PaperBLAST
PaperBLAST Hits for TCDB::A4HUI4 Proline/alanine transporter of 488 aas and 10 TMSs, AAP24. The first 18 amino acids of the negatively charged N-terminal LdAAP24 tail are required for alanine transport and may facilitate the electrostatic interactions of the entire negatively charged N-terminal tail with the positively charged internal loops in the transmembrane domain (Leishmania infantum) (488 a.a., MSRLPSTASD...)
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>TCDB::A4HUI4 Proline/alanine transporter of 488 aas and 10 TMSs, AAP24. The first 18 amino acids of the negatively charged N-terminal LdAAP24 tail are required for alanine transport and may facilitate the electrostatic interactions of the entire negatively charged N-terminal tail with the positively charged internal loops in the transmembrane domain (Leishmania infantum)
MSRLPSTASDNEPAHLTQMEDERYRETLIEGFMSVPEVEGDEGASNGDPSCQQKDQKAQE
YVEMDDDDDMTVVRLAAGELKENTNICKSAFHVFKANVGTGVFLLPTFYPDAGYVVSVIL
GVLIGAAVVDCTRLLVDVKIKINRSDVTTYSQVCRYVCGAGLGWFLFVAMCLAQFGFCLM
YTQLFGDTMVELANFKGSKYLWVSVVFFLCFPMTCFSDNLSLLAITSIIATVSVFYSLIC
CFAMSLMQLSQDGVHPSCDVAGNRIPVGWFNNLANNMMVLEGIAIILPVHAACTQKRLVP
KMATLVITGVIAWYILFGLTGYLAYGNSMTTSLVAKMAHSSWGTSVRVFFMLNLVFTYPV
QFMSAMQLIDQTVRCKPRSWMGIGLRLLINLVIWALAMGMPTSAVNTVVAFVGALPSVCM
VMIIPSILAMHVKYAVEHPDADRNTLQYWKKIFVTAPCFTFKRIRCYVYLVVAVLIMVIG
TYSIAETL
Running BLASTp...
Found 44 similar proteins in the literature:
TC 2.A.18.7.4 / A4HUI4 Proline/alanine transporter of 488 aas and 10 TMSs, AAP24. The first 18 amino acids of the negatively charged N-terminal LdAAP24 tail are required for alanine transport and may facilitate the electrostatic interactions of the entire negatively charged N-terminal tail with the positively charged internal loops in the transmembrane domain from Leishmania infantum
100% identity, 100% coverage
- substrates: Alanine, Proline
tcdb comment: This mechanism may underlie regulation of substrate flux rate for this and other transporters (Schlisselberg et al. 2015)
AVT3_SCHPO / Q10074 Vacuolar amino acid transporter 3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
TC 2.A.18.7.3 / Q10074 Vacuolar amino acid transporter 3, Avt3 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (see 4 papers)
avt3 vacuolar amino acid efflux transporter Avt3 from Schizosaccharomyces pombe (see 2 papers)
NP_593551 vacuolar amino acid transmembrane transporter Avt3 from Schizosaccharomyces pombe
23% identity, 53% coverage
CG16700 uncharacterized protein from Drosophila melanogaster
23% identity, 81% coverage
- Profiling neurotransmitter-evoked glial responses by RNA-sequencing analysis
Wang, Frontiers in neural circuits 2023 - “...+ FBgn0026438 Eaat2 FBgn0034911 GlyT + FBgn0001134 Grd + FBgn0001145 Gs2 + FBgn0039525 CG5646 FBgn0030816 CG16700 Alcohol metabolism FBgn0011768 Fdh FBgn0000055 Adh + FBgn0017482 T3dh + Genes are categorized into metabolism related to carbohydrates, lipid, amino acid, and alcohol. The changes in the expression of these...”
- Modulation of sleep by trafficking of lipids through the Drosophila blood-brain barrier
Li, eLife 2023 - “...acon, and MtnA ( Figure 2figure supplement 1D ). Meanwhile, knockdown of the transporter gene CG16700 ( Figure 2figure supplement 1A ), cytochrome P450 gene Cyp6a20 ( Figure 2figure supplement 1D ), and trafficking factor Cln7 decreased total sleep ( Figure 2figure supplement 1B ). Since...”
- “...CG3897 VDRC 101083 L(2)80717 GD VDRC 11117 CG6126 GD VDRC 7326 Lsd-2 KK VDRC 102269 CG16700 KK VDRC 110058 Mct1 KK VDRC 106773 JhI-21 KK VDRC 108509 Mnd KK VDRC 110217 Lrp1 KK VDRC 106364 CG5687 GD VDRC 33262 CG6386 KK VDRC 108502 CG4462 KK VDRC...”
- A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population
Lange, Molecular biology and evolution 2022 - “...0.0872 1.4E04 CG10182, CG33337, CG16723, CG10183, CG10184, CG31145 X 16919722 17013929 14 0.0849 1.6E04 CG4991, CG16700, Arpc3B, CG5004 3R 8856384 8882684 3 0.0848 2.2E04 ry, CG11668, snk, CG11670, Hsc70-2, CG31157, CG7966, pic, sim X 18020585 18110534 14 0.0782 2.3E04 CG32553, mir-369, mir-210, CG34133, ari-1, CG43229 X...”
- “...in on the window revealed a SNP pattern that localized over two genes, CG4991 and CG16700 ( supplementary fig. S2 C , Supplementary Material online). This region has previously been identified as a target of positive selection between African and non-African populations ( Svetec et al....”
- Natural variation in the transcriptional response of Drosophila melanogaster to oxidative stress
Ramnarine, G3 (Bethesda, Md.) 2022 - “...stress ( Figure3 ). Two genes within this module exhibit a particularly large negative fold-change: CG16700 and MFS9 ( Major Facilitator Superfamily Transporter 9 ), both of which are involved in transmembrane activity ( Gaudet et al. 2011 ). An additional three genes within this module...”
- Tadr is an axonal histidine transporter required for visual neurotransmission in Drosophila
Han, eLife 2022 - “...acid transmembrane transporter activity/SLC36A1 or A2 CG32081 Yes Amino acid transmembrane transporter activity/SLC36A1 or A2 CG16700 Yes Amino acid transmembrane transporter activity/SLC36A1 or A4 CG13384 Yes Amino acid transmembrane transporter activity/SLC36A1 or A4 CG43693 Yes Amino acid transmembrane transporter activity/SLC36A1 or A4 polyph Yes Amino acid...”
- Methionine restriction breaks obligatory coupling of cell proliferation and death by an oncogene Src in Drosophila
Nishida, eLife 2021 - “...Flybase FLYB: FBgn0030574 NA Gene Drosophila melanogaster CG8757 Flybase FLYB: FBgn0036380 NA Gene Drosophila melanogaster CG16700 Flybase FLYB: FBgn0030816 NA Gene Drosophila melanogaster path Flybase FLYB: FBgn0036007 NA Gene Drosophila melanogaster nprl3 Flybase FLYB: FBgn0036397 NA Gene Drosophila melanogaster nprl2 Flybase FLYB: FBgn0030800 NA Gene Drosophila...”
- “...et al., 2020 PMID: 32938923 F: 5'- AGAAACGATTGGATCGGGCA -3' R: 5'- ATCTGCCATCTTTTGGACCGA -3' Sequence-based reagent CG16700 (primer) FlyPrimerBank PP25676 F: 5'- CCTACAAGCTATCTGGAGACCA -3' R: 5'- GAGACCTCCGTTCTTGAAGGC -3' Sequence-based reagent path (primer) Newton et al., 2020 PMID: 32938923 F: 5'- TGTTTGATTTGCGCGGCATT -3' R: 5'- TTCGACCCGCTGTCCACTAT -3' Sequence-based...”
- Transcriptome Analysis of NPFR Neurons Reveals a Connection Between Proteome Diversity and Social Behavior
Ryvkin, Frontiers in behavioral neuroscience 2021 - “...Fru cells (vGAt, CG5549) and 6 enriched in NPFR neurons (Ncc69, CG7888, Eaat1, CG43693, CG8785, CG16700). Interestingly, Orct2 (Organic cation transporter 2), which is a transcriptional target of the insulin receptor pathway ( Herranz et al., 2006 ; Supplementary Figure 3 ) was enriched in NPFR...”
- Changes in Presynaptic Gene Expression during Homeostatic Compensation at a Central Synapse
Harrell, The Journal of neuroscience : the official journal of the Society for Neuroscience 2021 - “...CG5346 1828.19 0.5430 3.64E-06 1.89E-03 oxidation/reduction process Jhe 539.44 1.6050 8.94E-06 4.35E-03 hormone esterase activity CG16700 884.33 0.3650 1.18E-05 5.41E-03 amino acid transporter CG8303 573.39 0.7870 1.69E-05 7.29E-03 fatty acyl-CoA metabolism CG8788 1213.87 0.4020 2.57E-05 9.99E-03 no functional information Gmap 4141.22 0.4680 2.44E-05 9.99E-03 vesicle-mediated transport...”
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PGUG_00636 uncharacterized protein from Meyerozyma guilliermondii ATCC 6260
22% identity, 78% coverage
S36A4_HUMAN / Q6YBV0 Neutral amino acid uniporter 4; Solute carrier family 36 member 4 from Homo sapiens (Human) (see 2 papers)
TC 2.A.18.8.5 / Q6YBV0 H+-coupled amino acid transporter-4; SLC36A4 from Homo sapiens (see 3 papers)
NP_689526 neutral amino acid uniporter 4 isoform 1 from Homo sapiens
22% identity, 82% coverage
- function: Uniporter that mediates the transport of neutral amino acids like L-tryptophan, proline and alanine (PubMed:21097500). The transport activity is sodium ions-independent, electroneutral and therefore functions via facilitated diffusion (PubMed:21097500).
catalytic activity: L-tryptophan(in) = L-tryptophan(out) (RHEA:70947)
catalytic activity: L-alanine(in) = L-alanine(out) (RHEA:70719)
catalytic activity: L-proline(in) = L-proline(out) (RHEA:73811)
subunit: Interacts with CRYBA1. - substrates: Amino acids, H+
tcdb comment: SLC36A4 is widely distributed and has high-affinity (Km = 2-3 µM) for proline and tryptophan (Thwaites and Anderson 2011) - THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...Amino acid Transporter 4 Systematic nomenclature SLC36A3 SLC36A4 HGNC, UniProt SLC36A3 , Q495N2 SLC36A4 , Q6YBV0 Common abreviation PAT3 PAT4 Endogenous substrates Ltryptophan [ 423 ], Lproline [ 423 ] Stoichiometry Unknown Unknown Comments The function of the testesspecific PAT3 remains unknown. PAT4 is not protoncoupled...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...PAT3 PAT4 HGNC, UniProt SLC36A1 , Q7Z2H8 SLC36A2 , Q495M3 SLC36A3 , Q495N2 SLC36A4 , Q6YBV0 Substrates MeAIB [ 86 ], betaine , vigabatrin [ 1 ], 5aminolevulinic acid , guanidinopropionic acid , gaboxadol [ 299 ], Lazetidine2carboxylate [ 274 ], THPO [ 300 ] MeAIB...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...Common abbreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1, Q7Z2H8 SLC36A2, Q495M3 SLC36A3, Q495N2 SLC36A4, Q6YBV0 Endogenous substrates L-alanine, glycine, GABA, -alanine, taurine, L-proline, D-serine, D-cysteine, D-proline, D-alanine, trans-4-hydroxy-proline, sarcosine L-alanine, glycine, -alanine, L-proline, trans-4-hydroxy-proline, sarcosine L-tryptophan 381 , L-proline 381 Substrates THIP 378 , betaine,...”
