Family Search for PF08768 (THAP4_heme-bd)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

PF08768 hits 27 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

A1T297 Peroxynitrite isomerase 1 from Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 / PYR-1)
Aligns to 11:162 / 164 (92.7%), covers 99.3% of PF08768, 177.9 bits

• Characterization of the 2,6-Dimethylphenol Monooxygenase MpdAB and Evaluation of Its Potential in Vitamin E Precursor Synthesis.
  Ji, Applied and environmental microbiology 2022 (no snippet)
• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens.
  Bianchetti, Proteins 2011
  • “...acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and fatty acid-binding like protein from Mycobacterium vanbaalenii (A1T297). Residues that are within 4 A of the bound heme of cTHAP4 are highlighted in green. The strictly conserved histidine that coordinates the heme is highlighted in red. Table I...”

A0R6J8 Peroxynitrite isomerase 1 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
Aligns to 7:158 / 161 (94.4%), covers 99.3% of PF08768, 174.8 bits

• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens.
  Bianchetti, Proteins 2011
  • “...thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and fatty acid-binding like protein from Mycobacterium vanbaalenii (A1T297). Residues that are within 4 A of the bound heme of cTHAP4 are highlighted in green. The strictly conserved histidine that...”

NB_ARATH / O64527 Peroxynitrite isomerase Rv2717c; Ferric Arabidopsis thaliana nitrobindin; At-Nb(III); EC 5.99.-.- from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G79260 hypothetical protein from Arabidopsis thaliana
Aligns to 19:165 / 166 (88.6%), covers 99.3% of PF08768, 173.7 bits

• function: Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively) (PubMed:32295384). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo (PubMed:32295384, PubMed:19938152).
  catalytic activity: peroxynitrite = nitrate (RHEA:63116)
  cofactor: heme b (Binds 1 heme b group per subunit, that coordinates a highly solvent-exposed Fe(III) atom.)
  subunit: Homodimer.
• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...(Q8WY91), THAP4 from Callithrix jacchus (A6MKW1), THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and fatty acid-binding like protein from Mycobacterium vanbaalenii (A1T297). Residues that are within 4 A of...”
• Transcriptomic and proteomic analyses of Mangifera indica in response to Xanthomonas critis pv. mangiferaeindicae
  Liu, Frontiers in microbiology 2023
  • “...mango035105 SKP20 7.073 12.49 11.507 4.683 4.047 2.957 2534340.083 2353001.625 2375078.5 2237931.625 1963994.292 1739793.25 mango035149 At1g79260 14.97 26.47 26.68 4.42 10.743 11.28 2437932.083 2600219.792 1519332.604 2652060.667 1895509.958 2298095.917 TABLE 3 A total of 58 DEGs screened by WGCNA. DEGs express level Id Symbol RN0d RN2d RN6d...”
  • “...3.987 4.823 2.947 9.093 10.003 8.687 mango035105 SKP20 7.073 12.49 11.507 4.683 4.047 2.957 mango035149 At1g79260 14.97 26.47 26.68 4.42 10.743 11.28 TABLE 4 A total of 31 DEPs screened by WGCNA. Protein_id Symbol RN0d RN2d RN6d KT0d KT2d KT6d mango000296 CYP98A2 120449.669 336072.583 400800.042 254158.284...”
• A family of GFP-like proteins with different spectral properties in lancelet Branchiostoma floridae
  Baumann, Biology direct 2008
  • “...GFP-related models have p-values from 0.002 to 0.005. An apparently unrelated -barrel family, specified by At1g79260 protein from Arabidopsis thaliana , is seen with p-value 0.039, though the alignment is only partial and reciprocal search does not detect the G2 domain. G2 model also finds bacterial...”
• The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria
  Shepard, Journal of bacteriology 2007
  • “...3. (A) Structural superposition of Rv0813c (red) with At1g79260 (2A13; green) and Rv2717c (2FR2; light cyan). (B) Structural superposition (93 core Ca...”
  • “...structures of two of these proteins, Arabidopsis thaliana At1g79260 and M. tuberculosis Rv2717c (Protein Data Bank codes 2A13 and 2FR2) (Fig. 3A), have been...”

NP_001323382 nitrobindin heme-binding domain protein from Arabidopsis thaliana
Aligns to 33:179 / 180 (81.7%), covers 99.3% of PF08768, 173.3 bits

• The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1.
  Bianchetti, Proteins 2010
  • GeneRIF: Based on both structural and functional similarity to the nitrophorins, the protein was named as nitrobindin and hypothesized to play a role in NO transport.

