PaperBLAST

PaperBLAST Hits for biolip::9c4g2 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound () (67 a.a., PKMKSHSGTK...)

Show query sequence

>biolip::9c4g2 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound ()
PKMKSHSGTKKRFKVTGSGKVTARKAGKRHLNEHKSSRVTRRLTGETVLSKGEAAKVKKL
LAGHPGR

Running BLASTp...

Found 35 similar proteins in the literature:

9c4g2 / A0AAD0QKX2 Cutibacterium acnes 50s ribosomal subunit with clindamycin bound (see paper)
100% identity, 100% coverage

• Ligand: rna (9c4g2)

SCO1599 50S ribosomal protein L35 from Streptomyces coelicolor A3(2)
72% identity, 91% coverage

• The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production
  Vassallo, Frontiers in microbiology 2020
  • “...10 2 Transcription; Stress response SCO1505 30S ribosomal protein S4 1.82 8.98 10 5 Translation SCO1599 50S ribosomal protein L35 1.59 3.90 10 3 SCO4702 50S ribosomal protein L3 1.47 1.65 10 2 SCO4702 50S ribosomal protein L3 1.30 3.66 10 2 SCO4702 50S ribosomal protein...”
• Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes
  Kim, Molecular microbiology 2012
  • “...relA GTP pyrophosphokinase for ppGpp synthesis (S1) 3 SCO1598 rplT 50S ribosomal protein L20 3 SCO1599 rpmI 50S ribosomal protein L35 3 SCO1600 * infC Translation initiation factor IF-3 S1 6 SCO1618 Hypothetical protein, similar to cobalamin binding protein BtuF 6 SCO1619 * Possible transcriptional regulatory...”
• Comparative genomics of Streptomyces avermitilis, Streptomyces cattleya, Streptomyces maritimus and Kitasatospora aureofaciens using a Streptomyces coelicolor microarray system
  Hsiao, Antonie van Leeuwenhoek 2008
  • “...protein S4 0.36 0.35 0.76 0.31 SCO1598 50S ribosomal protein L20 1.50 0.63 0.89 0.34 SCO1599 50S ribosomal protein L35 0.23 0.41 0.49 0.51 SCO1998 30S ribosomal protein S1 1.39 0.77 0.99 0.91 SCO2563 30s ribosomal protein S20 0.34 0.34 0.77 0.33 SCO2596 50S ribosomal protein...”

SCAB_73971 50S ribosomal protein L35 from Streptomyces scabiei 87.22
C9Z4H9 Large ribosomal subunit protein bL35 from Streptomyces scabiei (strain 87.22)
72% identity, 91% coverage

• Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
  Komeil, Proteome science 2014
  • “...ribosomal protein S1 0.070.06 nd nd C9Z316 SCAB_73401 d tRNA (adenine-N(1)-)-methyltransferase 0.020.03 0.070.07 0.070.04 C9Z4H9 SCAB_73971 50S ribosomal protein L35 0.570.00 0.900.44 0.480.28 C9Z4I0 SCAB_73981 d 50S ribosomal protein L20 0.380.35 0.420.25 0.300.13 Transcription C9Z8G5 SCAB_28931 d Transcription termination factor 0.030.04 nd nd C9YWA1 SCAB_37181 d...”
• Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin
  Komeil, Proteome science 2014
  • “...30S ribosomal protein S1 0.070.06 nd nd C9Z316 SCAB_73401 d tRNA (adenine-N(1)-)-methyltransferase 0.020.03 0.070.07 0.070.04 C9Z4H9 SCAB_73971 50S ribosomal protein L35 0.570.00 0.900.44 0.480.28 C9Z4I0 SCAB_73981 d 50S ribosomal protein L20 0.380.35 0.420.25 0.300.13 Transcription C9Z8G5 SCAB_28931 d Transcription termination factor 0.030.04 nd nd C9YWA1 SCAB_37181...”

MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 from Mycolicibacterium smegmatis MC2 155
A0QYU7 Large ribosomal subunit protein bL35 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_3792 ribosomal protein L35 from Mycobacterium smegmatis str. MC2 155
51% identity, 94% coverage

• Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
  Ogbonna, Microbiology spectrum 2023
  • “...0.01 A0QSG0 rplX , MSMEG_1466, MSMEI_1430 50S ribosomal protein L24 0.02 0.02 A0QYU7 rpmI , MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 0.01 0.01 A0QSP8 rplM , MSMEG_1556, MSMEI_1519 50S ribosomal protein L13 0.08 0.07 A0QSD2 rplD , MSMEG_1437, MSMEI_1401 50S ribosomal protein L4 0.05 0.07 A0QSG6...”
  • “...A0QSG0 rplX , MSMEG_1466, MSMEI_1430 50S ribosomal protein L24 0.02 0.02 A0QYU7 rpmI , MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 0.01 0.01 A0QSP8 rplM , MSMEG_1556, MSMEI_1519 50S ribosomal protein L13 0.08 0.07 A0QSD2 rplD , MSMEG_1437, MSMEI_1401 50S ribosomal protein L4 0.05 0.07 A0QSG6 rpsE...”
• Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
  Ogbonna, Microbiology spectrum 2023
  • “...protein L22 0.03 0.01 A0QSG0 rplX , MSMEG_1466, MSMEI_1430 50S ribosomal protein L24 0.02 0.02 A0QYU7 rpmI , MSMEG_3792, MSMEI_3704 50S ribosomal protein L35 0.01 0.01 A0QSP8 rplM , MSMEG_1556, MSMEI_1519 50S ribosomal protein L13 0.08 0.07 A0QSD2 rplD , MSMEG_1437, MSMEI_1401 50S ribosomal protein L4...”
• Gene Expression, Bacteria Viability and Survivability Following Spray Drying of Mycobacterium smegmatis
  Lauten, Materials (Basel, Switzerland) 2010
  • “...L33 rpmG 0.6 11.6 0.045 9% MSMEG_6946 ribosomal protein L34 rpmH 0.3 11.5 0.282 0% MSMEG_3792 ribosomal protein L35 rpmI 0.8 13.6 0.004 46% MSMEG_1520 ribosomal protein L36 rpmJ 0.4 13.3 0.080 1% MSMEG_3833 ribosomal protein S1 -0.3 12.1 0.174 1% MSMEG_2519 ribosomal protein S2 rpsB...”