- PAT4 levels control amino-acid sensitivity of rapamycin-resistant mTORC1 from the Golgi and affect clinical outcome in colorectal cancer.
Fan, Oncogene 2016 - GeneRIF: Data predict that colorectal cancer cells with high PAT4 expression will be more resistant to depletion of serine and glutamine, allowing them to survive and outgrow neighbouring normal and tumorigenic cells.
- SLC36A4 (hPAT4) is a high affinity amino acid transporter when expressed in Xenopus laevis oocytes.
Pillai, The Journal of biological chemistry 2011 - GeneRIF: SLC36A4 (hPAT4) is a high affinity amino acid transporter when expressed in Xenopus laevis oocytes.
- Proton-assisted amino-acid transporters are conserved regulators of proliferation and amino-acid-dependent mTORC1 activation.
Heublein, Oncogene 2010 - GeneRIF: SLC36A4 has a similar in vivo growth regulatory activity to fly SLC36 family members when expressed in Drosophila and is also required for amino acid-dependent mTORC1 activation, and mTORC1-regulated proliferation in human cells.
AVT3B_ARATH / F4ILY9 Amino acid transporter AVT3B; AtAvt3B; Aromatic and neutral amino acid transporter-like protein 1 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G42005 amino acid transporter family protein from Arabidopsis thaliana
NP_850361 Transmembrane amino acid transporter family protein from Arabidopsis thaliana
24% identity, 73% coverage
LOC101745823 proton-coupled amino acid transporter-like protein pathetic from Bombyx mori
21% identity, 77% coverage
S36A1_MOUSE / Q8K4D3 Proton-coupled amino acid transporter 1; Proton/amino acid transporter 1; Solute carrier family 36 member 1 from Mus musculus (Mouse) (see paper)
TC 2.A.18.8.1 / Q8K4D3 The electrogenic, proton-dependent amino acid:H+ symporter, PAT1 or LYAAT-1 (Slc36A1). Catalyzes uptake of L-Gly, L-Ala, L-Pro, γ-amino butyrate, and short chain D-amino acids such as proline and hydroxyproline with an aa/ H+ ratio of 1:1 (found in lysosomes) In humans, this is the iminoglycinuria protein (Boll et al., 2004; from Mus musculus (Mouse) (see 2 papers)
Slc36a1 / RF|NP_694779.3 proton-coupled amino acid transporter 1 from Mus musculus (see paper)
NP_694779 proton-coupled amino acid transporter 1 from Mus musculus
23% identity, 85% coverage
- function: Electrogenic proton/amino acid symporter with selectivity for small apolar L-amino acids, their D-enantiomers and selected amino acid derivatives such as 4-aminobutanoate/GABA (PubMed:11959859). May be involved in the efflux from the lysosomal compartment of neutral amino acids resulting from proteolysis (By similarity). May play a role in specifying sites for exocytosis in neurons (By similarity).
catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
catalytic activity: L-proline(out) + H(+)(out) = L-proline(in) + H(+)(in) (RHEA:28963)
catalytic activity: D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) (RHEA:70643)
catalytic activity: L-serine(in) + H(+)(in) = L-serine(out) + H(+)(out) (RHEA:28887)
catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459) - substrates: Amino acids, Gamma-aminobutyric acid, H+
tcdb comment: Miyauchi et al., 2005; Broer, 2008). A disulfide bridge is essential for transport function (Dorn et al., 2009). Transports taurine and β-alanine by H+ symport with low affinity and high capacity across the intestinal brush boarder membrane (Anderson et al., 2009). Exhibits low affinity (Km= 1-10 mM) and transports amino acid-based drugs used to treat epilepsy, schizophrenia, bacterial infections, hyperglycemia and cancer (Thwaites and Anderson, 2011). It is regulated by the Birt-Hogg-Dubé (BHD) syndrome related protein FLCN that has been implicated in the vesicular trafficking processes by interacting with several Rab family GTPases. FLCN binds via its C-terminal DENN-like domain to the recycling transport regulator, Rab11A, and promoted the loading of PAT1 on Rab11A (Zhao et al. 2018) - A multi-hierarchical approach reveals d-serine as a hidden substrate of sodium-coupled monocarboxylate transporters.
Wiriyasermkul, eLife 2024 - “...0.01 1 131 2.6E+06 Slc1a5/Asct2 P51912 0.4 0.10 0.7 0.09 4 767 1.5E+07 Decreased Slc36a1/Pat1 Q8K4D3 1.2 0.08 1.0 0.12 3 103 5.4E+06 Slc2a5/Glut5 Q9WV38 1.2 0.01 0.8 0.04 2 1,140 6.5E+07 Slco4c1/Oatp-m1 Q8BGD4 1.1 0.00 0.9 0.00 9 4,011 1.5E+08 Slc22a13/Oat10 Q6A4L0 1.1 0.03 0.8...”
- Unraveling the Proteomic Landscape of Intestinal Epithelial Cell-Derived Exosomes in Mice.
Ding, Frontiers in physiology 2022 - “...34.59 1.314 0.053 Not 7 P53986 Slc16a1 Monocarboxylate transporter 1 208.23 0.764 0.028 Down 8 Q8K4D3 Slc36a1 Proton-coupled amino acid transporter 1 54.68 0.758 0.013 Down 9 Q9JIP7 Slc15a1 Solute carrier family 15 member 1 1489.24 0.756 0.022 Down 10 O35488 Slc27a2 Very long-chain acyl-CoA synthetase...”
- Insights into the Interaction of Lysosomal Amino Acid Transporters SLC38A9 and SLC36A1 Involved in mTORC1 Signaling in C2C12 Cells.
Wang, Biomolecules 2021 - GeneRIF: Insights into the Interaction of Lysosomal Amino Acid Transporters SLC38A9 and SLC36A1 Involved in mTORC1 Signaling in C2C12 Cells.
- Disturbed intestinal nitrogen homeostasis in a mouse model of high-fat diet-induced obesity and glucose intolerance.
Do, American journal of physiology. Endocrinology and metabolism 2014 (PubMed)- GeneRIF: Data suggest that a high-fat diet induces expression of two amino acid transporters (Slc36a1, Slc6a20a) in intestinal mucosa pointing to a specific and adaptive absorption of some amino acids in high-fat diet-induced obesity and glucose intolerance.
- Fructose-induced hypertension: essential role of chloride and fructose absorbing transporters PAT1 and Glut5.
Singh, Kidney international 2008 - GeneRIF: The essential role of chloride and fructose absorbing Slc36a1 is reported.
- Kinetics of bidirectional H+ and substrate transport by the proton-dependent amino acid symporter PAT1.
Foltz, The Biochemical journal 2005 - GeneRIF: detailed analysis of the transport mode of the murine PAT1 in oocytes; PAT1 is an electrogenic H+-coupled amino acid symporter with the capability for bidirectional amino acid transport
S36A1_RAT / Q924A5 Proton-coupled amino acid transporter 1; Proton/amino acid transporter 1; Lysosomal amino acid transporter 1; LYAAT-1; Neutral amino acid/proton symporter; Solute carrier family 36 member 1 from Rattus norvegicus (Rat) (see 2 papers)
XP_008765881 proton-coupled amino acid transporter 1 isoform X1 from Rattus norvegicus
22% identity, 85% coverage
- function: Electrogenic proton/amino acid symporter with selectivity for small apolar L-amino acids, their D-enantiomers and selected amino acid derivatives such as 4-aminobutanoate/GABA (PubMed:11390972, PubMed:12598615). May be involved in the efflux from the lysosomal compartment of neutral amino acids resulting from proteolysis (PubMed:12598615). May play a role in specifying sites for exocytosis in neurons (PubMed:12598615).
catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
catalytic activity: L-proline(out) + H(+)(out) = L-proline(in) + H(+)(in) (RHEA:28963)
catalytic activity: D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) (RHEA:70643)
catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
catalytic activity: L-serine(in) + H(+)(in) = L-serine(out) + H(+)(out) (RHEA:28887)
catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459) - PAT1 (SLC36A1) shows nuclear localization and affects growth of smooth muscle cells from rats.
Jensen, American journal of physiology. Endocrinology and metabolism 2014 (PubMed)- GeneRIF: knockdown of (PAT1) led to induced cellular growth, suggesting a role for PAT1 in regulating cellular proliferation of smooth muscle cells
- Sertraline inhibits the transport of PAT1 substrates in vivo and in vitro.
Nielsen, British journal of pharmacology 2013 - GeneRIF: Sertraline is an apparent non-competitive inhibitor of PAT1-mediated transport.
- Induction of amino acid transporters expression by endurance exercise in rat skeletal muscle.
Murakami, Biochemical and biophysical research communications 2013 (PubMed)- GeneRIF: Expression of proton-assisted amino acid transporter 1 (PAT1) mRNA was slightly but not significantly induced by a single bout of exercise in soleus and extensor digitorum longus muscles.
- Rectal absorption of vigabatrin, a substrate of the proton coupled amino acid transporter (PAT1, Slc36a1), in rats.
Holm, Pharmaceutical research 2012 (PubMed)- GeneRIF: PAT1(Slc36a1) protein was present in rat rectal epithelium.
- Fructose-induced hypertension: essential role of chloride and fructose absorbing transporters PAT1 and Glut5.
Singh, Kidney international 2008 - GeneRIF: The essential role of chloride and fructose absorbing Slc36a1 is reported.
- The H+-coupled electrogenic lysosomal amino acid transporter LYAAT1 localizes to the axon and plasma membrane of hippocampal neurons.
Wreden, The Journal of neuroscience : the official journal of the Society for Neuroscience 2003 - GeneRIF: The H+-coupled electrogenic lysosomal amino acid transporter LYAAT1 localizes to the axon and plasma membrane of hippocampal neurons.