3ia8A / Q8WY91 The structure of thE C-terminal heme nitrobindin domain of thap domain-containing protein 4 from homo sapiens (see paper)
Aligns to 7:160 / 162 (95.1%), covers 99.3% of PF08768, 173.0 bits

• Ligand: protoporphyrin ix containing fe (3ia8A)

A6MKW1 THAP domain containing protein 4-like protein (Fragment) from Callithrix jacchus
Aligns to 26:179 / 182 (84.6%), covers 99.3% of PF08768, 172.4 bits

• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...(Q6P3Z3), THAP4 from Rattus norvegicus (Q642B6), THAP4 from Homo sapiens (Q8WY91), THAP4 from Callithrix jacchus (A6MKW1), THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and fatty acid-binding like protein from...”

A5BBZ0 THAP4-like heme-binding beta-barrel domain-containing protein from Vitis vinifera
Aligns to 17:163 / 164 (89.6%), covers 99.3% of PF08768, 169.8 bits

• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and fatty acid-binding like protein from Mycobacterium vanbaalenii (A1T297). Residues that are within 4 A of the bound heme of cTHAP4 are...”
• The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
  Bianchetti, Proteins 2010
  • “...with the highest alignment scores correspond to hypothetical proteins from Vitis vinifera (grape, Uniprot code A5BBZ0), Musa balbisiana (banana, Uniprot code Q1EP49), and Oryza sativa (rice, Uniprot code Q0JKE7). The three hypothetical proteins had identities and similarities to nitrobindin ranging from 76%- 67% and 89%- 86%,...”

MAP2833c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
Aligns to 8:159 / 161 (94.4%), covers 100.0% of PF08768, 169.3 bits

• Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection
  Lamont, BMC genomics 2013
  • “...). The MAP profile in infected macrophages (single cell type infection) identified one fadD ( MAP2833c ) gene and one fadE gene ( MAP3651c ), indicating that beta-oxidation has just initiated within macrophages (Figure 6 ). Comparisons of infected co-cultured MAC-T cells against infected MAC-T cells,...”
  • “...the nascent strand. The implications of this are unclear. Nitric oxide may also interact with MAP2833c, which contains a nitrobindin binding domain that reversibly binds to nitric oxide, and cause further deleterious buildup within the cell [ 68 ]. The network implicates the involvement of MAP4216...”

THAP4_HUMAN / Q8WY91 Peroxynitrite isomerase THAP4; Ferric Homo sapiens nitrobindin; Hs-Nb(III); THAP domain-containing protein 4; EC 5.99.-.- from Homo sapiens (Human) (see 3 papers)
Aligns to 421:574 / 577 (26.7%), covers 99.3% of PF08768, 168.7 bits

• function: Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo, possibly modulating the transcriptional activity residing in the N- terminal region.
  catalytic activity: peroxynitrite = nitrate (RHEA:63116)
  cofactor: heme b (Binds 1 heme b group per subunit, that coordinates a highly solvent-exposed Fe(III) atom.)
  subunit: Homodimer.
• The Protective Action of Metformin against Pro-Inflammatory Cytokine-Induced Human Islet Cell Damage and the Mechanisms Involved.
  Giusti, Cells 2022
  • “...COMPONENT 2 (PTHR14237:SF27) MTARC2 0.01 0.01 Q9BZH6 WD REPEAT-CONTAINING PROTEIN 11 (PTHR14593:SF5) WDR11 0.01 0.01 Q8WY91 THAP DOMAIN-CONTAINING PROTEIN 4 (PTHR15854:SF4) THAP4 0.17 50.62 Q9Y2W1 THYROID HORMONE RECEPTOR-ASSOCIATED PROTEIN 3 (PTHR15268:SF16) THRAP3 0.41 0.22 P05408 NEUROENDOCRINE PROTEIN 7B2 (PTHR12738:SF0) SCG5 0.44 0.01 P48059 LIM AND SENESCENT...”
• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...of THAP4 from Mus musculus (Q6P3Z3), THAP4 from Rattus norvegicus (Q642B6), THAP4 from Homo sapiens (Q8WY91), THAP4 from Callithrix jacchus (A6MKW1), THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and...”