MT1680 50S ribosomal protein L35 from Mycobacterium tuberculosis CDC1551
Rv1642 50S ribosomal protein L35 from Mycobacterium tuberculosis H37Rv
MRA_1653 50S ribosomal protein L35 from Mycobacterium tuberculosis H37Ra
52% identity, 94% coverage

• Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
  Lin, Nucleic acids research 2002
  • “...MT0736, MT0728, MT0747, MT1337, MT2117.1, MT0663, MT4041.1, MT1680, MT3567.1, MT0729, MT0742, MT0744, MT0681, MT0062 Small subunit 22 MT1666, MT0727, MT3566,...”
• Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis
  Sinha, Frontiers in microbiology 2024
  • “...1995 ). In another example, MTB_ORF_16006 is an integral part of an operon comprising Rv1641, Rv1642, Rv1643 , and Rv1644 ( Supplementary Figure 12 ). The proteins in this operon share functions closely related to ribosome assembly and protein synthesis. Notably, MTB_ORF_16006 features a membrane-binding domain...”
  • “...MTB_ORF_54512. Supplementary Figure 12 Representation of MTB_ORF_16006 within an operon that includes the genes Rv1641, Rv1642, Rv1643 , and Rv1644 . Supplementary Table 1 The genomic locations of smORFs and the growth condition in which they were predicted. Supplementary Table 2 The accession numbers and the...”
• Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains
  Ullah, Pathogens (Basel, Switzerland) 2021
  • “...is possibly involved in a transcriptional process, metabolism, and cell development [ 59 ]. RpmI (Rv1642) is an active virulence operon involved in protein synthesis and is associated with invasion and intercellular resistance [ 60 ]. UreA (Rv1848) is involved in the conversion of urea to...”
  • “...PPE19 PE/PPE Rv1534 Rv1534 Possibly involved in a transcriptional mechanism Probable transcriptional regulator Regulatory proteins Rv1642 rpmI Translation 50S ribosomal protein L35 RpmI Information pathways Rv1848 ureA Involved in the conversion of urea to NH 3 [catalytic activity: urea + H 2 O = CO 2...”
• Transcriptional Profile of Mycobacterium tuberculosis in an in vitro Model of Intraocular Tuberculosis
  Abhishek, Frontiers in cellular and infection microbiology 2018
  • “...intracellular replication in ARPE-19 cells. Upregulation of ribosomal ( Rv2056c, Rv3459c, Rv3456c, Rv1630, Rv0720, Rv0979A, Rv1642 , and Rv0700 ), transcriptional ( Rv0823c, Rv1994c, Rv3765c, Rv3160c, Rv1963c, Rv3416, Rv0232, Rv0602c, Rv1129c, Rv2324, Rv3183 , and Rv3833 ), and translation initiation ( Rv3462c ) transcripts whose protein...”
• The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity?
  Pullan, BMC infectious diseases 2016
  • “...P41194 30S ribosomal protein S7 4.07 3.05 Rv0718 P66625 30S ribosomal protein S8 3.13 3.04 Rv1642 P66271 50S ribosomal protein L35 2.59 3.02 Rv0714 P66069 50S ribosomal protein L14 2.79 2.92 Rv0707 P0A5X6 30S ribosomal protein S3 1.06 2.91 5S_rRNA ribosomal RNA 2.44 2.91 Rv0721 P66574...”
• Osmosensory signaling in Mycobacterium tuberculosis mediated by a eukaryotic-like Ser/Thr protein kinase
  Hatzios, Proceedings of the National Academy of Sciences of the United States of America 2013
  • “...Rv1072 Rv1078 Rv1297 Rv1462 Rv1463 Rv1464 Rv1466 Rv1641 Rv1642 Rv1643 Rv1652 Rv1653 Rv1654 Rv1655 Rv1656 Rv1657 Rv1658 Rv1659 Rv1886c Rv1908c Rv1980c Rv1996...”
• The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome
  Santos, BMC genomics 2012
  • “...487 58.67 495 Rv1018c glmU NP_215534.1 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase plcpsec115 cpfrc_00945 64 63.33 64 Rv1642 rpmI NP_216158.1 50S ribosomal protein L35 plcppse080 cpfrc_01015 452 57.08 470 Rv0392c ndhA NP_214906.1 membrane NADH dehydrogenase plcppse080 cpfrc_01015 452 58.10 463 Rv1854c ndh NP_216370.1 NADH dehydrogenase plcpsec041 cpfrc_01074 403...”
• Mycobacterium tuberculosis modulates its cell surface via an oligopeptide permease (Opp) transport system
  Flores-Valdez, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2009
  • “...2.0 Annotationb or similarityc to protein domains Rv1594 Rv1596 Rv1623c Rv1642 Rv1653 Rv1687c 1.4 1.3 0.9 1.0 1.3 1.0 0.6 1.7 0.6 1.6 1.6 0.6 1.0 1.0 0.9 1.4...”
• The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
  Fu, BMC microbiology 2007
  • “...rplD 4868 415 Rv2159c - 3197 832 Rv0701 rplC 4822 429 Rv0640 rplK 3169 256 Rv1642 rpmI 4816 562 Rv2392 cysH 3147 663 Rv2244 acpM 4650 1053 Rv2196 qcrB 3137 578 Rv1884c rpfC 4642 615 Rv2391 nirA 3110 822 Rv1305 atpE 4488 679 Rv0289 - 3088...”
• More
• Rv2629 Overexpression Delays Mycobacterium smegmatis and Mycobacteria tuberculosis Entry into Log-Phase and Increases Pathogenicity of Mycobacterium smegmatis in Mice
  Liu, Frontiers in microbiology 2017
  • “...YP_001283215.1 Secreted antigen 85-B FbpB Up Down Up MRA_1706 YP_001283017.1 Hypothetical protein Up Up Up MRA_1653 YP_001282961.1 50S ribosomal protein L35 Up Up Up MRA_1624 YP_001282932.1 Prolipoprotein diacylglyceryl transferase Up Up Up MRA_1622 YP_001282930.1 Tryptophan synthase subunit beta Up Up Up MRA_1323 YP_001282626.1 UDP- N -acetylglucosamine...”