S36A1_HUMAN / Q7Z2H8 Proton-coupled amino acid transporter 1; Proton/amino acid transporter 1; hPAT1; Solute carrier family 36 member 1 from Homo sapiens (Human) (see 4 papers)
TC 2.A.18.8.7 / Q7Z2H8 Proton-coupled amino acid transporter 1 (Proton/amino acid transporter 1) (hPAT1 or LYAAT-1) (Solute carrier family 36 member 1) from Homo sapiens (see 6 papers)
XP_011535893 proton-coupled amino acid transporter 1 isoform X3 from Homo sapiens
22% identity, 85% coverage
- function: Electrogenic proton/amino acid symporter with selectivity for small apolar L-amino acids, their D-enantiomers and selected amino acid derivatives such as 4-aminobutanoate/GABA (PubMed:12527723, PubMed:12809675, PubMed:19549785). May be involved in the efflux from the lysosomal compartment of neutral amino acids resulting from proteolysis (By similarity). May play a role in specifying sites for exocytosis in neurons (By similarity).
catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
catalytic activity: L-proline(out) + H(+)(out) = L-proline(in) + H(+)(in) (RHEA:28963)
catalytic activity: D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) (RHEA:70643)
catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
catalytic activity: L-serine(in) + H(+)(in) = L-serine(out) + H(+)(out) (RHEA:28887)
catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459) - substrates: Amino acids, H+
tcdb comment: SLC36A1 is expressed at the luminal surface of the small intestine but is also commonly found in lysosomes in many cell types (including neurons), suggesting that it is a multipurpose carrier with distinct roles in different cells including absorption in the small intestine and as an efflux pathway following intralysosomal protein breakdown. SLC36A1 has a relatively low affinity (Km = 1-10 mM) for its substrates, which include zwitterionic amino and imino acids, heterocyclic amino acids and amino acid-based drugs and derivatives used experimentally and/or clinically to treat epilepsy, schizophrenia, bacterial infections, hyperglycaemia and cancer (Thwaites and Anderson 2011). hPAT1 transports the pyridine alkaloids, arecaidine, guvacine and isoguvacine, across the apical membrane of enterocytes and might be responsible for the intestinal absorption of these drug candidates (Voigt et al. 2013) - Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors.
Nielsen, Pharmaceutics 2025 - “...of hPAT1 (SLC36A1) was downloaded from the AlphaFold database [ 21 ] (AF-Q7Z2H8-F1-v4, UniProt ID: Q7Z2H8) and loaded into Maestro (13.6), which is part of the Schrdinger Suite [ 27 ]. Maestros Protein Preparation was used to add missing hydrogens, assign bond orders, generate protonation states...”
- Secretome profiling of human epithelial cells exposed to cigarette smoke extract and their effect on human lung microvascular endothelial cells
Seenak, Scientific reports 2024 - “...Cell migration 2.1262 Kelch-like protein 1 Q9NVR0 Protein folding 2.1998 Proton-coupled amino acid transporter 1 Q7Z2H8 Biological process 1. Proton transmembrane transport 2. Amino acid transmembrane transport Molecular function 1. Neutral amino acid transmembrane transporter activity 2. Organic anion transmembrane transporter activity 3. L-amino acid transmembrane...”
- Metformin directly targets the H3K27me3 demethylase KDM6A/UTX.
Cuyàs, Aging cell 2018 - “...P84022 Mothers against decapentaplegic homolog 3 (SMAD3) Q99720 Sigma nonopioid intracellular receptor 1 (OPRS1, SIGMAR1) Q7Z2H8 Protoncoupled amino acid transporter 1 (SLC36A1) P63092 Guanine nucleotidebinding protein G(s), subunit alpha (GNAS) P83916 Chromobox protein homolog 1 (CBX1) Q9H3R0 Lysinespecific demethylase 4C (KDM4C) P39748 Flap endonuclease 1 (FEN1)...”
- THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...Transporter 1 Protoncoupled Amino acid Transporter 2 Systematic nomenclature SLC36A1 SLC36A2 HGNC, UniProt SLC36A1 , Q7Z2H8 SLC36A2 , Q495M3 Common abreviation PAT1 PAT2 Substrates muscimol [ 525 ], arecaidine [ 525 ], betaine [ 525 ], Lcycloserine [ 525 ], 5aminolevulinic acid [ 525 ], gaboxadol...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...nomenclature SLC36A1 SLC36A2 SLC36A3 SLC36A4 Common abreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1 , Q7Z2H8 SLC36A2 , Q495M3 SLC36A3 , Q495N2 SLC36A4 , Q6YBV0 Substrates MeAIB [ 86 ], betaine , vigabatrin [ 1 ], 5aminolevulinic acid , guanidinopropionic acid , gaboxadol [ 299 ],...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...Systematic nomenclature SLC36A1 SLC36A2 SLC36A3 SLC36A4 Common abbreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1, Q7Z2H8 SLC36A2, Q495M3 SLC36A3, Q495N2 SLC36A4, Q6YBV0 Endogenous substrates L-alanine, glycine, GABA, -alanine, taurine, L-proline, D-serine, D-cysteine, D-proline, D-alanine, trans-4-hydroxy-proline, sarcosine L-alanine, glycine, -alanine, L-proline, trans-4-hydroxy-proline, sarcosine L-tryptophan 381 , L-proline...”
- Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity.
London, PLoS computational biology 2011 - “...CYVA Q9NTW7-3 - - + -2.88 MTO CFLT Q2UVF0 -- - + -2.74 MTO CAFI Q7Z2H8 -- + - -2.62 STO CWLS A6QL63-3 - + + -2.46 MTO CCLS Q9NZM3-3 -- -- ++ -2.37 MTO CTTE Q5T2R2-2 -- - - -2.14 STO CHFH Q8TCU3-2 --- +...”
- “...a mitochondrial protein is farnesylated in the cytosol. Finally, the proton-coupled amino acid transporter 1 (Q7Z2H8; CAFI) is likely not a farnesylation target, since mutation of the target cysteine to alanine did not affect its function [46] . As discussed above, the biological role of farnesylation...”
- Comparative Bioinformatics Analyses and Profiling of Lysosome-Related Organelle Proteomes
Hu, International journal of mass spectrometry 2007 - “...transporter 1 (proton/amino acid transporter 1) (Q7Z2H8) Q14789 Golgin subfamily B member 1 (Giantin) (Macrogolgin) Q99571 P2X purinoceptor 4 (ATP...”
- The amino acid transporter PAT1 regulates mTORC1 in a nutrient-sensitive manner that requires its transport activity.
Zhao, Cellular signalling 2019 (PubMed)- GeneRIF: Increasing the PAT1 level does not readily increase the mTORC1 activity. The lysosomal PAT1 was increased by starvation and decreased by nutrient replenishment. The lysosomal PAT1 plays a negative role on the mTORC1 activity.
- SLC36A1-mTORC1 signaling drives acquired resistance to CDK4/6 inhibitors.
Yoshida, Science advances 2019 - GeneRIF: SLC36A1-mTORC1 signaling drives acquired resistance to CDK4/6 inhibitors.
- Glycosylation affects the stability and subcellular distribution of human PAT1 protein.
Luo, FEBS letters 2017 (PubMed)- GeneRIF: Data indicate that the glycosylation-deficient mutant of amino acid transporter PAT1 (PAT1(3)(NQ) ) is unstable and is degraded mainly via the endoplasmic reticulum-associated degradation pathway in HEK293 cells.
- Amino acids suppress the expression of PAT1 on lysosomes via inducing the cleavage of a targeting signal.
Ji, FEBS letters 2017 (PubMed)- GeneRIF: A mechanism through which amino acids may suppress the expression of PAT1 on lysosomes by inducing protein cleavage to remove a targeting signal.
- Transport of the areca nut alkaloid arecaidine by the human proton-coupled amino acid transporter 1 (hPAT1).
Voigt, The Journal of pharmacy and pharmacology 2013 (PubMed)- GeneRIF: Data suggest that PAT1 in enterocytes is responsible for intestinal absorption of some of the alkaloids from areca nut (i.e., arecaidine, guvacine, isoguvacine).
- Sertraline inhibits the transport of PAT1 substrates in vivo and in vitro.
Nielsen, British journal of pharmacology 2013 - GeneRIF: Sertraline is an apparent non-competitive inhibitor of PAT1-mediated transport.
- Proton-assisted amino acid transporter PAT1 complexes with Rag GTPases and activates TORC1 on late endosomal and lysosomal membranes.
Ögmundsdóttir, PloS one 2012 - GeneRIF: PATs function as part of an amino acid-sensing engine that drives mTORC1 activation from endosomal and lysosomal membranes
- Intestinal drug transport via the proton-coupled amino acid transporter PAT1 (SLC36A1) is inhibited by Gly-X(aa) dipeptides.
Frølund, Molecular pharmaceutics 2012 (PubMed)- GeneRIF: In hPAT1 expressing oocytes Gly-Tyr, Gly-Pro, and Gly-Phe inhibited currents induced by drug substances.
- More
TGME49_227570 transmembrane amino acid transporter protein from Toxoplasma gondii ME49
22% identity, 81% coverage
- A Toxoplasma gondii putative amino acid transporter localizes to the plant-like vacuolar compartment and controls parasite extracellular survival and stage differentiation
Piro, mSphere 2024 - “...as amino acid transporters ( Fig. S1 ). The three genes encoding these proteins (TGME49_227430, TGME49_227570, and TGME49_227580) are all located on chromosome X. TGME49_227570 and TGME49_227580 are adjacent to one another in a head-to-tail arrangement, whereas TGME49_227430 is ~30 kbp away and in the opposite...”
- “...). Due to this homology, the protein encoded by TGME49_226060 was named TgAAT1, and TGME49_227430, TGME49_227570, and TGME49_227580 were named TgAAT2-4, respectively. Despite low amino acid conservation with SLC38A9, structural analysis of the TgAAT proteins using Alphafold2, TOPCONS, and I-TASSER software suggested the presence of 11...”
S36A4_MOUSE / Q8CH36 Neutral amino acid uniporter 4; Solute carrier family 36 member 4 from Mus musculus (Mouse) (see paper)
22% identity, 75% coverage
S36A3_MOUSE / Q811P0 Proton-coupled amino acid transporter 3; Proton/amino acid transporter 3; Solute carrier family 36 member 3; Tramdorin-2 from Mus musculus (Mouse) (see 2 papers)
23% identity, 70% coverage
XP_011247200 proton-coupled amino acid transporter 3 isoform X2 from Mus musculus
23% identity, 70% coverage
XP_005667282 proton-coupled amino acid transporter 4 isoform X1 from Sus scrofa
21% identity, 74% coverage
AVT3A_ARATH / Q9FKY3 Amino acid transporter AVT3A; AtAvt3A; Aromatic and neutral amino acid transporter-like protein 3 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G65990 amino acid transporter family protein from Arabidopsis thaliana
NP_201400 Transmembrane amino acid transporter family protein from Arabidopsis thaliana
25% identity, 60% coverage
- function: Translocates preferentially neutral amino acids and to a lesser extent aromatic amino acids from the vacuole to the cytoplasm. Requires ATP for function.