6r3wA / P9WFG7 M.Tuberculosis nitrobindin with a water molecule coordinated to the heme iron atom (see paper)
Aligns to 5:159 / 161 (96.3%), covers 99.3% of PF08768, 165.8 bits

• Ligand: protoporphyrin ix containing fe (6r3wA)

NB1_MYCTU / P9WFG7 Peroxynitrite isomerase 1; Ferric Mycobacterium tuberculosis nitrobindin; Mt-Nb(III); EC 5.99.-.- from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
Rv2717c hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 8:162 / 164 (94.5%), covers 99.3% of PF08768, 165.7 bits

• function: Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). In M.tuberculosis, could be part of the pool of proteins required to scavenge RNS and ROS produced by the host during the immunity response. Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo.
  catalytic activity: peroxynitrite = nitrate (RHEA:63116)
  cofactor: heme b (Binds 1 heme b group per subunit, that coordinates a highly solvent-exposed Fe(III) atom.)
  subunit: Homodimer.
• A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
  Bhagavat, Scientific reports 2017
  • “...5-phosphate oxidase (PNP/PMP oxidase) (pyridoxinephosphate oxidase) (PNPOX) (pyridoxine 5-phosphate oxidase) 0.52 0.79 TTP, UDP 8 Rv2717c Conserved protein 0.41 0.79 GTP, ATP Identification of additional fold types for a possible NTP binding A genome-wide survey for NTP binding sites carried out here enables an investigation of...”
• Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis
  Roychowdhury, Scientific reports 2015
  • “...Rv1755c (plcD) 25595002559600 97.87 3.92 Rv2286c (hypothetical) 26279002628000 97.87 3.92 Rv2349c (plcC) 30301003030200 97.87 3.92 Rv2717c (hypothetical) 30965003096600 97.87 3.92 Rv2787 (hypothetical) 34915003491600 97.87 3.92 Rv3125c (PPE49) Table 4 Spoligotype specific preferential insertion regions of IS 6110 in L4 isolates. LAM Percentage of LAM isolates (threshold...”
• Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
  van, BMC systems biology 2014
  • “...the STRING database [ 33 ] (gene neighbourhood and co-occurrence) allows us to functionally link Rv2717c with DNA repair and cell wall synthesis; NrdR is involved in the control of the synthesis of dNTP needed for DNA replication and/or DNA repair [ 69 ]; and the...”
• The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
  Bianchetti, Proteins 2010
  • “...the Vector Alignment Search Tool (VAST) [ 43 ]. The top hits from VAST were Rv2717c (PDB ID 2FR2) and Rv0813c (PDB ID 2FWV) from Mycobacterium tuberculosis , which were previously solved in the absence of heme by structural genomic groups and were hypothesized to be...”
• The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria
  Shepard, Journal of bacteriology 2007
  • “...linens; Lx, Leifsonia xyli; Mtb, M. tuberculosis Rv2717c; At, Arabidopsis thaliana Atlg79260. 1902 SHEPARD ET AL. FIG. 3. (A) Structural superposition...”
  • “...of Rv0813c (red) with At1g79260 (2A13; green) and Rv2717c (2FR2; light cyan). (B) Structural superposition (93 core Ca positions) of Rv0813c (red) with human...”
• The mycobacterium-specific gene Rv2719c is DNA damage inducible independently of RecA
  Brooks, Journal of bacteriology 2006
  • “...cotranscribed with the two downstream genes Rv2718c and Rv2717c, and microarray analysis indicated that expression of all three of these genes is increased...”
  • “...also the case for the cotranscribed genes Rv2718c and Rv2717c; in each case the induction ratio for the recA deletion strain was approximately 64% that observed...”
• Mycobacterium tuberculosis genes induced during infection of human macrophages
  Dubnau, Infection and immunity 2002
  • “...Unknown Rv0036c, Rv0406c, Rv0811c, Rv1778c, Rv2273, Rv2468c, Rv2632c, Rv2717c, Rv3427c, Rv3493c, Rv3717 a The Rv number is the number assigned to the open...”

Q642B6 Peroxynitrite isomerase THAP4 from Rattus norvegicus
Aligns to 413:566 / 569 (27.1%), covers 99.3% of PF08768, 164.9 bits

• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...sticks. Figure 2 Sequence alignment of THAP4 from Mus musculus (Q6P3Z3), THAP4 from Rattus norvegicus (Q642B6), THAP4 from Homo sapiens (Q8WY91), THAP4 from Callithrix jacchus (A6MKW1), THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein...”