7f0d3 / A5U2Z9 Cryo-em structure of mycobacterium tuberculosis 50s ribosome subunit bound with clarithromycin (see paper)
52% identity, 91% coverage

• Ligand: rna (7f0d3)

RL35_THET8 / Q5SKU1 Large ribosomal subunit protein bL35; 50S ribosomal protein L35 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see paper)
56% identity, 91% coverage

• subunit: Part of the 50S ribosomal subunit

BAB1_2123 Ribosomal protein L35 from Brucella melitensis biovar Abortus 2308
49% identity, 91% coverage

• Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
  Lamontagne, BMC genomics 2010
  • “...membrane BAB1_0659 Omp2a BAB1_0707 OstA BAB1_0963 TolC Unknown localization BAB1_0030 Unknown BAB1_0991 Unknown BAB1_1543 DUF526 BAB1_2123 RpmI; L35 BAB1_0170 GrpE BAB1_1070 WrbA BAB1_1559 FbcF BAB1_2176 YaeC/NLPA lipoprotein BAB1_0389 CcoP BAB1_1113 Unknown; conserved BAB1_1641 Unknown BAB1_2186 RpsT; S20 BAB1_0413 AtpB BAB1_1152 PdhA BAB1_1647 FabG domain BAB2_0207 Unknown...”

cg1564 50S ribosomal protein L35 from Corynebacterium glutamicum ATCC 13032
NCgl1325 50S ribosomal protein L35 from Corynebacterium glutamicum ATCC 13032
52% identity, 90% coverage

• Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
  Follmann, BMC genomics 2009
  • “...Ketol-acid reductoisomerase 0 -1.44 -0.91 4.0 3.8 3.9 2.9 3.9 3.3 -0.9 1.7 -0.6 58 cg1564 u rpmI 50S ribosomal protein L35 0 -1.04 -0.31 - -0.8 - 1.6 1.4 2.4 - - - 59 cg1565 u rplT 50S ribosomal protein L20 0 -1.26 -0.29 1.2...”
• Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
  Sun, PloS one 2017
  • “...proteins. Eleven genes encoded ribosomal proteins (NCgl1304, NCgl0538, NCgl1901, NCgl2261, NCgl0518, NCgl0515, NCgl0495, NCgl0487, NCgl0833, NCgl1325, NCgl0488); however, most of them were down-regulated under C . glutamicum EGFP, indicating that the translation process was suppressed with EGFP expression. There were two genes (NCgl0303, NCgl1526) up-regulated in...”

CLIBASIA_01020 50S ribosomal protein L35 from Candidatus Liberibacter asiaticus str. psy62
47% identity, 85% coverage

• MESSA: MEta-Server for protein Sequence Analysis
  Cong, BMC biology 2012
  • “...was essential to ensure reliable predictions. In one case, the hypothetical ribosomal protein L35 (locus: CLIBASIA_01020; gi: 254780319) [ 46 ] is predicted to have a signal peptide by three out of four predictors. However, all the closely related proteins and protein families identified by MESSA...”

BL1366a 50S ribosomal protein L35 from Bifidobacterium longum NCC2705
48% identity, 91% coverage

• Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum
  Ventura, Microbiology and molecular biology reviews : MMBR 2007
  • “...initiation factor If3; PFAM_ID, IF3 BL1366a ....................................RpmI; COG family, ribosomal protein L35; PFAM_ID, Ribosomal_L35p BL1367...”

RL35_DEIRA / Q9RSW6 Large ribosomal subunit protein bL35; 50S ribosomal protein L35 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1) (see 6 papers)
49% identity, 91% coverage

• function: Binds the 23S rRNA
  subunit: Part of the 50S ribosomal subunit. Contacts proteins L15 and L33.

5dm63 / Q9RSW6 Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans (see paper)
49% identity, 91% coverage

• Ligand: rna (5dm63)

8buu3 / P55874 8buu3 (see paper)
44% identity, 94% coverage

• Ligand: rna (8buu3)

RL35_BACSU / P55874 Large ribosomal subunit protein bL35; 50S ribosomal protein L35 from Bacillus subtilis (strain 168) (see paper)
BSU28860 50S ribosomal protein L35 from Bacillus subtilis subsp. subtilis str. 168
44% identity, 94% coverage