- Amino Acid Transporters in Plants: Identification and Function
Yao, Plants (Basel, Switzerland) 2020 - “...ant1 mutants: Essential amino acids within the SEs [ 78 , 88 , 111 ] At5g65990 AVT3A neutral amino acids various tissues of whole plants tonoplast [ 78 ] At, Arabidopsis thaliana ; UMAMIT, usually multiple acids move in and out; BAT, bidirectional amino acid transporter;...”
- Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress
Rasheed, Frontiers in plant science 2016 - “...11.8 2.3 At5g11110 Sucrose phosphate synthase 2F/SPSA2 5.8 15.5 32.6 64.4 1.2 1.5 5.5 10.6 At5g65990 Transmembrane amino acid transporter 6.7 13.5 24.6 20.0 1.3 1.1 2.3 1.8 At2g19410 U-box domain-containing protein kinase 5.1 2.9 2.6 1.9 0.9 0.8 1.0 0.8 At1g21240 Wall associated kinase 3/WAK3...”
- Functional Expression and Characterization of Schizosaccharomyces pombe Avt3p as a Vacuolar Amino Acid Exporter in Saccharomyces cerevisiae
Chardwiriyapreecha, PloS one 2015 - “...homologs according to CLUSTALW: Saccharomyces cerevisiae Avt3p and Avt4p (P36062 and P50944, respectively), Arabidopsis thaliana At5G65990 (ABH04593), and human hPAT1and hPAT2 (AAI36439 and AAI01104, respectively). Identical and similar residues are denoted by black boxes and gray boxes , respectively. The conserved glutamate residue is indicated by...”
- The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
Elashry, Plant physiology and biochemistry : PPB 2013 - “...3.3 0.2 0.36 At5g41800 AtProT5 5.7 6 0.3 0.14 At3g11900 ANT1 6.7 6 0.7 0.06 At5g65990 ANT2 4.5 6.9 2.4 a 0.00 At4g38250 ANT3 8.6 7 1.6 a 0.00 At2g41190 AVT1L1 5.2 6.2 1 0.05 At3g09340 AVT1L2 not available on GeneChip At3g09330 AVT1L3 not available on...”
- Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses
Brenner, BMC plant biology 2012 - “...AT1G31320 LOB domain protein 4 (LBD4) CATMA5a61330 18 2.56 8.17 5.68 1.21 0.84 1.02 5.89E-04 AT5G65990 amino acid transporter family protein CATMA4a30310 28 0.99 0.86 5.08 0.65 0.54 0.81 1.31E-06 AT4G28660 photosystem II reaction centre W (PsbW) family protein CATMA5a50360 21 0.49 0.64 5.65 1.00 0.56...”
- “...Col-0 FDR p-value genotype effect AGI Description Root Shoot root-specific CATMA5a61330 11 18.32 1.26 7.99E-04 AT5G65990 amino acid transporter family protein CATMA3a43475 5 7.63 1.57 9.62E-06 AT3G50410 Dof-type zinc finger domain-containing protein CATMA1a62410 4 5.66 0.63 4.99E-02 AT1G73165 Clavata3 / ESR-Related-1 (CLE1) CATMA5a37900 7 4.72 1.07...”
- Functional identification of AtAVT3, a family of vacuolar amino acid transporters, in Arabidopsis.
Fujiki, FEBS letters 2017 (PubMed)- GeneRIF: AtAVT3 family represents the long sought-for vacuolar amino acid exporters in plants.[AtAVT3A]
S36A_DROME / Q9W056 Proton-coupled amino acid transporter-like protein acs; Protein arcus from Drosophila melanogaster (Fruit fly) (see 3 papers)
NP_647686 arcus from Drosophila melanogaster
25% identity, 76% coverage
- function: Amino acid transporter which has pH-dependent electrogenic transport activity for alanine, glycine and proline (PubMed:15843412). Plays a role in positive regulation of growth by directly or indirectly modulating the effects of the TOR signaling pathway (PubMed:15843412, PubMed:22574197). Required in enterocytes for the efficient recovery of gut epithelium following the cytoplasmic purge response to bacterial infection (PubMed:37636057). Acts cell-autonomously to promote the retrograde transport of amino acids into the intestinal epithelium (PubMed:37636057). Acts non-cell-autonomously through the insulin signaling pathway to stimulate Myc expression and the release of amino acids from nutrient stores into the hemolymph (PubMed:37636057).
disruption phenotype: Viable (PubMed:37636057). Adult flies show delayed recovery of the midgut epithelial wall following the cytoplasmic purge response to intestinal bacterial infection (PubMed:37636057). RNAi-mediated ubiquitous knockdown or tissue specific knockdown in enterocytes or epithelial progenitor cells impairs recovery of intestinal wall thickness after the cytoplasmic purge response to intestinal bacterial infection (PubMed:37636057). RNAi-mediated tissue specific knockdown in Malpighian tubules, visceral muscles, enteroendocrine cells or the fat body has no effect on recovery from intestinal bacterial infection (PubMed:37636057). - PAT-related amino acid transporters regulate growth via a novel mechanism that does not require bulk transport of amino acids.
Goberdhan, Development (Cambridge, England) 2005 (PubMed)- GeneRIF: This study shows that CG1139 has similar transport properties to other SLC36 proton-assisted amino acid permeases and highlights for the first time a role for this family in promoting growth via interaction with the TOR and PI3K pathways in Drosophila. It may regulate growth independently of bulk amino acid transport.
S36A3_HUMAN / Q495N2 Proton-coupled amino acid transporter 3; Proton/amino acid transporter 3; Solute carrier family 36 member 3; Tramdorin-2 from Homo sapiens (Human) (see paper)
TC 2.A.18.8.4 / Q495N2 H+-coupled amino acid transporter-3 (SLC36A3) from Homo sapiens (see 5 papers)
NP_861439 proton-coupled amino acid transporter 3 isoform 2 from Homo sapiens
23% identity, 74% coverage
- substrates: Amino acids, H+
tcdb comment: SLC36A3 is expressed only in testes and has no known function (Thwaites and Anderson 2011) - THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...Transporter 3 Protoncoupled Amino acid Transporter 4 Systematic nomenclature SLC36A3 SLC36A4 HGNC, UniProt SLC36A3 , Q495N2 SLC36A4 , Q6YBV0 Common abreviation PAT3 PAT4 Endogenous substrates Ltryptophan [ 423 ], Lproline [ 423 ] Stoichiometry Unknown Unknown Comments The function of the testesspecific PAT3 remains unknown. PAT4...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...abreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1 , Q7Z2H8 SLC36A2 , Q495M3 SLC36A3 , Q495N2 SLC36A4 , Q6YBV0 Substrates MeAIB [ 86 ], betaine , vigabatrin [ 1 ], 5aminolevulinic acid , guanidinopropionic acid , gaboxadol [ 299 ], Lazetidine2carboxylate [ 274 ], THPO [...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...SLC36A3 SLC36A4 Common abbreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1, Q7Z2H8 SLC36A2, Q495M3 SLC36A3, Q495N2 SLC36A4, Q6YBV0 Endogenous substrates L-alanine, glycine, GABA, -alanine, taurine, L-proline, D-serine, D-cysteine, D-proline, D-alanine, trans-4-hydroxy-proline, sarcosine L-alanine, glycine, -alanine, L-proline, trans-4-hydroxy-proline, sarcosine L-tryptophan 381 , L-proline 381 Substrates THIP 378...”
- Mechanisms of lysophosphatidic acid (LPA) mediated stimulation of intestinal apical Cl-/OH- exchange.
Singla, American journal of physiology. Gastrointestinal and liver physiology 2010 - GeneRIF: lysophosphatidic acid stimulates apical Cl(-)/OH(-) exchange activity and surface levels of SLC36A3 and SLC26A6 in intestinal epithelial cells
- A cluster of proton/amino acid transporter genes in the human and mouse genomes.
Boll, Genomics 2003 (PubMed)- GeneRIF: PAT3 was isolated and identified, but its function is not yet known.
AVT3C_ARATH / Q9SVG0 Amino acid transporter AVT3C; AtAvt3C; Aromatic and neutral amino acid transporter-like protein 2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_195538 Transmembrane amino acid transporter family protein from Arabidopsis thaliana
AT4G38250 amino acid transporter family protein from Arabidopsis thaliana
25% identity, 71% coverage
AVT3_YEAST / P36062 Vacuolar amino acid transporter 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
TC 2.A.18.7.1 / P36062 The vacuolar amino acid transporter, AVT3 (catalyzes efflux from yeast vacuoles of large neutral amino acids such as tyr, gln, asn, leu and ile) (see 6 papers)
AVT3 / RF|NP_012776.1 vacuolar amino acid transporter 3 from Saccharomyces cerevisiae
YKL146W Avt3p from Saccharomyces cerevisiae
21% identity, 53% coverage
- function: Involved in amino acid efflux from the vacuole to the cytoplasm. Capable of transporting large neutral amino acids including tyrosine, glutamine, asparagine, isoleucine and leucine.
- substrates: Amino acids
- Functional Expression and Characterization of Schizosaccharomyces pombe Avt3p as a Vacuolar Amino Acid Exporter in Saccharomyces cerevisiae
Chardwiriyapreecha, PloS one 2015 - “...451477) and analogous regions in the homologs according to CLUSTALW: Saccharomyces cerevisiae Avt3p and Avt4p (P36062 and P50944, respectively), Arabidopsis thaliana At5G65990 (ABH04593), and human hPAT1and hPAT2 (AAI36439 and AAI01104, respectively). Identical and similar residues are denoted by black boxes and gray boxes , respectively. The...”
- Regulation of Amino Acid Transport in Saccharomyces cerevisiae
Bianchi, Microbiology and molecular biology reviews : MMBR 2019 (secret) - Widespread Cumulative Influence of Small Effect Size Mutations on Yeast Quantitative Traits
Hua, Cell systems 2018 - “...YNL049C, YMR015C, YDL052C, YJR134C, YKL096W, YNL280C, YLR194C, YER113C, YDR077W, YDR055W, YNR021W, YNL327W, YLR130C, YNR039C, YJL099W, YKL146W, YPR003C, YHL017W, YOR245C, YER166W, YBR132C, YOR016C, YPR090W, YNL300W, YLR250W, YGR038W, YPL259C, YPR071W, YKL065C, YKL046C, YPL274W, YEL048C, YOR317W, YDR100W, YNL146W, YMR253C, YJR031C, YER011W, YJL078C, YIL016W, YML037C, YGR247W, YFL004W, YBR023C, YIL044C, YMR052W,...”