Q2TBI2 Peroxynitrite isomerase THAP4 from Bos taurus
Aligns to 428:581 / 584 (26.4%), covers 99.3% of PF08768, 164.6 bits

• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...(Q642B6), THAP4 from Homo sapiens (Q8WY91), THAP4 from Callithrix jacchus (A6MKW1), THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera (A5BBZ0), fatty acid-binding like protein from Mycobacterium smegmatis (A0R6J8), and fatty acid-binding like protein from Mycobacterium vanbaalenii (A1T297). Residues that...”

Q6P3Z3 Peroxynitrite isomerase THAP4 from Mus musculus
Aligns to 413:566 / 569 (27.1%), covers 99.3% of PF08768, 163.9 bits

• Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens
  Bianchetti, Proteins 2011
  • “...interface are shown as black sticks. Figure 2 Sequence alignment of THAP4 from Mus musculus (Q6P3Z3), THAP4 from Rattus norvegicus (Q642B6), THAP4 from Homo sapiens (Q8WY91), THAP4 from Callithrix jacchus (A6MKW1), THAP4 from Bos taurus (Q2TBI2), Nitrobindin from Arabidopsis thaliana (O64527), uncharacterized protein from Vitis vinifera...”

7bbmA / O64527 Mutant nitrobindin m75l/h76l/q96c/m148l (nb4h) from arabidopsis thaliana with cofactor mnppix
Aligns to 6:152 / 153 (96.1%), covers 99.3% of PF08768, 162.3 bits

• Ligand: manganese protoporphyrin ix (7bbmA)

Q1EP49 THAP4-like heme-binding beta-barrel domain-containing protein from Musa balbisiana
Aligns to 18:162 / 191 (75.9%), covers 99.3% of PF08768, 159.8 bits

• The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
  Bianchetti, Proteins 2010
  • “...to hypothetical proteins from Vitis vinifera (grape, Uniprot code A5BBZ0), Musa balbisiana (banana, Uniprot code Q1EP49), and Oryza sativa (rice, Uniprot code Q0JKE7). The three hypothetical proteins had identities and similarities to nitrobindin ranging from 76%- 67% and 89%- 86%, respectively. The BLAST search also revealed...”

SCO4179 hypothetical protein from Streptomyces coelicolor A3(2)
Aligns to 11:164 / 191 (80.6%), covers 100.0% of PF08768, 155.3 bits

• Recent advances in understanding Streptomyces
  Chater, F1000Research 2016
  • “...WhiA protein 71 . It is speculated that the Wbl proteins are denitrosylated by the SCO4179 (nitrobindin?)-mediated transfer of nitric oxide to mycothiol (MSH) to generate MSNO 51 . MSNO is denitrosylated by MSNO reductase, with the resulting oxidised mycothiol then being reduced to MSH by...”
• Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences
  Chandra, FEMS microbiology reviews 2014
  • “...et al ., 2003 ). The second potentially NO-related protein with a very similar distribution, SCO4179, has clearcut similarity to nitrobindins of plants and animals (Bianchetti et al ., 2010 ; Bianchetti et al ., 2011 ). Nitrobindins are haem-containing proteins that bind NO in the...”

ML1006 conserved hypothetical protein from Mycobacterium leprae TN
Aligns to 8:159 / 161 (94.4%), covers 100.0% of PF08768, 154.4 bits

• Identification of a novel multidrug efflux pump of Mycobacterium tuberculosis
  Danilchanka, Antimicrobial agents and chemotherapy 2008
  • “...fadD23 rv3826 544 2,000 Group B ML1069 ML1013 ML1009 ML1006 gmhA cpsY* cyp121* bcg3787* rv0113 rv0806c rv2276 rv3727 205 923 368 720 2,000 2,000 2,000 2,000...”