• subunit: Part of the 50S ribosomal subunit.
• Arginine phosphorylation marks proteins for degradation by a Clp protease
  Trentini, Nature 2016
  • “...O31461 ilvE Branched-chain aa transaminase 1 T249 P42956 mtlA PTS system mannitol-specific EIICB S365 S365 P55874 rpmI 50S ribosomal prot. L35 S47 S47 P21476 rpsS 30S ribosomal prot. S19 T77 O34607 sdaAA Probable L-serine dehydratase, chain T99 P54334 xkdO Phage-like element PBSX prot. XkdO S295 O34833...”
• Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone
  Reddy, Omics : a journal of integrative biology 2015
  • “...OS O34967 50S ribosomal protein L31 type B OS P55874 50S ribosomal protein L35 OS a Gene name Q-TOF Unique Plumbagin/ Unique Plumbagin/ Coverage peptides...”
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU01340 BSU37070 BSU15080 BSU24900 BSU00990 BSU41060 BSU28860 BSU01400 BSU16490 BSU01220 BSU29660 BSU01330 BSU40910 BSU01110 BSU01300 BSU01500 BSU01150...”

ruthe_01785 50S ribosomal protein L35 from Rubellimicrobium thermophilum DSM 16684
43% identity, 91% coverage

• Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade
  Fiebig, Standards in genomic sciences 2013
  • “...[ 45 ]. Several other genes involved in this process were also detected (e.g. ruthe_01784, ruthe_01785 and ruthe_01786). Genome analysis of strain R. thermophilum DSM 16684 T further revealed the presence of several genes encoding proteins associated with the utilization of urease (ruthe_02149 to 02151, ruthe_02153...”

SMc00363 PROBABLE 50S RIBOSOMAL PROTEIN L35 from Sinorhizobium meliloti 1021
47% identity, 88% coverage

• Antimicrobial nodule-specific cysteine-rich peptides induce membrane depolarization-associated changes in the transcriptome of Sinorhizobium meliloti
  Tiricz, Applied and environmental microbiology 2013
  • “...ribosomes SMc01049 SMc02695 SM_b20995 SMc00323 SMc00335 SMc00363 SMc00364 SMc00485 SMc00565 SMc00567 SMc00568 SMc00704 SMc01152 SMc01283 SMc01286 SMc01287...”
• Sinorhizobium meliloti ExoR and ExoS proteins regulate both succinoglycan and flagellum production
  Yao, Journal of bacteriology 2004
  • “...control genes (sma1118, smb21183, smb21295, smc00323, smc00335, smc00363, smc00646, smc01106, smc02857, smc03859, smc03979, and smc04040), which were printed in...”

Q71YN4 Large ribosomal subunit protein bL35 from Listeria monocytogenes serotype 4b (strain F2365)
lmo1784 ribosomal protein L35 from Listeria monocytogenes EGD-e
39% identity, 93% coverage

• Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach
  Srivastava, International journal of peptide research and therapeutics 2021
  • “...0.628 Non-allergen 133 Q721Y1 0.988 Non-allergen 134 Q71YM9 1.733 Non-allergen 135 Q71WG4 2.217 Non-allergen 136 Q71YN4 2.371 Non-allergen 137 Q71WH3 2.224 Non-allergen 138 Q71ZY7 0.968 Non-allergen 139 Q71XW7 1.979 Non-allergen 140 Q720A1 0.577 Non-allergen 141 Q723G3 2.038 Non-allergen 142 Q71WV3 0.925 Non-allergen 143 Q71ZJ5 0.952 Non-allergen...”
  • “...RRGKVRRAK 20.2 1.3055 Antigen DRB1_1301 LRGKAARIK 17.4 2.0521 Antigen Q71WG4 DRB1_1301 AKLEITLKR 51.3 1.1423 Antigen Q71YN4 DRB1_0701 FKRTGSGKL 34.3 1.1993 Antigen DRB1_1301 THRGSAKRF 43.7 1.0624 Antigen DRB1_1301 QKQKRKLRK 46.1 1.1816 Antigen Q71WH3 DRB1_1301 LGRTSSQRK 33.5 1.2846 Antigen Q71ZY7 DRB1_1301 LKKYCPRLR 50.8 2.0807 Antigen DRB1_1301 KKYCPRLRR 61.5...”
• Comparison of Surface Proteomes of Adherence Variants of Listeria Monocytogenes Using LC-MS/MS for Identification of Potential Surface Adhesins
  Tiong, Pathogens (Basel, Switzerland) 2016
  • “...protein S20 (9) CY CY 0.33 (E,C,CM) CY No No 0 No No <1.8 0.83 lmo1784 (3.7.1) 50S ribosomal protein L35 (8) CY CY 0.33 (E,C,CM) CY No No 0 Yes No <1.8 1.22 lmo2156 (5.1) Hypothetical protein (13) S M (Equal score to all) Unknown...”
  • “...--- 10 19 lmo1699 * ,1 lmo1699 Mobility and chemotaxis 1.5 --- >10 --- 20 lmo1784 rpmI Ribosomal proteins 3.7.1 --- --- 21 lmo1860 msrA Protein modification reductase A 3.8 --- 10x --- 22 lmo1953 pnp Metabolism of nucleotides and nucleic acids 2.3 --- >10 ---...”
• Characterisation of the transcriptomes of genetically diverse Listeria monocytogenes exposed to hyperosmotic and low temperature conditions reveal global stress-adaptation mechanisms
  Durack, PloS one 2013
  • “...lmo1707 1.95 *** 1.56 ** 1.10 *** 1.81 *** 1.08 *** 1.26 *** unknown protein lmo1784 rpmI 2.39 *** 1.32 *** 1.80 *** 1.66 ** 1.38 *** 2.32 *** ribosomal protein L35 lmo1816 rpmB 3.27 *** 4.34 *** 3.01 *** 3.58 ** 1.84 *** 4.11 ***...”
  • “...were rplK ( lmo0248 ), rplA ( lmo0249 ), rpsD ( lmo1596 ), rpmI ( lmo1784 ), rpmB ( lmo1816 ) and rpmE ( lmo2548 ). Although different physical stresses, both high Na + concentration and low temperature have a damaging effect on ribosome function. While...”
• Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes
  Hu, Applied and environmental microbiology 2007
  • “...lmo1523 lmo1542 lmo1541 lmo1657 lmo1658 lmo1683 lmo1785 lmo1784 lmo1859 lmo1879 lmo1921 lmo1956 lmo2048 lmo2047 lmo2055 lmo2054 lmo2261 lmo2340 lmo2362 lmo2363...”