- Functional Expression and Characterization of Schizosaccharomyces pombe Avt3p as a Vacuolar Amino Acid Exporter in Saccharomyces cerevisiae
Chardwiriyapreecha, PloS one 2015 - “...Avt3p ( SPAC3H1 . 09c , SpAvt3p), a homologue of S . cerevisiae Avt3p ( YKL146w ) and Avt4p ( YNL101w ), is involved in spore formation by S . pombe cells [ 23 ]. In this study, the avt3 + gene of S . pombe...”
- “...Intracellular localization of GFP-Avt3p in S . pombe cells Recently, we showed that Avt3p ( YKL146w ) and Avt4p ( YNL101w ) are involved in amino acid export from the vacuoles in S . cerevisiae [ 12 ]. Based on phylogenetic relationships with Avt3p and Avt4p,...”
- A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells
Alver, G3 (Bethesda, Md.) 2013 - “...MRPL22 YNL177c SSH4 YKL124w YHL044W YHL044w ATO3 YDR384c NCE102 YPR149w SWT21 YNL187w YHR022C YHR022c AVT3 YKL146w NFI1 YOR156c THI72 YOR192c YJL049W YJL049w BMH2 YDR099w NKP1 YDR383c THP1 YOL072w YKL070W YKL070w BSC1 YDL037c NNK1 YKL171w TIM21 YGR033c YKL136W YKL136w BUD2 YKL092c NUP2 YLR335w TMT1 YER175c YKL151C YKL151c...”
- Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae
Ljungdahl, Genetics 2012 - “...proteins Systematic name AVT subfamily YJR001w YEL064c YKL146w YNL101w YBL089w YER119c YIL088c VBA subfamily YMR088c YBR293w YCL069w YDR119w YKR105c Other...”
- Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening
Mah, BMC biochemistry 2005 - “...0.4755 YDR299W BFR2 0.47 YPL211W NIP7 0.4521 YML037C 0.4503 YDR171W HSP42 0.442 YOL104C NDJ1 0.3611 YKL146W AVT3 0.3592 YGL245W 0.2863 YIL010W DOT5 0.2606 YNL007C SIS1 0.2239 YHL021C 0.2094 YMR196W 0.2089 YJR142W 0.2005 YGR220C MRPL9 0.1976 YLR177W 0.1626 YJL211C 0.1594 YML035C AMD1 0.1384 YGL105W ARC1 0.1332 YGR264C...”
- The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation--via a newly identified Glc7/Bud14 type I protein phosphatase module--and TFIID promoter distribution
Lenssen, Molecular and cellular biology 2005 - “...YBR280C YBL075C YNL125C YJL225C YPR026W YDL078C YCLX05C YKL146W YIR043C YOR005C YHR033W YLR178C YER060W-A YJL082W YHR006W YBR139W Gene 496 LENSSEN ET AL....”
- Identification and characterization of a lysosomal transporter for small neutral amino acids
Sagné, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...T27A1.5, and S. cerevisiae predicted proteins YNL101w and YKL146w was performed with the PILEUP software of the GCG 10.0-UNIX package. Black boxes indicate...”
- “...of the seven AAAP family members, YNL101w (40% over 311) and YKL146w (32% over 466), PNAS June 19, 2001 vol. 98 no. 13 7209 BIOCHEMISTRY Fig. 3. LYAAT-1 is a...”
FOXG_11334 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
20% identity, 73% coverage
AVT4_YEAST / P50944 Vacuolar amino acid transporter 4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
TC 2.A.18.7.2 / P50944 Vacuolar amino acid transporter 4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 6 papers)
NP_014298 Avt4p from Saccharomyces cerevisiae S288C
YNL101W Avt4p from Saccharomyces cerevisiae
23% identity, 43% coverage
- function: Involved in amino acid efflux from the vacuole to the cytoplasm. Capable of transporting large neutral amino acids including tyrosine, glutamine, asparagine, isoleucine and leucine.
- substrates: Amino acids
- Vacuolar transporter Avt4 is involved in excretion of basic amino acids from the vacuoles of Saccharomyces cerevisiae.
Sekito, Bioscience, biotechnology, and biochemistry 2014 (PubMed)- GeneRIF: Avt4p is a vacuolar amino acid exporter involving in the recycling of basic amino acids
- Functional Expression and Characterization of Schizosaccharomyces pombe Avt3p as a Vacuolar Amino Acid Exporter in Saccharomyces cerevisiae
Chardwiriyapreecha, PloS one 2015 - “...analogous regions in the homologs according to CLUSTALW: Saccharomyces cerevisiae Avt3p and Avt4p (P36062 and P50944, respectively), Arabidopsis thaliana At5G65990 (ABH04593), and human hPAT1and hPAT2 (AAI36439 and AAI01104, respectively). Identical and similar residues are denoted by black boxes and gray boxes , respectively. The conserved glutamate...”
- Regulation of Amino Acid Transport in Saccharomyces cerevisiae
Bianchi, Microbiology and molecular biology reviews : MMBR 2019 (secret) - Functional Expression and Characterization of Schizosaccharomyces pombe Avt3p as a Vacuolar Amino Acid Exporter in Saccharomyces cerevisiae
Chardwiriyapreecha, PloS one 2015 - “..., SpAvt3p), a homologue of S . cerevisiae Avt3p ( YKL146w ) and Avt4p ( YNL101w ), is involved in spore formation by S . pombe cells [ 23 ]. In this study, the avt3 + gene of S . pombe was heterologously expressed in S...”
- “...S . pombe cells Recently, we showed that Avt3p ( YKL146w ) and Avt4p ( YNL101w ) are involved in amino acid export from the vacuoles in S . cerevisiae [ 12 ]. Based on phylogenetic relationships with Avt3p and Avt4p, we found that Avt3p in...”
- Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
Sen, Genome research 2015 - “...than the reductions in ribosome density observed for the corresponding native genes ( YPR159W , YNL101W , YIL090W , YDL145C , YML035C , and YBL102W ) (Supplemental Table S2). One possible explanation for this discrepancy is that Ded1 function is relatively less impaired in ded1-cs cells...”
- Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae
Ljungdahl, Genetics 2012 - “...Systematic name AVT subfamily YJR001w YEL064c YKL146w YNL101w YBL089w YER119c YIL088c VBA subfamily YMR088c YBR293w YCL069w YDR119w YKR105c Other transport...”
- A novel pathway that coordinates mitotic exit with spindle position
Nelson, Molecular biology of the cell 2007 - “...yjr056c, ykl056c, ykl063c, ymr071c, ymr181c, ymr196w, ymr226c, ynl101w, ynl116w, ynl187w, ynl335w, yor033w, and ypl070w. A mild phenotype was seen for 18...”
- An intimate collaboration between peroxisomes and lipid bodies
Binns, The Journal of cell biology 2006 - “...Act1p , Adh2p Fba1p, Gvp36p, Hom3p, Pgk1p Proteins also in nucleus Bmh2p, Crm1p, Pdc1p, Rib1p, Ynl101w, Ypr127w Others Hhf1/2p (n), Htb(1a/o2)p (n), Pma2p (pm) Organelle assignments are based on data accumulated at www.yeastgenome.org . Underlined identifications correspond to the 20 best (lowest) logE scores ( Fenyo...”
- Substrate specificity analysis of protein kinase complex Dbf2-Mob1 by peptide library and proteome array screening
Mah, BMC biochemistry 2005 - “...3.1016 YMR229C RRP5 2.6954 YBR118W TEF2 2.619 YJL108C PRM10 2.5802 YPR091C 2.5784 YKL168C KKQ8 2.5013 YNL101W AVT4 2.1486 YBR285W 1.9355 YMR239C RNT1 1.593 YNR047W 1.4015 YJL076W NET1 1.3521 YNL155W 1.2912 YNR006W VPS27 1.1429 YIL135C VHS2 1.116 YMR184W 1.1144 YDL220C CDC13 1.0274 YBR108W 1.0216 YDL019C OSH2 0.9962...”
- “...0 YJL108C PRM10 2.5802 41 0 YPR091C 2.5784 87 3 YKL168C KKQ8 2.5013 84 14 YNL101W AVT4 2.1486 80 7 YBR285W 1.9355 17 0 YMR239C RNT1 1.593 54 2 YNR047W 1.4015 100 21 YJL076W NET1 1.3521 128 11 YNL155W 1.2912 31 1 YNR006W VPS27 1.1429 71...”
- Genome-wide coexpression dynamics: theory and application
Li, Proceedings of the National Academy of Sciences of the United States of America 2002 - “...PFK1 and PFK2 (glycolysis), and two genes, ECM1 and YNL101W, the functions of which are newly revealed. The complexity in computation is eased by a new result...”
- “...relevance of the LA approach in protein-function prediction. YNL101W is another LA-scouting leader that is still considered as an unknown gene in SGD and...”
- More
S36A2_HUMAN / Q495M3 Proton-coupled amino acid transporter 2; Proton/amino acid transporter 2; Solute carrier family 36 member 2; Transmembrane domain rich protein 1; Tramdorin-1 from Homo sapiens (Human) (see 3 papers)
TC 2.A.18.8.6 / Q495M3 Proton-coupled amino acid transporter 2 (Proton/amino acid transporter 2) (Solute carrier family 36 member 2) (Tramdorin-1) from Homo sapiens (see 5 papers)
NP_861441 proton-coupled amino acid transporter 2 from Homo sapiens
20% identity, 83% coverage
- function: Electrogenic proton/amino acid symporter with a high selectivity for the small side chains amino acids glycine, alanine and proline, where both L- and D-enantiomers are transported. Extension of the backbone length, as in beta-alanine and 4-aminobutanoate or methylation of the amino group, as in sarcosine and N,N- dimethylglycine, are also tolerated but decrease transport efficiency. A free carboxyl group is preferred.
catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
catalytic activity: L-proline(out) + H(+)(out) = L-proline(in) + H(+)(in) (RHEA:28963)
catalytic activity: D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) (RHEA:70643)
catalytic activity: 4-hydroxy-L-proline(in) + H(+)(in) = 4-hydroxy-L-proline(out) + H(+)(out) (RHEA:70663)
catalytic activity: L-serine(in) + H(+)(in) = L-serine(out) + H(+)(out) (RHEA:28887)
catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459)
catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
catalytic activity: sarcosine(in) + H(+)(in) = sarcosine(out) + H(+)(out) (RHEA:70655)
catalytic activity: N,N-dimethylglycine(in) + H(+)(in) = N,N-dimethylglycine(out) + H(+)(out) (RHEA:70659) - substrates: Amino acids, H+
- Compendium of causative genes and their encoded proteins for common monogenic disorders.