NB2_MYCTU / P9WFG9 Peroxynitrite isomerase 2; Ferric nitrobindin; Nb(III); EC 5.99.-.- from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
Rv0813c hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 64:223 / 226 (70.8%), covers 99.3% of PF08768, 137.6 bits

• function: Heme-binding protein able to scavenge peroxynitrite and to protect free L-tyrosine against peroxynitrite-mediated nitration, by acting as a peroxynitrite isomerase that converts peroxynitrite to nitrate. Therefore, this protein likely plays a role in peroxynitrite sensing and in the detoxification of reactive nitrogen and oxygen species (RNS and ROS, respectively). Is able to bind nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo.
  catalytic activity: peroxynitrite = nitrate (RHEA:63116)
  cofactor: heme b (Binds 1 heme b group per subunit, that coordinates a highly solvent-exposed Fe(III) atom.)
  subunit: Homodimer.
• Discovery of novel amino acid production traits by evolution of synthetic co-cultures
  Zuchowski, Microbial cell factories 2023
  • “...r.m.s.d. of 1.89 and 1.85 for WT and mutant, respectively) and 48% sequence identity with Rv0813c (PDB code 2fwv), a fatty acid binding protein-like protein of Mycobacterium tuberculosis [ 29 ]. Rv0813c belongs to the calycin superfamily implicated in the transport and storage of small and...”
  • “...or their metabolites, e.g. to/from membrane transporters. In the predicted Cg2850 structure, as observed in Rv0813c, residues 80229 appear to form an anti-parallel -barrel which could provide a cavity for non-covalent interactions (binding of ligands), while residues 2879 constitute a partly helical N-terminal segment that mostly...”
• New Insights into the Methylation of Mycobacterium tuberculosis Heparin Binding Hemagglutinin Adhesin Expressed in Rhodococcus erythropolis
  Parada, Pathogens (Basel, Switzerland) 2021
  • “...In prokaryotes, they are present only within the order of Actinomycetales. In M. tuberculosis , Rv0813c protein was identified as a FABP, on the grounds of its crystal structure. These proteins in bacteria may have roles in the recognition, transport and/or storage of small molecules [...”
  • “...A. Graa M. Buschiazzo A. Betton J.-M. Cole S.T. Alzari P.M. The Crystal Structure of Rv0813c from Mycobacterium tuberculosis Reveals a New Family of Fatty Acid-Binding Protein-Like Proteins in Bacteria J. Bacteriol. 2007 189 1899 1904 10.1128/JB.01435-06 17172346 34. Choi J.-A. Lim Y.-J. Cho S.-N. Lee...”
• Lipid and fatty acid metabolism in trypanosomatids
  Parreira, Microbial cell (Graz, Austria) 2021
  • “...-barrel fold were also observed in some Gram-positive bacteria. For instance, M. tuberculosis studies identified Rv0813c as a hypothetical protein with high similarity to the -barrel FABPs of mammals. Such findings uncovered a new family of bacterial proteins structurally similar to eukaryotic cellular retinol-binding proteins (CRBPs),...”
  • “...A Graa M Buschiazzo A Betton JM Cole ST Alzari PM The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria. J Bacteriol 2007 189 5 1899 1904 10.1128/JB.01435-06 17172346 44 Parsons JB Broussard TC Bose JL...”
• A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
  Bhagavat, Scientific reports 2017
  • “...Protein Name PMSmax PMSmin Ligands 1 Rv0674 Conserved hypothetical protein 0.41 0.82 ATP, GTP 2 Rv0813c Conserved protein 0.49 0.83 ATP 3 Rv1340 Probable ribonuclease RphA (RNase PH) (tRNA nucleotidyltransferase) 0.58 0.76 TTP 4 Rv1626 Probable two-component system transcriptional regulator regulatory proteins 0.51 0.89 ATP, GTP...”
• Exploration of novel cellular and serological antigen biomarkers in the ORFeome of Mycobacterium tuberculosis
  Liu, Molecular & cellular proteomics : MCP 2014
  • “...Pulmonary TB Extrapulmonary TB Annotation Rv0388c Rv0415 Rv0582 Rv0813c Rv0819 Rv1455 Rv1773c Rv1853 Rv1864c Rv2234 0.993 0.443 0.855 0.164 0.923 0.162 1.263...”
  • “...ThiO Hypothetical protein Rv0582 Hypothetical protein Rv0813c Hypothetical protein Rv0819 Hypothetical protein Rv1455 Transcriptional regulatory protein Urease...”
• The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1
  Bianchetti, Proteins 2010
  • “...(VAST) [ 43 ]. The top hits from VAST were Rv2717c (PDB ID 2FR2) and Rv0813c (PDB ID 2FWV) from Mycobacterium tuberculosis , which were previously solved in the absence of heme by structural genomic groups and were hypothesized to be FABPs based on structural homology...”
  • “...cores Proteins 1995 23 3 356 369 8710828 44 Shepard W The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria J Bacteriol 2007 189 5 1899 1904 17172346 45 Andersen JF The crystal structure of nitrophorin...”
• The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid-binding protein-like proteins in bacteria
  Shepard, Journal of bacteriology 2007
  • “...Vol. 189, No. 5 The Crystal Structure of Rv0813c from Mycobacterium tuberculosis Reveals a New Family of Fatty Acid-Binding Protein-Like Proteins in Bacteria...”
  • “...10 September 2006/Accepted 5 December 2006 The gene Rv0813c from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is...”

MAB_0732c hypothetical protein from Mycobacterium abscessus ATCC 19977
Aligns to 43:202 / 205 (78.0%), covers 99.3% of PF08768, 136.7 bits

• Hierarchy and interconnected networks in the WhiB7 mediated transcriptional response to antibiotic stress in Mycobacterium abscessus
  Hurst-Hess, PLoS genetics 2023
  • “...strains upon exposure to TET (16g/mL for 45 mins). Region of complementarity between ncRNA1 and MAB_0732c transcript is shown using dashed vertical lines. p adj = 0 (***) and <0.01 (*). Identification of chromosomal binding sites of MabWhiB7 using CHIP-Seq The 181 genes comprising the MabWhiB7...”
  • “...orientation of motif; antisense RNA detected ncRNA:1.4 1,2,3 MAB_3471: 1.4 1,2,3 55 736028 9 MAB_0731/ MAB_0732c MAB_0732 Wrong direction for both ORFs; antisense RNA detected ncRNA:99 1,2,3 MAB_0732c: 10.3 1,2,3 56 3252670 1 upstream of MAB_3211c opposite direction Wrong orientation for MAB_3211c; antisense to MAB_3212c? 1,2,3...”

cg2850 hypothetical protein from Corynebacterium glutamicum ATCC 13032
Aligns to 73:226 / 229 (67.2%), covers 99.3% of PF08768, 133.5 bits

• Discovery of novel amino acid production traits by evolution of synthetic co-cultures
  Zuchowski, Microbial cell factories 2023
  • “...ttaagg ttgagg P argT * 1 SNV G1767718A cg1874 Cg1874 G93D Cg1874 G93D SNV G2712428C cg2850 Cg2850 G30R Cg2850 G30R ARG LEU ++ evo2 DEL 13990261401854 P cg1504 , cg1505, cg1506 deletion of 2829bp upstream of cg1504 b P argT * 2 SNV G1767718A cg1874 Cg1874...”
  • “...codon GAGGAA, synonymous mutation argT * SNV G1767718A cg1874 Cg1874 G93D Cg1874 G93D SNV G2712428C cg2850 Cg2850 G30R Cg2850 G30R a Reads were mapped using GenBank accession number CP017995 (for LEU ARG + ) or BX927147 (for ARG LEU ++ ) as reference. Mutations are given...”
• The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase
  Larisch, BMC genomics 2007
  • “...1.41 cg2057 secreted protein 1.35 cg2105 conserved hypothetical protein 1.14 cg2797 conserved hypothetical protein 1.21 cg2850 conserved hypothetical protein 1.14 cg3022 conserved hypothetical protein 1.15 cg3329 conserved hypothetical protein 1.09 cg3330 putative secreted protein 1.71 cg0177 hypothetical protein -1.21 cg0757 conserved hypothetical protein -1.20 cg0838 DEAD-box...”

ML2200 conserved hypothetical protein from Mycobacterium leprae TN
Aligns to 66:225 / 228 (70.2%), covers 99.3% of PF08768, 131.0 bits

• Analysis of antigens of Mycobacterium leprae by interaction to sera IgG, IgM, and IgA response to improve diagnosis of leprosy
  Kumar, BioMed research international 2014
  • “...weight of 24521Da and contains about 228 amino acids. It is a product of gene ML2200 ( http://www.sanger.ac.uk/Projects/M_leprae/CDS/ML2200.shtml ). The M. leprae surface shows a marked protein (SDS predicted MW 28kDa) for myelin producing Schwann cells; a surface-exposed laminin binding protein (LBP) of molecular mass 21kDa...”

CBG11199 Protein CBG11199 from Caenorhabditis briggsae
Aligns to 77:235 / 238 (66.8%), covers 100.0% of PF08768, 119.8 bits

• Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes
  Beadell, Genome biology and evolution 2014
  • “...Few germ cells; aberrant oocytes 36 CBG10477 CBG10809 Aberrant proximal oocytes and postpachytene cells 37 CBG11199 Cbr-mes-3 38 CBG20654 Cbr-moe-3 Slow-growing, Sma, Egl, Pvl; abnormal somatic gonad migration, aberrant oocytes 39 CBG12306 CBG07050 Delayed gametogenesis, aberrant oocytes, abnormal embryonic cell divisions 40 Cbr-puf-3.1 Cbr-puf-3.2 41 CBG13131...”

Tsp_09560 cuticle collagen dpy-7 from Trichinella spiralis
Aligns to 63:221 / 256 (62.1%), covers 100.0% of PF08768, 107.8 bits

• Label-free quantitative proteomic analysis of molting-related proteins of Trichinella spiralis intestinal infective larvae
  Ren, Veterinary research 2019
  • “...collagen trimer; integral component of membrane; MF: structural constituent of cuticle Cuticle collagen dpy-7 E5SR67 Tsp_09560 29.37 6 26.60 CC: collagen trimer Cuticle collagen 6 Protein roller-8 E5SAG9 rol-8 35.18 3 9.50 CC: collagen trimer; integral component of membrane; MF: structural constituent of cuticle Cuticle collagen...”

BAB1_0227 hypothetical protein from Brucella melitensis biovar Abortus 2308
Aligns to 43:219 / 221 (80.1%), covers 99.3% of PF08768, 80.2 bits

• Brucella modulates secretory trafficking via multiple type IV secretion effector proteins
  Myeni, PLoS pathogens 2013
  • “...host cells ( Fig. 1 , S1 and S2 ). Ten of these Brucella proteins, BAB1_0227, BAB1_0678, BAB1_0712, BAB1_0847, BAB1_1611, BAB1_1671, BAB1_1864, BAB1_1948, BAB2_0119 and BAB2_0541 were newly identified as translocated by Brucella into host cells, while translocation of BAB1_1865 (also named BPE865) was previously reported...”
  • “...with TEM1 ( Fig. 1AD ). However, only the N-terminal TEM1 fusions of BAB2_0541 and BAB1_0227 showed translocation ( Fig. 1AD ). While BAB2_0541 fusion constructs were expressed to comparable levels, the BAB1_0227-TEM1 fusion protein was not detected by Western blot analysis ( Fig. 1E ),...”

BMEI1724 Hypothetical Protein from Brucella melitensis 16M
Aligns to 38:214 / 216 (81.9%), covers 99.3% of PF08768, 74.0 bits

• Immuno-profiling of Brucella proteins for developing improved vaccines and DIVA capable serodiagnostic assays for brucellosis
  Nandini, Frontiers in microbiology 2023
  • “...BMEI0375 Glycolate oxidase subunit GLCD BMEI1527 High-affinity zinc uptake system protein ZNUA BMEII0178 Hypothetical protein BMEI1724 Leucine- isoleucine- valine- threonine- and alanine-binding protein precursor BMEI1930 CobT protein BMEI0050 AsnC family transcriptional regulator BMEI0357 Outer membrane lipoprotein BMEII0017 Hypothetical protein BMEI0641 ABC transporter substrate-binding protein BMEI1954 Carnitine...”

MAB7_CAEEL / Q95Q39 Protein male abnormal 7 from Caenorhabditis elegans (see paper)
NP_508174 Protein male abnormal 7 from Caenorhabditis elegans
Aligns to 124:277 / 287 (53.7%), covers 86.8% of PF08768, 33.4 bits

• function: Plays an important role in determining body shape and sensory ray morphology, possibly by acting as a signaling molecule outside the expressing cell.
• Potassium channel modulation by a toxin domain in matrix metalloprotease 23
  Rangaraju, The Journal of biological chemistry 2010
  • “...number Data Bank (42) with code 2K72. NP_508174). PMP1-Jellyfish, Podocoryne metalloproteinase 1 (58). Structural figures were prepared using the programs...”
• mab-7 encodes a novel transmembrane protein that orchestrates sensory ray morphogenesis in C. elegans.
  Tsang, Developmental biology 2007 (PubMed)
  • GeneRIF: The characterization of another component essential for morphogenetic process encoded by mab-7, is reported.

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