A8JEP1 50S ribosomal protein L35 from Chlamydomonas reinhardtii
47% identity, 53% coverage

• Scaling-up and proteomic analysis reveals photosynthetic and metabolic insights toward prolonged H₂ photoproduction in Chlamydomonas hpm91 mutant lacking proton gradient regulation 5 (PGR5)
  Liu, Photosynthesis research 2022
  • “...KEGG pathway Uniprot accession Gene ID Protein name Ratio (Mu0/Wt0) p -value (<0.05) Ribosomal proteins A8JEP1 PRPL35 50S ribosomal protein L35 1.80 3.73E02 A8IQE3 RPL14 Ribosomal protein L14 1.60 2.06E02 A8J9D9 PRPL24 Plastid ribosomal protein L24 1.63 2.23E03 A8JGK1 RPS17 Ribosomal protein S17 3.41 3.43E03 A8HVP2...”

8uu97 / A0A660JIB9 8uu97 (see paper)
39% identity, 93% coverage

• Ligand: rna (8uu97)

ISORED2_02500 50S ribosomal protein L35 from Acetobacterium wieringae
44% identity, 91% coverage

• Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae
  Kronen, mSystems 2023
  • “...Stress response ISORED2_01001 VUZ28314.1 2.39 1.01 10 2 556 ENOG4105CKU Formyltetrahydrofolate synthetase One-carbon metabolic process ISORED2_02500 VUZ24737.1 2.44 2.62 10 2 67 ENOG4105VJV 50s ribosomal protein L35 Structural constituent of ribosome ISORED2_00772 VUZ28022.1 2.46 2.85 10 2 513 ENOG410ND7V Xylulokinase Carbohydrate metabolic process ISORED2_00996 VUZ28309.1 4.48...”

SYNW0058 50S ribosomal protein L35 from Synechococcus sp. WH 8102
38% identity, 91% coverage

• Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains
  Stuart, Applied and environmental microbiology 2009
  • “...1.11 SYNW1960 SYNW0144 SYNW0334 SYNW2232 SYNW1303 SYNW2224 SYNW0058 SYNW0546 SYNW0521 SYNW2442 SYNW2375 SYNW0233 SYNW2103 SYNW1730 SYNW1778 SYNW2489 0.46 0.59...”

RL35_RHOPA / Q6NDR5 Large ribosomal subunit protein bL35; 50S ribosomal protein L35; RRP-L35 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (see paper)
RPA0039 50S ribosomal protein L35 from Rhodopseudomonas palustris CGA009
41% identity, 91% coverage

• ATP Is a Major Determinant of Phototrophic Bacterial Longevity in Growth Arrest
  Yin, mBio 2023
  • “...an individual gene under light and dark-incubated conditions. From left to right, 50S ribosome: RPA0038, RPA0039, RPA0158, RPA0159, RPA0241, RPA0493, RPA0526, RPA0634, RPA0918, RPA2767, RPA3080, RPA3129, RPA3225, RPA3231, RPA3232, RPA3234, RPA3235, RPA3238, RPA3239, RPA3240, RPA3242, RPA3243, RPA3245, RPA3247-RPA3250, RPA3269, RPA3270, RPA3272, RPA3273, RPA4197, RPA4356; 30S ribosome:...”

Q67W51 50S ribosomal protein L35 from Oryza sativa subsp. japonica
41% identity, 38% coverage

• Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments
  Ling, Scientific reports 2019
  • “...1 0.733 0.012 Uncharacterized protein B9FFK4 5.32 1 1 0.736 0.014 50S ribosomal protein L35 Q67W51 4.11 1 1 0.748 0.019 Os01g0717000 protein (Fragment) A0A0P0V7D0 9.09 1 1 0.751 0.020 ATP-dependent 6-phosphofructokinase A2ZQ69 12.33 1 5 0.757 0.024 Glutathione peroxidase B7FAE9 30.34 1 6 0.765 0.030...”

NGO0297 putative 50s ribosomal protein L35 from Neisseria gonorrhoeae FA 1090
NMB0722 50S ribosomal protein L35 from Neisseria meningitidis MC58
NGFG_00442 50S ribosomal protein L35 from Neisseria gonorrhoeae MS11
43% identity, 91% coverage

• Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium
  Ducey, Journal of bacteriology 2005
  • “...NGO0043c NGO0057 NGO0191 NGO0199c NGO0260 NGO0295 NGO0296 NGO0297 NGO0584 NGO0905 NGO1246c NGO1413 NGO1748c NGO1776 NGO1818c Conserved hypothetical protein 50S...”
• Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium
  Ducey, Journal of bacteriology 2005
  • “...NMB1862 NMB1845 NMB0609 NMB0617 NMB0687 NMB0720 NMB0721 NMB0722 NMB1320 NMB1437 NMB1587 NMB0569 NMB0244 NMB0207 NMB0168 NGO1822c NGO1824.1c NGO1826.1c NGO1828c...”
• Transcriptional landscape and essential genes of Neisseria gonorrhoeae
  Remmele, Nucleic acids research 2014
  • “...sequence 117 bp upstream of a transcript encoding the 50S ribosomal proteins L35 and L20 (NGFG_00442 and NGFG_00443) was exchanged by a Kanamycin-P trc cassette. The P trc promoter is IPTG-inducible as lacI q can bind there as a repressor. In the recombinant strains the expression...”
  • “...show growth defects when IPTG is omitted. These data indicate that the ribosomal protein-encoding genes NGFG_00442 and NGFG_00443 ( P = 0.00061 and 0.00245, respectively) are essential for GC growth (Supplementary Figure S6B). In addition to conditional knockout assays and DNA footprinting analysis, several putative essential...”