Apgar, Protein science : a publication of the Protein Society 2022 - THE CONCISE GUIDE TO PHARMACOLOGY 2017/18: Transporters
Alexander, British journal of pharmacology 2017 - “...Amino acid Transporter 2 Systematic nomenclature SLC36A1 SLC36A2 HGNC, UniProt SLC36A1 , Q7Z2H8 SLC36A2 , Q495M3 Common abreviation PAT1 PAT2 Substrates muscimol [ 525 ], arecaidine [ 525 ], betaine [ 525 ], Lcycloserine [ 525 ], 5aminolevulinic acid [ 525 ], gaboxadol [ 330 ,...”
- The Concise Guide to PHARMACOLOGY 2015/16: Transporters
Alexander, British journal of pharmacology 2015 - “...SLC36A3 SLC36A4 Common abreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1 , Q7Z2H8 SLC36A2 , Q495M3 SLC36A3 , Q495N2 SLC36A4 , Q6YBV0 Substrates MeAIB [ 86 ], betaine , vigabatrin [ 1 ], 5aminolevulinic acid , guanidinopropionic acid , gaboxadol [ 299 ], Lazetidine2carboxylate [ 274...”
- The Concise Guide to PHARMACOLOGY 2013/14: transporters
Alexander, British journal of pharmacology 2013 - “...SLC36A1 SLC36A2 SLC36A3 SLC36A4 Common abbreviation PAT1 PAT2 PAT3 PAT4 HGNC, UniProt SLC36A1, Q7Z2H8 SLC36A2, Q495M3 SLC36A3, Q495N2 SLC36A4, Q6YBV0 Endogenous substrates L-alanine, glycine, GABA, -alanine, taurine, L-proline, D-serine, D-cysteine, D-proline, D-alanine, trans-4-hydroxy-proline, sarcosine L-alanine, glycine, -alanine, L-proline, trans-4-hydroxy-proline, sarcosine L-tryptophan 381 , L-proline 381 Substrates...”
- Identification of Key Biomarkers and Immune Infiltration in Sporadic Vestibular Schwannoma Basing Transcriptome-Wide Profiling.
Shi, World neurosurgery 2022 (PubMed)- GeneRIF: Identification of Key Biomarkers and Immune Infiltration in Sporadic Vestibular Schwannoma Basing Transcriptome-Wide Profiling.
- ASC-1, PAT2, and P2RX5 are cell surface markers for white, beige, and brown adipocytes.
Ussar, Science translational medicine 2014 - GeneRIF: The amino acid transporter PAT2 and the purinergic receptor P2RX5 are cell surface markers expressed in classical brown and beige adipocytes.
- Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
Trynka, Gut 2009 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Fine mapping of the CELIAC2 locus on chromosome 5q31-q33 in the Finnish and Hungarian populations.
Koskinen, Tissue antigens 2009 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
LOC105049578 amino acid transporter ANT1-like from Elaeis guineensis
24% identity, 69% coverage
- Genes, pathways and networks responding to drought stress in oil palm roots
Wang, Scientific reports 2020 - “...oil palm seedlings. Gene Annotation Expression Ion transport LOC105045862 Ammonium transporter 2 member 1 Up LOC105049578 Amino acid transporter ANT1 Up LOC105037902 Receptor-like protein kinase HSL1 Down LOC105033828 Cation/H(+) antiporter 20 Up LOC105039277 Plasma membrane ATPase Down LOC105052943 Plasma membrane ATPase 4 Up LOC105047848 Potassium channel...”
NCU05775 amino acid transporter from Neurospora crassa OR74A
20% identity, 55% coverage
- RNAseq and targeted metabolomics implicate RIC8 in regulation of energy homeostasis, amino acid compartmentation, and asexual development in <i>Neurospora crassa</i>
Quinn, mBio 2024 - “...AVT3 ) leads to slightly higher arginine levels in nitrogen-replete medium. ( 58 ) aap-13 NCU05775 AVT3 and AVT4 Out MFS (major facilitator superfamily) mdr-7 NCU01095 VBA2 In Basic amino acid importer in the vacuolar membrane. Vacuoles from the mutant have a defect in arginine uptake....”
- Systems biology of the qa gene cluster in Neurospora crassa
Tang, PloS one 2011 - “...valine, isoleucine degradation (1.05.01, 01.01.11.04.02); aromatic amino acid metabolism (1.01.09.05.02, NCU04072, NCU09429, 1.01.09.04.01); transport (20.01.03, NCU05775, 20.01.03.01); carbohydrate metabolism (1.05.01.01.01, 1.05.01.01.02, 2.01, NCU09429); unidirectional cell growth morphogenesis (40.01.03); membrane-related (16.09, 14.07.04, 20.03.01.01; QA metabolism (1.20, qa gene cluster encoded proteins; unclassified (99 and no KEGG assignment...”
- “...in Table 3 ; one of these is thought to be an amino acid transporter (NCU05775). Another is thought to be a lactose transporter (NCU00801). Ensemble fitting of 7 distinct genetic networks to the profiling data from the different microarray experiments In this section we specifically...”
NCU03783 transmembrane domain transporter from Neurospora crassa OR74A
21% identity, 44% coverage
NP_647555 proton-coupled amino acid transporter 2 from Rattus norvegicus
21% identity, 58% coverage
S36A2_MOUSE / Q8BHK3 Proton-coupled amino acid transporter 2; Proton/amino acid transporter 2; Solute carrier family 36 member 2; Transmembrane domain rich protein 1; Tramdorin-1 from Mus musculus (Mouse) (see 5 papers)
TC 2.A.18.8.2 / Q8BHK3 Electrogenic, proton-coupled, amino acid symporter 2 (PAT2; Tramdorin-1; SLC36A2) (transports small amino acids: glycine, alanine and proline; found in the ER, not in lysosomes, of neuronal cells in the brain and spinal cord; it can catalyze bidirectional transport depending on the driving force) (Boll et al., 2004; from Mus musculus (Mouse) (see 9 papers)
Slc36a2 / RF|NP_694810.1 proton-coupled amino acid transporter 2 from Mus musculus (see paper)
NP_694810 proton-coupled amino acid transporter 2 from Mus musculus
20% identity, 58% coverage
- function: Electrogenic proton/amino acid symporter with a high selectivity for the small side chains amino acids glycine, alanine and proline, where both L- and D-enantiomers are transported. Extension of the backbone length, as in beta-alanine and 4-aminobutanoate or methylation of the amino group, as in sarcosine and N,N- dimethylglycine, are also tolerated but decrease transport efficiency. A free carboxyl group is preferred.
catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
catalytic activity: L-proline(out) + H(+)(out) = L-proline(in) + H(+)(in) (RHEA:28963)
catalytic activity: D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) (RHEA:70643)
catalytic activity: 4-hydroxy-L-proline(in) + H(+)(in) = 4-hydroxy-L-proline(out) + H(+)(out) (RHEA:70663)
catalytic activity: L-serine(in) + H(+)(in) = L-serine(out) + H(+)(out) (RHEA:28887)
catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459)
catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
catalytic activity: sarcosine(in) + H(+)(in) = sarcosine(out) + H(+)(out) (RHEA:70655)
catalytic activity: N,N-dimethylglycine(in) + H(+)(in) = N,N-dimethylglycine(out) + H(+)(out) (RHEA:70659) - substrates: Amino acids, H+
tcdb comment: Rubio-Aliaga et al., 2004).SLC36A2 is expressed at the apical surface of the human renal proximal tubule where it functions in the reabsorption of glycine, proline, hydroxyproline and amino acid derivatives with narrower substrate selectivity and higher affinity (Km0.1-0.7 mM) than SLC36A1. Mutations in SLC36A2 lead to hyperglycinuria and iminoglycinuria - ASC-1, PAT2, and P2RX5 are cell surface markers for white, beige, and brown adipocytes.
Ussar, Science translational medicine 2014 - GeneRIF: The amino acid transporter PAT2 and the purinergic receptor P2RX5 are cell surface markers expressed in classical brown and beige adipocytes.
- Transport of L-proline by the proton-coupled amino acid transporter PAT2 in differentiated 3T3-L1 cells.
Zebisch, Amino acids 2013 (PubMed)- GeneRIF: During the 14 day differentiation period the uptake of the prototype PAT2 substrate L-[(3)H]proline increased ~5-fold.
- Substrate specificity and transport mode of the proton-dependent amino acid transporter mPAT2.
Foltz, European journal of biochemistry 2004 (PubMed)- GeneRIF: proton binding affinity to PAT2 is substrate-independent, favouring a sequential binding of proton followed by substrate
- Association of PAT proteins with lipid storage droplets in term fetal membranes.
Ackerman, Placenta (PubMed)- GeneRIF: Classification of lipid storage droplets based on this protein suggests that these organelles may serve specialized functions within individual cells.
LOC100168251 proton-coupled amino acid transporter-like protein CG1139 from Acyrthosiphon pisum
20% identity, 75% coverage
LOC100644921 proton-coupled amino acid transporter-like protein CG1139 from Bombus terrestris
22% identity, 65% coverage
S36A2_RAT / Q8K415 Proton-coupled amino acid transporter 2; Proton/amino acid transporter 2; rPAT2; Solute carrier family 36 member 2; Transmembrane domain rich protein 1; Tramdorin-1 from Rattus norvegicus (Rat) (see 2 papers)
22% identity, 71% coverage
- function: Electrogenic proton/amino acid symporter with a high selectivity for the small side chains amino acids glycine, alanine and proline, where both L- and D-enantiomers are transported. Extension of the backbone length, as in beta-alanine and 4-aminobutanoate or methylation of the amino group, as in sarcosine and N,N- dimethylglycine, are also tolerated but decrease transport efficiency. A free carboxyl group is preferred.
catalytic activity: glycine(in) + H(+)(in) = glycine(out) + H(+)(out) (RHEA:28899)
catalytic activity: L-alanine(in) + H(+)(in) = L-alanine(out) + H(+)(out) (RHEA:29443)
catalytic activity: D-alanine(in) + H(+)(in) = D-alanine(out) + H(+)(out) (RHEA:28903)
catalytic activity: L-proline(out) + H(+)(out) = L-proline(in) + H(+)(in) (RHEA:28963)
catalytic activity: D-proline(out) + H(+)(out) = D-proline(in) + H(+)(in) (RHEA:70643)
catalytic activity: 4-hydroxy-L-proline(in) + H(+)(in) = 4-hydroxy-L-proline(out) + H(+)(out) (RHEA:70663)
catalytic activity: L-serine(in) + H(+)(in) = L-serine(out) + H(+)(out) (RHEA:28887)
catalytic activity: D-serine(out) + H(+)(out) = D-serine(in) + H(+)(in) (RHEA:70647)
catalytic activity: beta-alanine(in) + H(+)(in) = beta-alanine(out) + H(+)(out) (RHEA:29459)
catalytic activity: 4-aminobutanoate(in) + H(+)(in) = 4-aminobutanoate(out) + H(+)(out) (RHEA:28915)
catalytic activity: sarcosine(in) + H(+)(in) = sarcosine(out) + H(+)(out) (RHEA:70655)
catalytic activity: N,N-dimethylglycine(in) + H(+)(in) = N,N-dimethylglycine(out) + H(+)(out) (RHEA:70659)
LOC105841453 proton-coupled amino acid transporter 1 from Bombyx mori
20% identity, 72% coverage
LOC100642564 proton-coupled amino acid transporter-like protein pathetic from Bombus terrestris
21% identity, 58% coverage
ANT1_ARATH / Q9SF09 Amino acid transporter ANT1; Aromatic and neutral amino acid transporter 1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT3G11900 ANT1 (AROMATIC AND NEUTRAL TRANSPORTER 1); amino acid transmembrane transporter/ aromatic amino acid transmembrane transporter/ neutral amino acid transmembrane transporter from Arabidopsis thaliana
21% identity, 65% coverage
- function: Translocates aromatic and neutral amino acids such as tyrosine, tryptophan, phenylalanine, histidine, proline, leucine, valine, glutamine, as well as arginine. Transports the auxins indole-3- acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D).