GBAA_4818 50S ribosomal protein L35 from Bacillus anthracis str. 'Ames Ancestor'
41% identity, 91% coverage

• Microevolution of Anthrax from a Young Ancestor (M.A.Y.A.) Suggests a Soil-Borne Life Cycle of Bacillus anthracis
  Braun, PloS one 2015
  • “...Phe comG operon protein 4 GBAA_4463 6 4380690 A C - 1 ribosomal protein L35 GBAA_4818 1 silent mutation HRM for analysis of SNP distribution in Pollino isolates SNP discovery in the genome-sequenced Pollino isolates yielded a number of 6 point mutations that appeared to be...”

F452_RS0103380 50S ribosomal protein L35 from Porphyromonas gulae DSM 15663
PGN_0964 probable 50S ribosomal protein L35 from Porphyromonas gingivalis ATCC 33277
PG0990 ribosomal protein L35 from Porphyromonas gingivalis W83
40% identity, 93% coverage

• Antibacterial effects of sodium tripolyphosphate against Porphyromonas species associated with periodontitis of companion animals
  Lee, Journal of veterinary science 2019
  • “...50S ribosomal protein L20 1.97E-26 +3.66 * F452_RS0100210 50S ribosomal protein L21 4.76E-35 +3.65 * F452_RS0103380 50S ribosomal protein L35 9.81E-24 +3.60 * F452_RS0102545 50S ribosomal protein L33 3.07E-20 +3.48 * F452_RS0102540 50S ribosomal protein L28 1.35E-14 +2.74 * F452_RS0101135 30S ribosomal protein S1 7.48E-15 +2.56...”
• Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database
  Hendrickson, BMC microbiology 2009
  • “...(1) PGN_0035 PGN_0167 PGN_0640 PGN_0965 PGN_0394 PGN_0188 PGN_0279 PGN_1572 PGN_1589 PGN_0636 PGN_0639 PGN_1647 PGN_1648 PGN_0641 PGN_0964 PGN_1698 PGN_1844 PGN_1088 PGN_1219 PGN_1651 PGN_1852 PGN_1573 PGN_1575 PGN_1853 PGN_1854 PGN_1588 PGN_1590 PGN_1855 PGN_1861 PGN_1832 PGN_1840 PGN_1863 PGN_1868 PGN_1842 PGN_1843 PGN_1872 PGN_1890 PGN_1849 PGN_1850 PGN_1891 PGN_1856 PGN_1857 PGN_1857 PGN_1858 PGN_1860...”
• Molecular pathways underlying inhibitory effect of antimicrobial peptide Nal-P-113 on bacteria biofilms formation of Porphyromonas gingivalis W83 by DNA microarray
  Wang, BMC microbiology 2017
  • “...synthetase is one of the key enzymes in protein synthesis [ 17 ]. PG2117 and PG0990 both encoding ribosomal proteins were shown to be up-regulated by 3.32-fold and 2.52-fold, respectively. Moreover, transporting and binding protein pathway was also significantly inhibited by Nal-P-113 treatment. 4 out of...”
• Microarray analysis of the transcriptional responses of Porphyromonas gingivalis to polyphosphate
  Moon, BMC microbiology 2014
  • “...protein L31 4.01 PG0656 50S ribosomal protein L34 6.80 PG0989 50S ribosomal protein L20 3.43 PG0990 Ribosomal protein L35 1.74 PG1723 Ribosomal protein S20 2.94 PG1758 Ribosomal protein S15 6.23 PG1959 Ribosomal protein L33 2.02 PG1960 Ribosomal protein L28 2.03 PG2117 30S ribosomal protein S16 2.93...”

SACOL1726 ribosomal protein L35 from Staphylococcus aureus subsp. aureus COL
P66276 Large ribosomal subunit protein bL35 from Staphylococcus aureus (strain N315)
Q6GG26 Large ribosomal subunit protein bL35 from Staphylococcus aureus (strain MRSA252)
SA1503 50S ribosomal protein L35 from Staphylococcus aureus subsp. aureus N315
SAV1679 50S ribosomal protein L35 from Staphylococcus aureus subsp. aureus Mu50
MW1623 50S ribosomal protein L35 from Staphylococcus aureus subsp. aureus MW2
EKM74_RS01860 50S ribosomal protein L35 from Staphylococcus aureus
42% identity, 93% coverage

• Tea tree oil-induced transcriptional alterations in Staphylococcus aureus
  Cuaron, Phytotherapy research : PTR 2013
  • “...adenylosuccinate synthase SACOL0018 5-GAGGTTGGTCGTGAATACGG-3 5-TGGGTACTCAGTAATTTCTTTACCG-3 purM phosphoribosylaminoimidazole synthetase SACOL1080 5-AATATGGGTATTGGCTATACGG-3 5-CACAATATGACCAATTTGATAGGC-3 rpmI ribosomal protein L35 SACOL1726 5-TGCCAAAAATGAAAACTCACC-3 5-GAGATGTGAAAGCTCTTGAACG-3 tenA transcriptional regulator, TenA family SACOL2086 5-TAGGAGCTGACGCATTACGC-3 5-CCCATTGTTCTAGTGTCATAGCC-3 vraR DNA-binding response regulator VraR SACOL1942 5-AAAGAAGCAATTGCCAAAGC-3 5-TGAGTCGTCGCTTCTACACC-3 vraS histidine kinase sensor SACOL1943 5-AGTGCCGATGAAAGTTGTGC-3 5-TTTTGTACCGTTTGAATGACG-3 vraX VraX protein SACOL0625 5-TCGACAGTATCACCATGAAGG-3...”
  • “...dehydrogenase SACOL2628 7.0 1.5 1.6 hypothetical protein (191 aa) SACOL1086 7.0 rpmI ribosomal protein L35 SACOL1726 5.9 2.0 1.8 thiD phosphomethylpyrimidine kinase SACOL2085 5.1 purQ phosphoribosylformylglycinamidine synthase I SACOL1077 4.9 purC phosphoribosylaminoimidazole-succinocarboxamide synthase SACOL1075 4.6 thiE putative thiamine-phosphate pyrophosphorylase SACOL2083 3.8 thiM hydroxyethylthiazole kinase SACOL2084 3.2...”
• The Staphylococcus aureus LytSR two-component regulatory system affects biofilm formation
  Sharma-Kuinkel, Journal of bacteriology 2009
  • “...SACOL2234 SACOL2237 SACOL2228 SACOL2231 SACOL2221 SACOL1726 SACOL1274 SACOL2233 SACOL2222 SACOL0592 SACOL2240 SACOL2214 SACOL0591 SACOL2226 SACOL1292 SACOL2230...”
• Identification of N-terminal protein processing sites by chemical labeling mass spectrometry
  Misal, Rapid communications in mass spectrometry : RCM 2019
  • “...24 M AIKKYKPITNGR R P60432 Ribosomal protein L2 Cytoplasm 21 19 25 M PKMKTHR G P66276 Ribosomal protein L35 Cytoplasm 5 5 26 M TKGILGR K P60449 Ribosomal protein L3 Cytoplasm 12 12 27 M TMTDPIADMLTR V P66630 Ribosomal protein S8 Cytoplasm 16 16 28 M...”
• Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
  Hiltunen, Microorganisms 2019
  • “...Q6GEI3 50S ribosomal protein L30 Q6GEK1 50S ribosomal protein L31 Q6GEV5 50S ribosomal protein L35 Q6GG26 50S ribosomal protein L4 Q6GEI4 50S ribosomal protein L5 Q99S33 50S ribosomal protein L6 Q99S36 50S ribosomal protein L7/L12 Q6GJC8 50S ribosomal protein L9 Q6GKT0 Elongation factor TuEfTU Q6GJC0 Elongation...”
• Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids
  Chung, PloS one 2013
  • “...50S ribosomal protein L33 1,2,3 8.4 Translation SAS093 rpmH 50S ribosomal protein L34 6.3 Translation SA1503 rpmI 50S ribosomal protein L35 6.0 Translation SAS078 rpmJ 50S ribosomal protein L36 21.0 Translation SA2035 rplE 50S ribosomal protein L5 6.3 Translation SA0498 rplL 50S ribosomal protein L7/L12 8.3...”
• Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
  Even, Applied and environmental microbiology 2009
  • “...and cellular division genes SAV0535 SAV0547 SAV0548 SAV1678 SAV1679 SAV1128 IGS2 SAV1180 SAV0511 Corresponding ORF (MW2)c 4464 EVEN ET AL. APPL. ENVIRON....”
• Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
  Even, Applied and environmental microbiology 2009
  • “...SAV1433 SAV1474 SAV1261 SAV1228 MW0491 MW0502 MW0503 MW1622 MW1623 MW1010 nusG fus tufA rplT rpmI rpmF MW1063 MW0466 ftsL ftsH MW0284 MW1323 MW1363 MW1144...”
• Transcriptomic Analysis Revealed Antimicrobial Mechanisms of Lactobacillus rhamnosus SCB0119 against Escherichia coli and Staphylococcus aureus
  Peng, International journal of molecular sciences 2022
  • “...ribosomal protein L21 EKM74_RS01855 19.42 10.05 621.08 94.23 4.999194 rplT ; 50S ribosomal protein L20 EKM74_RS01860 51.94 21.24 5478.49 45.03 6.720704 rpmI ; 50S ribosomal protein L35 EKM74_RS02080 80.66 17.27 3451.94 642.32 5.419314 rpsD ; 30S ribosomal protein S4 EKM74_RS05465 190.13 11.18 3317.01 500.37 4.124828 rpsI...”

CT834 L35 Ribosomal Protein from Chlamydia trachomatis D/UW-3/CX
36% identity, 91% coverage

• Simultaneous transcriptional profiling of bacteria and their host cells
  Humphrys, PloS one 2013
  • “...assays were designed for genes CT81, CT500, CT229, CT875, CT734, CT446, CT577, CT18, CT864, CT665, CT834, CT391, CT216, CT705, and CT416. Chlamydial gene expression is plotted against the RPKM for each gene. qRT-PCR data is expressed as 1/log2 Ct and normalized to 16S rRNA. (PDF) Click...”

5nrg3 / Q2FXQ0 The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with rb02 (see paper)
42% identity, 93% coverage

• Ligands: rna; manganese (ii) ion (5nrg3)

prpl35-1 / CAD24038.1 putative plastid ribosomal protein L35, partial from Zea mays (see paper)
41% identity, 47% coverage

CCNA_01098 LSU ribosomal protein L35P from Caulobacter crescentus NA1000
CC1046 ribosomal protein L35 from Caulobacter crescentus CB15
41% identity, 91% coverage

• Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry
  Lalanne, Cell 2018
  • “...from C. crescentus (CCNA_00370 and CCNA_00371) were included, and ribosomal protein L35 from C. crescentus (CCNA_01098) was included. We note that the S12 operon (including EF-G and EF-Tu) displayed in Fig. 2E and S4FH was assembled outside of the current described framework due to the multiple...”
• Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus
  Badger, Journal of bacteriology 2006
  • “...Putative lipoprotein CC0136 CC3602 CC3601 CC1116 CC1485 CC0224 CC1046 CC0241 CC2977 CC1840 CC2493 CC3309 CC3551 CC0356 CC1285 CC1987 CC0948 CC0922 CC0699 CC0636...”
• Use of the Caulobacter crescentus genome sequence to develop a method for systematic genetic mapping
  West, Journal of bacteriology 2002
  • “...(phenylalanyl-tRNA synthetase subunits). Product 2 contained CC1045 and CC1046 (ribosomal subunits L20 and L35). Product 3 contained CC1049 to CC1052. Product 4...”

RK35_SPIOL / P23326 Large ribosomal subunit protein bL35c; 50S ribosomal protein L35, chloroplastic; CL35 from Spinacia oleracea (Spinach) (see 2 papers)
39% identity, 35% coverage

• function: Component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus.
  subunit: Component of the chloroplast large ribosomal subunit (LSU). Mature 70S chloroplast ribosomes of higher plants consist of a small (30S) and a large (50S) subunit. The 30S small subunit contains 1 molecule of ribosomal RNA (16S rRNA) and 24 different proteins. The 50S large subunit contains 3 rRNA molecules (23S, 5S and 4.5S rRNA) and 33 different proteins.
• Adaptive responses along a depth and a latitudinal gradient in the endemic seagrass Posidonia oceanica.
  Jahnke, Heredity 2019
• Cryo-EM structure of the large subunit of the spinach chloroplast ribosome
  Ahmed, Scientific reports 2016
  • “...57 bL33c c P28805 166 959 55 bL34c d P82244 92152 92148 46 bL35c e P23326 87159 91157 65 bL36c f P12230 137 137 38 PSRP5 g P27684 63142 79121 PSRP variant 5, pI=10.01 PSRP6 h P82411 48116 4893 pI=9.87 Protein residues and signal peptide positions...”

Q9Z6R8 Large ribosomal subunit protein bL35 from Chlamydia pneumoniae
36% identity, 91% coverage

• Prediction of Chlamydia pneumoniae protein localization in host mitochondria and cytoplasm and possible involvements in lung cancer etiology: a computational approach
  Alshamsan, Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society 2017
  • “...(Q9Z6V3), L4 (Q9Z7Q8), L5 (Q9Z7R9), L29 (Q9Z7R5), L27 (Q9Z807), L33 (Q9Z8T4), L34 (Q9Z6X1) and L35 (Q9Z6R8), L36 (Q9Z6X0), which potentially involved in various steps of translation and ribosome biogenesis in C. pneumoniae . Control of translation is a critical component for the progress and advancement of...”

ssl1426 50S ribosomal protein L35 from Synechocystis sp. PCC 6803
43% identity, 91% coverage

• Proteomic analysis of the regulatory networks of ClpX in a model cyanobacterium Synechocystis sp. PCC 6803
  Zhang, Frontiers in plant science 2022
  • “...large subunit), including rplB (sll1802), rplX (sll1807), rpsK (sll1817), rplT (sll0767), rpsL (sll1096), and rpmI (ssl1426). Furthermore, many proteases, such as hhoA (sll1679), ymxG (slr1331), htrA (slr1204), methionine aminopeptidase (sll0555), and putative carboxypeptidase (sll0777), were significantly upregulated. As mentioned above, ClpX functions as a chaperone for...”
  • “...from 50S ribosomal protein L2 (sll1802), 50S ribosomal protein L24 (sll1807), 50S ribosomal protein L35 (ssl1426), and 30S ribosomal protein S11 (sll1817) are shown in Figure5C . Figure5 Validation of DEPs using Parallel Reaction Monitoring (PRM) analysis. (A) Pairwise correlation of peak area of transitions for...”
• A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803
  Song, Molecular & cellular proteomics : MCP 2014
  • “...Slr1597 Slr1727 Slr1838 Slr1856 Slr1974 Slr2041 Slr2059 Ssl1426 Ssl1784 Ssl3044 Ssl3432 Ssl3441 Ssl3445 Ssr0482 Ssr1604 Ssr2799 Mutant_r1 vs. Control_r1...”
• Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803
  Liu, Biotechnology for biofuels 2012
  • “...Sll1813 1.60 50S ribosomal protein L15 Ssl3436 2.58 2.06 1.72 1.71 50S ribosomal protein L29 Ssl1426 2.07 50S ribosomal protein L35 Ssl2084 3.11 3.46 3.55 5.13 1.95 Acyl carrier protein Sll1017 1.93 Ammonium/methylammonium permease Slr0242 1.58 1.66 Bacterioferritin co migratory protein Slr0043 2.56 Bicarbonate transport system...”
• RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
  Wang, Biotechnology for biofuels 2012
  • “...4.12E+05 6.41E+05 9.77E+05 1.72E+05 3.12E+05 5.68E+05 2.51E+05 6.14E+05 5.94E+05 50S ribosomal protein L24 Protein synthesis ssl1426 5.89E+06 2.35E+06 5.49E+06 4.31E+06 4.18E+06 2.74E+06 2.30E+06 2.22E+06 2.17E+06 50S ribosomal protein L35 Protein synthesis slr2067 1.00E+06 2.39E+06 4.47E+06 3.52E+05 1.16E+06 2.61E+06 8.80E+05 3.28E+06 3.45E+06 Allophycocyanin alpha subunit Energy metabolism...”
• Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803
  Zhang, BMC genomics 2008
  • “...( rpl5 ), sll1809 ( rps8 ), sll1810 ( rpl6 ), sll1813 ( rpl15 ), ssl1426 ( rpl35 )) 13 RNA polymerase subunits (sll1787( rpoB ), sll1789( rpoC2 ), sll1818( rpoA )), Translation (sll1820( truA ), sll1099( tufA ), Ribosomal proteins (sll0767( rpl20 ), sll1745( rpl10...”

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Statistics

How It Works

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.

Secrets

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.

Omissions from the PaperBLAST Database

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.