- Transcription factor OsMYB2 triggers amino acid transporter OsANT1 expression to regulate rice growth and salt tolerance
Nie, Plant physiology 2025 (no snippet) - Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis
Zhang, BMC genomic data 2021 - “...AT3G10810 zinc finger (C3HC4-type RING finger) family protein 6.4 AT3G11280 Duplicated homeodomain-like superfamily protein 5.9 AT3G11900 aromatic and neutral transporter 1 7.1 AT3G12120 fatty acid desaturase 2 7.8 AT3G22160 JAV1 is a repressor of jasmonate-mediated defense responses 11.3 AT3G22170 far-red elongated hypocotyls 3 9.5 AT3G27503 Encodes...”
- Amino Acid Transporters in Plants: Identification and Function
Yao, Plants (Basel, Switzerland) 2020 - “...At2g01170 BAT1 Ala, Arg, Glu, Lys vascular tissues plasma membrane [ 39 , 110 ] At3g11900 ANT1 aromatic and neutral amino acid, Arg flowers and cauline leaves ER in the perinuclear region ant1 mutants: Essential amino acids within the SEs [ 78 , 88 , 111...”
- The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
Elashry, Plant physiology and biochemistry : PPB 2013 - “...2.7 0.2 0.34 At1g08230 AtProT4 3.1 3.3 0.2 0.36 At5g41800 AtProT5 5.7 6 0.3 0.14 At3g11900 ANT1 6.7 6 0.7 0.06 At5g65990 ANT2 4.5 6.9 2.4 a 0.00 At4g38250 ANT3 8.6 7 1.6 a 0.00 At2g41190 AVT1L1 5.2 6.2 1 0.05 At3g09340 AVT1L2 not available on...”
PATH_DROME / Q9VT04 Proton-coupled amino acid transporter-like protein pathetic from Drosophila melanogaster (Fruit fly) (see 4 papers)
TC 2.A.18.8.3 / Q9VT04 Amino acid transporter (low capacity, high affinity) and amino acid-dependent signal transduction protein, Pathetic (Path) from Drosophila melanogaster (Fruit fly) (see 2 papers)
path / RF|NP_648327.1 RH24992p from Drosophila melanogaster (see paper)
NP_648327 pathetic, isoform A from Drosophila melanogaster
21% identity, 67% coverage
- function: Amino acid transporter which has pH-dependent electrogenic transport activity for alanine and glycine but not for proline (PubMed:15843412). Plays a role in positive regulation of growth by directly or indirectly modulating the effects of the TOR signaling pathway (PubMed:15843412, PubMed:22574197). Required in a cell- autonomous manner for dendrite growth in neurons with large dendrite arbors (PubMed:26063572, PubMed:26735916).
disruption phenotype: Severe dendrite growth defects in class IV da neurons which normally have large dendrite arbors, moderate defects in class III neurons which normally have medium-sized dendrite arbors and no effect in class I or III neurons which normally have small dendrite arbors (PubMed:26063572). Induction of starvation response and altered protein homeostasis in class III and IV neurons (PubMed:26063572). Severe defects in axon growth with mutants showing no defects 48 hours after egg laying (AEL) but severe defects apparent by 120 hours AEL (PubMed:26735916). - substrates: Amino acids
- Proteomic Analysis of Red Ginseng on Prolonging the Life Span of Male Drosophila melanogaster
Hou, Frontiers in pharmacology 2021 - “...0.029160556 Up 27 Q8SYU2 RpL7-like 1.211114 0.031963084 Up 28 M9WDW1 Lds-RA 1.210729 0.007067795 Up 29 Q9VT04 Path 1.207497 0.012074239 Up 30 Q9VNX8 CG7414 1.205446 0.00520136 Up 31 P40301 Prosalpha2 1.201562 0.026267051 Up 32 Q8MS69 Dmel\CG9596 1.201365 0.043806106 Up 33 A8YPP4 CG30296 0.832942 0.015104015 Down 34 Q9VS47...”
- The SLC36 transporter Pathetic is required for neural stem cell proliferation and for brain growth under nutrition restriction.
Feng, Neural development 2020 - GeneRIF: The SLC36 transporter Pathetic is required for neural stem cell proliferation and for brain growth under nutrition restriction.
- The SLC36 transporter Pathetic is required for extreme dendrite growth in Drosophila sensory neurons.
Lin, Genes & development 2015 - GeneRIF: mutation of pathetic impinges on nutrient responses and protein homeostasis specifically in neurons with large dendrite arbors but not in other cells.
- Functions of the SLC36 transporter Pathetic in growth control.
Lin, Fly 2015 - GeneRIF: Path is a nutrient sensor with widespread function in Drosophila.
LOC113506931 proton-coupled amino acid transporter-like protein pathetic from Trichoplusia ni
22% identity, 80% coverage
cgd7_4800 ABC transporter, amino acid transporter 12 transmembrane spanning subunit from Cryptosporidium parvum Iowa II
21% identity, 45% coverage
J7RA72 Putative lysine/histidine transporter from Hordeum vulgare
22% identity, 72% coverage
TGME49_227580 transmembrane amino acid transporter protein from Toxoplasma gondii ME49
20% identity, 68% coverage
- A Toxoplasma gondii putative amino acid transporter localizes to the plant-like vacuolar compartment and controls parasite extracellular survival and stage differentiation
Piro, mSphere 2024 - “...acid transporters ( Fig. S1 ). The three genes encoding these proteins (TGME49_227430, TGME49_227570, and TGME49_227580) are all located on chromosome X. TGME49_227570 and TGME49_227580 are adjacent to one another in a head-to-tail arrangement, whereas TGME49_227430 is ~30 kbp away and in the opposite orientation. The...”
- “...to this homology, the protein encoded by TGME49_226060 was named TgAAT1, and TGME49_227430, TGME49_227570, and TGME49_227580 were named TgAAT2-4, respectively. Despite low amino acid conservation with SLC38A9, structural analysis of the TgAAT proteins using Alphafold2, TOPCONS, and I-TASSER software suggested the presence of 11 transmembrane domains...”
AT3G01760 lysine and histidine specific transporter, putative from Arabidopsis thaliana
20% identity, 72% coverage
- Amino acids biosynthesis in root hair development: a mini-review
Montiel, Biochemical Society transactions 2024 - “...differentiation zone where the RHs are formed [ 86 , 87 ]. A related LHT6 (At3g01760) A. thaliana gene, expressed in root tissues, including the RHs, encodes a transporter involved in uptake of acidic amino acids, Ala and Glu [ 85 ]. Rice ( Oryza sativa...”
- The tea plant CsLHT1 and CsLHT6 transporters take up amino acids, as a nitrogen source, from the soil of organic tea plantations
Li, Horticulture research 2021 - “...IDs are as follows: AtLHT1 (AT5G40780), AtLHT2 (AT1G24400), AtLHT3 (AT1G61270), AtLHT4 (AT1G47670), AtLHT5 (AT1G67640), AtLHT6 (AT3G01760), AtLHT7 (AT4G35180), AtLHT8 (AT1G71680), AtLHT9 (AT1G25530), AtLHT10 (AT1G48640), CsLHT1 (TEA026462), CsLHT2 (TEA021847), CsLHT3 (TEA033469), CsLHT4 (TEA029168), CsLHT5 (TEA016092), CsLHT6 (TEA003706), and CsLHT7 (TEA021821). Multiple sequence alignment of full-length proteins was...”
- Organic nitrogen nutrition: LHT1.2 protein from hybrid aspen (Populus tremula L. x tremuloides Michx) is a functional amino acid transporter and a homolog of Arabidopsis LHT1
Gratz, Tree physiology 2021 - “...( AtLHT2 ); At1g61270 ( AtLHT3 ); At1g47670 ( AtLHT4 ); At1g67640 ( AtLHT5 ); At3g01760 ( AtLHT6 ); At4g35180 ( AtLHT7 ); At1g71680 ( AtLHT8 ); At1g25530 ( AtLHT9 ); At1g48640 ( AtLHT10 ); At2g18960 ( AtAHA1 ); At3g53090 ( AtUPL7 ). Poplar sequence data...”
- Different and overlapping functions of Arabidopsis LHT6 and AAP1 transporters in root amino acid uptake
Perchlik, Journal of experimental botany 2014 - “...and Tegeder, 2004 ; Hirner et al. , 2006 ). It was found that LHT6 (At3g01760) is strongly expressed in roots and this transporter was examined further with respect to its function in amino acid root uptake using localization analyses, as well as growth and transport...”
- The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
Elashry, Plant physiology and biochemistry : PPB 2013 - “...on GeneChip At1g47670 AtLHT4 5.9 5 0.9 a 0.00 At1g67640 AtLHT5 3.6 3.2 0.4 0.17 At3g01760 AtLHT6 not available on GeneChip At4g35180 AtLHT7 3.4 3.6 0.2 0.42 At1g71680 AtLHT8 3.9 3.4 0.5 0.09 At2g39890 AtProT1 6.8 7.4 0.6 0.20 At3g55740 AtProT2 4.4 4.6 0.2 0.45 At2g36590...”
- Molecular Evolution of Plant AAP and LHT Amino Acid Transporters
Tegeder, Frontiers in plant science 2012 - “...At1G24400 Arabidopsis thaliana 441 AtLHT3 At1G61270 Arabidopsis thaliana 451 AtLHT5 At1G67640 Arabidopsis thaliana 441 AtLHT6 At3G01760 Arabidopsis thaliana 455 AtLHT8 At1G71680 Arabidopsis thaliana 448 AtLHT9 At1G25530 Arabidopsis thaliana 440 AtLHT10 At1G48640 Arabidopsis thaliana 453 MtLHT1A Medtr2g122930 Medicago truncatula 453 MtLHT1B Medtr6g025000 Medicago truncatula 484 MtLHT2A AC233656_24.1...”
LOC105051602 lysine histidine transporter 1 from Elaeis guineensis
20% identity, 69% coverage
LDBPK_071340 amino acid transporter, putative from Leishmania donovani
21% identity, 68% coverage
- Comprehensive proteomic analysis of autophagosomes derived from Leishmania-infected macrophages
Nandan, PloS one 2023 - “...LDBPK_170170 A0A0R4J963 Elongation factor 1-alpha LDBPK_050510 E9B8E1 ATPase alpha subunit LDBPK_051190 E9B8K9 Prefoldin subunit, putative LDBPK_071340 E9B9C1 Amino acid transporter, putative LDBPK_100960 E9BAE1 Small GTP-binding protein Rab11, putative LDBPK_130330 E9BBA8 Tubulin alpha chain LDBPK_190200 E9BE16 ADP/ATP translocase LDBPK_190710 E9BE66 Glycosomal Malate dehydrogenase LDBPK_201350 E9BET4 Calpain-like cysteine...”
- “...identified five Leishmania integral membrane proteins according to their UniProt annotations: amino acid transporter ( LDBPK_071340 ), ADP/ATP translocase ( LDBPK_190200 ), glycosomal membrane like protein ( LDBPK_240140 ), glycosomal membrane protein ( LDBPK_282430 ), and uncharacterized protein ( LDBPK_350150 ). These membrane proteins may be...”
Q4DMS3 ABC-type polar-amino-acid transporter (EC 7.4.2.1) from Trypanosoma cruzi (see paper)
21% identity, 67% coverage
LHT1_ARATH / Q9FKS8 Lysine histidine transporter 1 from Arabidopsis thaliana (Mouse-ear cress) (see 4 papers)
TC 2.A.18.2.2 / Q9FKS8 Lysine/histidine transporter, LHT1 (see 8 papers)
NP_851109 lysine histidine transporter 1 from Arabidopsis thaliana
AT5G40780, NP_851109 LHT1; amino acid transmembrane transporter from Arabidopsis thaliana
20% identity, 79% coverage
- function: Amino acid-proton symporter. Transporter with a broad specificity for histidine, lysine, glutamic acid, alanine, serine, proline and glycine. Involved in both apoplastic transport of amino acids in leaves and their uptake by roots.
disruption phenotype: Lower biomass at the time of harvest, but no visible phenotype until bolting. Decreased uptake of L-histidine, L- glutamine, glutamic acid, L-serine, glycine, L-asparagine, aspartic acid, L-proline and L- or D-alanine. - substrates: Histidine, lysine
- Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature
Valadares, Journal of fungi (Basel, Switzerland) 2020 - “...cationic amino acid transporter (ID Q84MA5, FC = 6.7), and a lysine histidine transporter (ID Q9FKS8, FC = 4.5), all likely located on the plasma membrane, were also up-regulated in Myc roots ( Table S7 ). The most abundant transcripts up-regulated in Myc roots ( Table...”
- Subgroup 4 R2R3-MYBs in conifer trees: gene family expansion and contribution to the isoprenoid- and flavonoid-oriented responses
Bedon, Journal of experimental botany 2010 - “...ABC transporter, PDR-like Q0IRX8 1E-30 FV 2.3 3.4E-06 1.8 1.7E-03 GQ03238_I01 BT111495 Amino acid permease Q9FKS8 1E-16 2.2 2.5E-07 1.6 8.0E-04 GQ04005_E15 DV983142.2* Sulphate transporter (SULTR1;3) Q9AT12 5E-58 1.7 3.7E-05 1.5 5.4E-03 GO:0006118 Electron transport GQ03709_B14 BT115936 UDP-glucose dehydrogenase Q6RK07 0E+00 1.5 1.2E-05 1.3 5.1E-03 GQ03510_P10...”
- AtLHT1 Transporter Can Facilitate the Uptake and Translocation of a Glycinergic-Chlorantraniliprole Conjugate in Arabidopsis thaliana.
Chen, Journal of agricultural and food chemistry 2018 (PubMed)- GeneRIF: Seedlings deficient in LHT1 exhibited a reduction with respect to both the uptake and root-to-shoot transfer of chlorantraniliprole-glycine conjugate
- Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil.
Ganeteg, Plant, cell & environment 2017 (PubMed)- GeneRIF: LHT1 expression is crucial for plant uptake of organic Nitrogen from soil.
- Genetic identification of ACC-RESISTANT2 reveals involvement of LYSINE HISTIDINE TRANSPORTER1 in the uptake of 1-aminocyclopropane-1-carboxylic acid in Arabidopsis thaliana.
Shin, Plant & cell physiology 2015 (PubMed)- GeneRIF: Map-based cloning of ARE2 demonstrated that LYSINE HISTIDINE TRANSPORTER1 (LHT1), encoding an amino acid transporter, is the gene responsible.
- GeneRIF: A class of amino acid transporters including LHT1 takes part in transport of 1-Aminocyclopropane-1-carboxylic acid (ACC), thereby influencing exogenous ACC-induced ethylene responses in A. thaliana.[LHT1]
- Arabidopsis LHT1 is a high-affinity transporter for cellular amino acid uptake in both root epidermis and leaf mesophyll.
Hirner, The Plant cell 2006 - GeneRIF: LHT1 functions in the uptake of amino acids in roots and the supply of leaf mesophyll with xylem-derived amino acids.
- Amino acids biosynthesis in root hair development: a mini-review
Montiel, Biochemical Society transactions 2024 - “...in soil [ 84 , 85 ]. Another amino acid transporter, LYSINE HISTIDINE TRANSPORTER1, (LHT1, AT5G40780) is involved in Gln, Ala, Glu and Asp uptake in A. thaliana roots, especially when present at low soil concentrations, which can be as low as 2M [ 84 ]....”
- Transporter-mediated depletion of extracellular proline directly contributes to plant pattern-triggered immunity against a bacterial pathogen
Rogan, Nature communications 2024 - “...oligonucleotides for qRT-PCR to measure transcripts from the indicated genes: AT2G28390 , 5-AACTCTATGCAGCATTTGATCCACT-3 and 5-TGATTGCATATCTTTATCGCCATC-3; AT5G40780 ( LHT1 ), 5-CGTTGAAATCGGTGTTTGCATCGT-3 and 5-GCGATTGTTGAGTAGCTGAGAGAC-3. Statistics Statistical analyses of data were done using Microsoft Excel, Metaboanalyst 5.0 73 , R with the MetaboAnalyst for R package 74 , and...”
- Root-based inorganic carbon uptake increases the growth of Arabidopsis thaliana and changes transporter expression and nitrogen and sulfur metabolism
Gamarra, Frontiers in plant science 2024 - “...OCT2 1.37 2.59 218.72 AT1G16390 Organic cation/carnitine transporter 3 OCT3 1.09 2.13 642.40 Aminoacid transporter AT5G40780 Lysine histidine transporter 1 LHT1 1.12 2.17 5278.25 Magnesium transporter AT1G29830 Magnesium transporter CorA-like family protein - 1.10 2.14 83.20 Potassium transporter AT5G14880 Potassium transporter POT8 1.09 2.13 5594.82 Metal...”
- The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites
Scholz, International journal of molecular sciences 2023 - “...Amino acid (GDU family) GDU7 At5g38770 x x 1.81 x Amino acid (LHT family) LHT1 At5g40780 x 2.16 x x Amino acid (LHT family) LHT2/AATL2 At1g24400 x x x 2.06 Amino acid (LHT family) LHT3 At1g61270 x x x 1.53 Amino acid (LHT family) LHT7 At4g35180...”
- The EXO70 inhibitor Endosidin2 alters plasma membrane protein composition in Arabidopsis roots
Li, Frontiers in plant science 2023 - “...0 NO AT5G35940 Mannose-binding lectin superfamily protein 0.38 organic acid metabolic process (GO:0006082) 0 NO AT5G40780 LYSINE HISTIDINE TRANSPORTER 1 LHT1 0.39 amino acid transmembrane transport (GO:0003333) 11 NO AT1G17260 AUTOINHIBITED H(+)-ATPASE 10 AHA10 0.40 proton transmembrane transport (GO:1902600) 10 NO AT2G01520 MLP-LIKE PROTEIN 328 MLP328...”
- A 1-aminocyclopropane-1-carboxylic-acid (ACC) dipeptide elicits ethylene responses through ACC-oxidase mediated substrate promiscuity
Vaughan-Hirsch, Frontiers in plant science 2022 - “...ecotype Col-0 was used as wild-type control, the etr1-1 (AT1G66340; N237) EMS mutant and lht1-5 (AT5G40780; SALK_115555C) mutant were obtained from NASC. Seeds were surface sterilized by incubation with 70% ethanol (v/v) for 2 mins, followed incubation in 5% bleach (NaOCl) (v/v) for 5 mins. Seeds...”
- Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration
Kanapin, International journal of molecular sciences 2022 - “...AT5G67140 [ 58 ] SCF ubiquitin ligase complex Chr4:14879575 Chr4:14879658 Lus10041581 lysine histidine transporter 1 AT5G40780, LHT1 [ 30 ] solute transporter Chr4:15210519 Lus10041644 fucosyltransferase 1 AT2G03220, ATFT1, ATFUT1, FT1, MUR2 [ 59 ] xyloglucan synthesis Lus10041651 cinnamoyl CoA reductase 1 AT1G15950, ATCCR1, IRX4 [ 60...”
- Transcriptomics Using the Enriched Arabidopsis Shoot Apex Reveals Developmental Priming Genes Involved in Plastic Plant Growth under Salt Stress Conditions
Cha, Plants (Basel, Switzerland) 2022 - “...] AT4G27260 GH3.5 3.81 0.21 UP 2.47 0.29 UP IAA-dependent salt tolerance [ 47 ] AT5G40780 LHT1 3.33 0.32 DOWN 4.62 0.41 DOWN uptake of amino acid [ 51 ] AT1G75780 TUB1 4.61 0.48 UP 3.36 0.44 UP - AT1G62300 WRKY6 2.89 0.16 DOWN 3.91 0.49...”
- More
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory