PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST Hits for VIMSS3615187 iron-containing alcohol dehydrogenase (387 a.a., MSHDLSQLRK...)

Found 250 similar proteins in the literature:

PA1991 probable iron-containing alcohol dehydrogenase (NCBI) from Pseudomonas aeruginosa PAO1 (90% identity, 100% coverage)

AO356_28020 ethanol oxidation regulatory protein ercA from Pseudomonas fluorescens FW300-N2C3 (90% identity, 99% coverage)

PP_2682 alcohol dehydrogenase, iron-containing (NCBI ptt file) from Pseudomonas putida KT2440 (90% identity, 100% coverage)

PS417_17420 ethanol oxidation regulatory protein ercA from Pseudomonas simiae WCS417 (89% identity, 100% coverage)

HP15_3135 ethanol oxidation regulatory protein ercA from Marinobacter adhaerens HP15 (69% identity, 100% coverage)

DVU2545 alcohol dehydrogenase, iron-containing (TIGR) from Desulfovibrio vulgaris Hildenborough (52% identity, 98% coverage)

MSMEG_6239 1,3-propanediol dehydrogenase (NCBI) from Mycobacterium smegmatis str. MC2 155 (43% identity, 96% coverage)

SSCH_1120010 alcohol dehydrogenase from Syntrophaceticus schinkii (43% identity, 98% coverage)

Pcar_0257 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (41% identity, 98% coverage)

DSOUD_1067 alcohol dehydrogenase from Desulfuromonas soudanensis (40% identity, 98% coverage)

Csac_0407 Alcohol dehydrogenase (RefSeq) from Caldicellulosiruptor saccharolyticus DSM 8903 (40% identity, 99% coverage)

Pcar_2847 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (41% identity, 98% coverage)

SO1490 alcohol dehydrogenase II (NCBI ptt file) from Shewanella oneidensis MR-1 (41% identity, 98% coverage)

PflSS101_1413 L-threonine dehydrogenase from Pseudomonas fluorescens SS101 (42% identity, 92% coverage)

AOLE_06670 alcohol dehydrogenase from Acinetobacter oleivorans DR1 (39% identity, 98% coverage)

Q7NUH0 Probable alcohol dehydrogenase from Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (41% identity, 97% coverage)

dhaT / GB|AAB48848.1 1,3-propanediol dehydrogenase; EC 1.1.1.202 from Citrobacter freundii (38% identity, 98% coverage) (see paper)

Pcar_1594 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (41% identity, 97% coverage)

Pcar_0251 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (40% identity, 97% coverage)

RPA1205 putative alcohol dehydrogenase (NCBI) from Rhodopseudomonas palustris CGA009 (39% identity, 97% coverage)

Pcar_0255 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (40% identity, 97% coverage)

Dde_3523 alcohol dehydrogenase, iron-containing (RefSeq) from Desulfovibrio desulfuricans G20 (39% identity, 96% coverage)

WP_011953356 1,3-propanediol dehydrogenase from Lactobacillus reuteri JCM 1112 (39% identity, 96% coverage)
LAR_0029 1,3-propanediol dehydrogenase (RefSeq) from Lactobacillus reuteri JCM 1112

DVU2405, ORF02977 alcohol dehydrogenase, iron-containing (TIGR) from Desulfovibrio vulgaris Hildenborough (40% identity, 97% coverage)

YP_005228921 1,3-propanediol oxidoreductase from Klebsiella pneumoniae subsp. pneumoniae HS11286 (36% identity, 98% coverage)

DSOUD_1075 alcohol dehydrogenase from Desulfuromonas soudanensis (38% identity, 98% coverage)

CLPA_c22740 1,3-propanediol dehydrogenase from Clostridium pasteurianum DSM 525 = ATCC 6013 (37% identity, 98% coverage)

PBPRA2519 putative alcohol dehydrogenase (NCBI) from Photobacterium profundum SS9 (37% identity, 97% coverage)

ZMO1596 iron-containing alcohol dehydrogenase (RefSeq) from Zymomonas mobilis subsp. mobilis ZM4 (39% identity, 90% coverage)

SOV_1c02190 alcohol dehydrogenase from Sporomusa ovata DSM 2662 (37% identity, 97% coverage)

Pcar_2510 1,3-propanediol dehydrogenase (NCBI) from Pelobacter carbinolicus str. DSM 2380 (39% identity, 98% coverage)

Asuc_0403 iron-containing alcohol dehydrogenase (RefSeq) from Actinobacillus succinogenes 130Z (38% identity, 97% coverage)

Z5010 putative oxidoreductase (NCBI ptt file) from Escherichia coli O157:H7 EDL933 (38% identity, 97% coverage)

YP_003034403 iron-containing alcohol dehydrogenase (RefSeq) from Escherichia coli 'BL21-Gold(DE3)pLysS AG' (38% identity, 97% coverage)

YiaY / b3589 L-threonine dehydrogenase from Escherichia coli K-12 substr. MG1655 (38% identity, 97% coverage) (see 6 papers)
P37686 L-threonine dehydrogenase from Escherichia coli (strain K12) (see 5 papers)
b3589 predicted Fe-containing alcohol dehydrogenase (NCBI) from Escherichia coli str. K-12 substr. MG1655

ADH4_SCHPO / Q09669 Alcohol dehydrogenase 4; EC 1.1.1.1; Alcohol dehydrogenase IV from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (40% identity, 88% coverage) (see 3 papers)
adh4 / RF|NP_592819.1 alcohol dehydrogenase Adh4; EC 1.1.1.1 from Schizosaccharomyces pombe (see 3 papers)
SPAC5H10.06c alcohol dehydrogenase Adh4 (RefSeq) from Schizosaccharomyces pombe

Halsa_0672 alcohol dehydrogenase from Halanaerobium hydrogeniformans (38% identity, 98% coverage)

A1S_2098 putative alcohol dehydrogenase (RefSeq) from Acinetobacter baumannii ATCC 17978 (39% identity, 90% coverage)

MEDH_BACMT / P31005 NAD-dependent methanol dehydrogenase; MDH; MEDH; EC 1.1.1.244; Type 3 alcohol dehydrogenase from Bacillus methanolicus (36% identity, 97% coverage) (see 6 papers)
mdh methanol dehydrogenase; EC 1.1.1.244 from Bacillus methanolicus (see paper)

CBY_0500 1,3-propanediol dehydrogenase (RefSeq) from Clostridium butyricum 5521 (37% identity, 98% coverage)

WP_003593433 1,3-propanediol dehydrogenase from Lactobacillus brevis ATCC 367 (36% identity, 96% coverage)

YGL256W Adh4p (RefSeq) from Saccharomyces cerevisiae (36% identity, 82% coverage)

ADH4_YEAST / P10127 Alcohol dehydrogenase 4; EC 1.1.1.1; Alcohol dehydrogenase IV; ADHIV from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (37% identity, 97% coverage) (see 8 papers)

Dde_3534 alcohol dehydrogenase (Chris Hemme) from Desulfovibrio desulfuricans G20 (39% identity, 97% coverage)

Pcar_2848 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (36% identity, 98% coverage)

lp_3051 1,3-propanediol dehydrogenase (NCBI ptt file) from Lactobacillus plantarum WCFS1 (36% identity, 96% coverage)

fucO / RF|NP_417279 propanediol oxidoreductase from Escherichia coli K12 (36% identity, 97% coverage) (see 5 papers)
b2799 L-1,2-propanediol oxidoreductase (NCBI) from Escherichia coli str. K-12 substr. MG1655
Z4116 L-1,2-propanediol oxidoreductase (NCBI ptt file) from Escherichia coli O157:H7 EDL933

FucO / b2799 L-1,2-propanediol oxidoreductase from Escherichia coli K-12 substr. MG1655 (36% identity, 97% coverage) (see 22 papers)
FUCO_ECOLI / P0A9S1 Lactaldehyde reductase; EC 1.1.1.77; Propanediol oxidoreductase from Escherichia coli (strain K12) (see paper)
P0A9S1 L-1,2-propanediol oxidoreductase from Escherichia coli (strain K12) (see 21 papers)
NP_417279 L-1,2-propanediol oxidoreductase from Escherichia coli str. K-12 substr. MG1655

CD3006 probable alcohol dehydrogenase (RefSeq) from Clostridium difficile 630 (37% identity, 93% coverage)

GBSB_BACSU / P71017 Alcohol dehydrogenase; EC 1.1.1.1 from Bacillus subtilis (strain 168) (36% identity, 94% coverage) (see 2 papers)
P71017 choline dehydrogenase from Bacillus subtilis (strain 168) (see paper)
gbsB alcohol dehydrogenase; EC 1.1.1.1 from Bacillus subtilis (see 3 papers)

DCF50_p2281 alcohol dehydrogenase from Dehalobacter sp. CF (36% identity, 96% coverage)

Halsa_2285 alcohol dehydrogenase from Halanaerobium hydrogeniformans (37% identity, 82% coverage)

Pcar_2506 alcohol dehydrogenase, class IV (NCBI) from Pelobacter carbinolicus str. DSM 2380 (39% identity, 79% coverage)

KLMA_20005 alcohol dehydrogenase 4 from Kluyveromyces marxianus DMKU3-1042 (37% identity, 89% coverage)

Q8ZKS2 L-lactaldehyde reductase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (36% identity, 97% coverage) (see paper)
STM4044 putative iron-containing alcohol dehydrogenase (NCBI ptt file) from Salmonella typhimurium LT2

PP_2803 1,3-propanediol dehydrogenase (NCBI ptt file) from Pseudomonas putida KT2440 (35% identity, 92% coverage)

YPTB0382 probable alcohol dehydrogenase (NCBI) from Yersinia pseudotuberculosis IP 32953 (36% identity, 92% coverage)

Dhaf_2180 iron-containing alcohol dehydrogenase (RefSeq) from Desulfitobacterium hafniense DCB-2 (33% identity, 91% coverage)

P13604 NADPH-dependent butanol dehydrogenas from Clostridium saccharobutylicum (32% identity, 97% coverage) (see paper)
adh1 / GB|AAA83520.1 NADPH-dependent butanol dehydrogenase; EC 1.1.1.1 from Clostridium saccharobutylicum (see paper)

T260_06755 alcohol dehydrogenase EutG from Geobacillus sp. MAS1 (38% identity, 81% coverage)

BL1673 possible lactaldehyde reductase (NCBI) from Bifidobacterium longum NCC2705 (33% identity, 95% coverage)

SPD_1985 alcohol dehydrogenase, iron-containing (NCBI) from Streptococcus pneumoniae D39 (33% identity, 97% coverage)
spr1963 Probable alcohol dehydrogenase. (NCBI ptt file) from Streptococcus pneumoniae R6

BpOF4_21519 hypothetical protein (RefSeq) from Bacillus pseudofirmus OF4 (32% identity, 99% coverage)

SP_2157 alcohol dehydrogenase, iron-containing (RefSeq) from Streptococcus pneumoniae TIGR4 (33% identity, 97% coverage)

Gura_3568 iron-containing alcohol dehydrogenase (RefSeq) from Geobacter uraniumreducens Rf4 (33% identity, 93% coverage)

SOV_3c00580 alcohol dehydrogenase from Sporomusa ovata DSM 2662 (34% identity, 97% coverage)

CBY_3751 NADPH-dependent butanol dehydrogenase (RefSeq) from Clostridium butyricum 5521 (32% identity, 97% coverage)

I3VSF1 Aldehyde-alcohol dehydrogenase from Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485) (32% identity, 44% coverage)

pRL100135 putative 1,3-propanediol dehydrogenase (NCBI) from Rhizobium leguminosarum bv. viciae 3841 (35% identity, 97% coverage)

Dtox_4270 iron-containing alcohol dehydrogenase (RefSeq) from Desulfotomaculum acetoxidans DSM 771 (32% identity, 95% coverage)

NP_396070 gamma hydroxybutyrate dehydrogenase from Agrobacterium fabrum str. C58 (34% identity, 97% coverage)

CAETHG_0555, CLJU_c24880 NADPH-dependent butanol dehydrogenase from Clostridium autoethanogenum DSM 10061 (31% identity, 96% coverage)

Teth39_0206 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq) from Thermoanaerobacter ethanolicus ATCC 33223 (32% identity, 43% coverage)

CBY_3747 NADPH-dependent butanol dehydrogenase (RefSeq) from Clostridium butyricum 5521 (33% identity, 88% coverage)

Cbei_2181 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (31% identity, 97% coverage)

Cbei_1722 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (32% identity, 91% coverage)

CAETHG_1841, CLJU_c39950 NADPH-dependent butanol dehydrogenase from Clostridium ljungdahlii DSM 13528 (31% identity, 94% coverage)

SOV_3c00590 alcohol dehydrogenase from Sporomusa ovata DSM 2662 (31% identity, 99% coverage)

TepiRe1_0393 alcohol dehydrogenase from Tepidanaerobacter acetatoxydans Re1 (30% identity, 97% coverage)

CAETHG_3954 alcohol dehydrogenase from Clostridium autoethanogenum DSM 10061 (32% identity, 97% coverage)

CD1907 putative ethanolamine/propanediol utilization propanol dehydrogenase (RefSeq) from Clostridium difficile 630 (32% identity, 95% coverage)

ADH1_GEOTN / A4IP64 Long-chain-alcohol dehydrogenase 1; EC 1.1.1.192; Alcohol dehydrogenase 1; ADH1; Fatty alcohol oxidoreductase 1; Glycerol dehydrogenase; EC 1.1.1.6 from Geobacillus thermodenitrificans (strain NG80-2) (33% identity, 93% coverage) (see paper)
GTNG_1754 Alcohol dehydrogenase (RefSeq) from Geobacillus thermodenitrificans NG80-2

Cbei_0305 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (33% identity, 40% coverage)

SMB_P058 alcohol dehydrogenase from Clostridium acetobutylicum EA 2018 (29% identity, 92% coverage)

TCEL_01373 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Thermobrachium celere DSM 8682 (31% identity, 44% coverage)

cgd8_1720 acetaldehyde reductase plus alcohol dehydrogenase (AdhE) of possible bacterial origin from Cryptosporidium parvum Iowa II (30% identity, 43% coverage)

CAP0059 Alcohol dehydrogenase (NCBI ptt file) from Clostridium acetobutylicum ATCC 824 (29% identity, 92% coverage)

Q9ANR5 aldehyde/alcohol dehydrogenase from Clostridium acetobutylicum (30% identity, 43% coverage) (see 2 papers)
Q7DFN2 Aldehyde-alcohol dehydrogenase from Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787)
CAP0035, CA_P0035 Aldehyde-alcohol dehydrogenase, ADHE1 (NCBI ptt file) from Clostridium acetobutylicum ATCC 824
CEA_P0034 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Clostridium acetobutylicum EA 2018

YffV / b2453 putative alcohol dehydrogenase in ethanolamine utilization from Escherichia coli K-12 substr. MG1655 (32% identity, 97% coverage) (see 2 papers)
eutG / GB|AAC75506.2 ethanolamine utilization protein eutG; EC 1.1.-.- from Escherichia coli K12 (see 3 papers)
b2453 ethanolamine utilization; homolog of Salmonella enzyme, similar to iron-containing alcohol dehydrogenase (VIMSS) from Escherichia coli str. K-12 substr. MG1655

Dde_3267 Alcohol dehydrogenase, class IV (VIMSS-AUTO) from Desulfovibrio desulfuricans G20 (30% identity, 91% coverage)

Clocl_0117 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from [Clostridium] clariflavum DSM 19732 (31% identity, 44% coverage)

Cthe_0423 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium thermocellum ATCC 27405 (31% identity, 40% coverage)
Cthe_0423 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Ruminiclostridium thermocellum DSM 1313

CBY_3753 aldehyde-alcohol dehydrogenase 2 (RefSeq) from Clostridium butyricum 5521 (31% identity, 40% coverage)

EF0900 aldehyde-alcohol dehydrogenase (NCBI ptt file) from Enterococcus faecalis V583 (30% identity, 42% coverage)

Entcl_1314 ethanolamine utilization ethanol dehydrogenase EutG from Enterobacter lignolyticus SCF1 (33% identity, 97% coverage)

CLJU_RS05830 alcohol dehydrogenase from Clostridium ljungdahlii DSM 13528 (31% identity, 97% coverage)

lmo1171 similar to NADPH-dependent butanol dehydrogenase (NCBI ptt file) from Listeria monocytogenes EGD-e (29% identity, 92% coverage)

BAS4267 aldehyde-alcohol dehydrogenase (NCBI) from Bacillus anthracis str. Sterne (29% identity, 43% coverage)
BA4599 aldehyde-alcohol dehydrogenase (NCBI ptt file) from Bacillus anthracis str. Ames

MSMEG_6242 alcohol dehydrogenase, iron-containing (NCBI) from Mycobacterium smegmatis str. MC2 155 (31% identity, 86% coverage)

NP_461396 alcohol dehydrogenase EutG from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (31% identity, 97% coverage)

Cphy_3925 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium phytofermentans ISDg (32% identity, 40% coverage)

Csal_0681 iron-containing alcohol dehydrogenase (NCBI) from Chromohalobacter salexigens DSM 3043 (32% identity, 95% coverage)

LSA0379 Bifunctional enzyme: alcohol dehydrogenase, acetaldehyde dehydrogenase (NCBI) from Lactobacillus sakei subsp. sakei 23K (31% identity, 41% coverage)

LGG_00757 NAD-dependent alcohol-acetaldehyde dehydrogenase and iron-binding alcohol dehydrogenase (RefSeq) from Lactobacillus rhamnosus GG (30% identity, 42% coverage)

SSU05_0280 NAD-dependent aldehyde dehydrogenase (RefSeq) from Streptococcus suis 05ZYH33 (31% identity, 41% coverage)

YPTB2103 aldehyde-alcohol dehydrogenase (NCBI) from Yersinia pseudotuberculosis IP 32953 (31% identity, 38% coverage)

Dtur_1632 iron-containing alcohol dehydrogenase (RefSeq) from Dictyoglomus turgidum DSM 6724 (30% identity, 95% coverage)

RPC_4481 iron-containing alcohol dehydrogenase (NCBI) from Rhodopseudomonas palustris BisB18 (31% identity, 38% coverage)

AMETH_5577 NDMA-dependent methanol dehydrogenase from Amycolatopsis methanolica 239 (30% identity, 86% coverage)

STM1749 iron-dependent alcohol dehydrogenase of the multifunctional alcohol dehydrogenase AdhE (NCBI ptt file) from Salmonella typhimurium LT2 (31% identity, 38% coverage)

Entcl_2072 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Enterobacter lignolyticus SCF1 (30% identity, 38% coverage)

AKI40_3351 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Enterobacter sp. FY-07 (30% identity, 38% coverage)

lp_3662 bifunctional protein: alcohol dehydrogenase; acetaldehyde dehydrogenase (NCBI ptt file) from Lactobacillus plantarum WCFS1 (30% identity, 42% coverage)

MNO_AMYME / Q9RCG0 Methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase; MNO; EC 1.1.99.37; Methanol dehydrogenase (nicotinoprotein); Methanol:NDMA oxidoreductase from Amycolatopsis methanolica (34% identity, 72% coverage) (see paper)

AN479_RS20355 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Serratia marcescens (30% identity, 40% coverage)

Cphy_1029 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium phytofermentans ISDg (30% identity, 94% coverage)

VC2033 alcohol dehydrogenase/acetaldehyde dehydrogenase (NCBI ptt file) from Vibrio cholerae O1 biovar eltor str. N16961 (31% identity, 38% coverage)

SACOL0135 alcohol dehydrogenase, iron-containing (NCBI) from Staphylococcus aureus subsp. aureus COL (31% identity, 39% coverage)
SAOUHSC_00113 alcohol dehydrogenase, iron-containing, putative (NCBI) from Staphylococcus aureus subsp. aureus NCTC 8325

NP_465159 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Listeria monocytogenes EGD-e (29% identity, 43% coverage)
lmo1634 similar to Alcohol-acetaldehyde dehydrogenase (NCBI ptt file) from Listeria monocytogenes EGD-e

LMRG_01332 alcohol dehydrogenase, iron-containing (RefSeq) from Listeria monocytogenes 10403S (29% identity, 43% coverage)

SA0143 alcohol-acetaldehyde dehydrogenase (NCBI) from Staphylococcus aureus subsp. aureus N315 (31% identity, 39% coverage)

NP_213782 1,3 propanediol dehydrogenase from Aquifex aeolicus VF5 (29% identity, 89% coverage)

CtherDRAFT_0616 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium thermocellum DSM 4150 (31% identity, 91% coverage)

CLJU_c16510 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Clostridium ljungdahlii DSM 13528 (30% identity, 43% coverage)

EHI_150490 alcohol dehydrogenase, putative from Entamoeba histolytica HM-1:IMSS (29% identity, 44% coverage)

EHI_160940 alcohol dehydrogenase, putative from Entamoeba histolytica HM-1:IMSS (29% identity, 44% coverage)

AdhC / b1241 aldehyde-alcohol dehydrogenase from Escherichia coli K-12 substr. MG1655 (30% identity, 38% coverage) (see 5 papers)
adhE / MB|P0A9Q7 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 from Escherichia coli K12 (see 12 papers)
P0A9Q7 Aldehyde-alcohol dehydrogenase from Escherichia coli (strain K12)
NP_415757 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase from Escherichia coli str. K-12 substr. MG1655
b1241 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase (NCBI) from Escherichia coli str. K-12 substr. MG1655

CAETHG_3747, CLAU_3655 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Clostridium autoethanogenum DSM 10061 (30% identity, 43% coverage)

ADH2_ENTHI / Q24803 Aldehyde-alcohol dehydrogenase 2 from Entamoeba histolytica (29% identity, 44% coverage) (see 2 papers)
adh2 / GB|AAA81906.1 aldehyde-alcohol dehydrogenase 2; EC 1.1.1.1; EC 1.2.1.10 from Entamoeba histolytica (see paper)

SERP0389 alcohol dehydrogenase, iron-containing (NCBI) from Staphylococcus epidermidis RP62A (31% identity, 39% coverage)

Ccel_1083 NADPH-dependent butanol dehydrogenase from [Clostridium] cellulolyticum H10 (30% identity, 94% coverage)
Ccel_1083 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium cellulolyticum H10

A1S_2053 putative iron-containing alcohol dehydrogenase (RefSeq) from Acinetobacter baumannii ATCC 17978 (34% identity, 83% coverage)

KPN_02199 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase (RefSeq) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (30% identity, 38% coverage)

SpyM3_0036 putative alcohol dehydrogenase II (NCBI ptt file) from Streptococcus pyogenes MGAS315 (29% identity, 40% coverage)

CD0334 aldehyde-alcohol dehydrogenase [includes: alcohol dehydrogenase; acetaldehyde dehydrogenase [acetylating]; pyruvate-formate-lyase deactivase (RefSeq) from Clostridium difficile 630 (28% identity, 42% coverage)

M5005_Spy_0039 alcohol dehydrogenase/acetaldehyde dehydrogenase (acetylating) (NCBI) from Streptococcus pyogenes MGAS5005 (29% identity, 40% coverage)

Cthe_2579 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium thermocellum ATCC 27405 (31% identity, 91% coverage)

CBO0345 aldehyde-alcohol dehydrogenase (RefSeq) from Clostridium botulinum A str. ATCC 3502 (30% identity, 41% coverage)

plu2496 Aldehyde-alcohol dehydrogenase [includes: alcohol dehydrogenase (ADH) and acetaldehyde dehydrogenase [acetylating] (ACDH); pyruvate-formate-lyase deactivase (PFL deactivase)] (NCBI) from Photorhabdus luminescens subsp. laumondii TTO1 (31% identity, 39% coverage)

SE0506 alcohol dehydrogenase (NCBI ptt file) from Staphylococcus epidermidis ATCC 12228 (31% identity, 39% coverage)

SAR11_1287 iron-containing alcohol dehydrogenase (NCBI) from Candidatus Pelagibacter ubique HTCC1062 (27% identity, 98% coverage)

CD2966 aldehyde-alcohol dehydrogenase [includes: alcohol dehydrogenase and pyruvate-formate-lyase deactivase (RefSeq) from Clostridium difficile 630 (31% identity, 40% coverage)

CD0274 putative 1,3-propanediol dehydrogenase (RefSeq) from Clostridium difficile 630 (28% identity, 96% coverage)

MNO_RHOER / Q53062 Methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase; MNO; EC 1.1.99.37; Methanol dehydrogenase (nicotinoprotein); Methanol:NDMA oxidoreductase from Rhodococcus erythropolis (Arthrobacter picolinophilus) (32% identity, 86% coverage) (see paper)

SGO_0113 alcohol-acetaldehyde dehydrogenase (RefSeq) from Streptococcus gordonii str. Challis substr. CH1 (30% identity, 40% coverage)

Cbei_4552 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (32% identity, 79% coverage)

A1S_2702 putative alcohol dehydrogenase (RefSeq) from Acinetobacter baumannii ATCC 17978 (31% identity, 74% coverage)

AHA_1331 alcohol dehydrogenase, iron-containing (NCBI) from Aeromonas hydrophila subsp. hydrophila ATCC 7966 (30% identity, 97% coverage)

Ccel_3198 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium cellulolyticum H10 (30% identity, 40% coverage)
Ccel_3198 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from [Clostridium] cellulolyticum H10

EHI_024240, XP_001913653 aldehyde-alcohol dehydrogenase 2, putative from Entamoeba histolytica HM-1:IMSS (30% identity, 46% coverage)

CLAU_3656 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Clostridium autoethanogenum DSM 10061 (30% identity, 41% coverage)

spr1837 Alcohol-acetaldehyde dehydrogenase (NCBI ptt file) from Streptococcus pneumoniae R6 (30% identity, 39% coverage)

SPD_1834 alcohol dehydrogenase, iron-containing (NCBI) from Streptococcus pneumoniae D39 (30% identity, 40% coverage)

SAG0053 aldehyde-alcohol dehydrogenase (NCBI ptt file) from Streptococcus agalactiae 2603V/R (28% identity, 40% coverage)

pRL100103 putative alcohol dehydrogenase (NCBI) from Rhizobium leguminosarum bv. viciae 3841 (32% identity, 97% coverage)

Cbei_4354 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (26% identity, 96% coverage)

MNO_MYCS8 / C5MRT8 Methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase; MDO; EC 1.1.99.37; Methanol dehydrogenase (nicotinoprotein); Methanol:NDMA oxidoreductase from Mycobacterium sp. (strain DSM 3803 / JC1) (30% identity, 88% coverage) (see paper)

BAB2_0506 Iron-containing alcohol dehydrogenase (NCBI) from Brucella melitensis biovar Abortus 2308 (32% identity, 77% coverage)

SSA_0514 PduQ protein, putative (NCBI) from Streptococcus sanguinis SK36 (28% identity, 96% coverage)

TM0111 alcohol dehydrogenase, iron-containing (NCBI ptt file) from Thermotoga maritima MSB8 (29% identity, 96% coverage)

PA5186 probable iron-containing alcohol dehydrogenase (NCBI) from Pseudomonas aeruginosa PAO1 (35% identity, 95% coverage)

CTN_0580 Alcohol dehydrogenase, iron-containing (RefSeq) from Thermotoga neapolitana DSM 4359 (28% identity, 96% coverage)

Cbei_1937 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (27% identity, 95% coverage)

Cthe_0394 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium thermocellum ATCC 27405 (30% identity, 77% coverage)

EF1635 propanol dehydrogenase PduQ, putative (NCBI ptt file) from Enterococcus faecalis V583 (27% identity, 96% coverage)

Tpet_0813 iron-containing alcohol dehydrogenase (RefSeq) from Thermotoga petrophila RKU-1 (28% identity, 98% coverage)

Csac_0711 iron-containing alcohol dehydrogenase (RefSeq) from Caldicellulosiruptor saccharolyticus DSM 8903 (29% identity, 89% coverage)

A8JI07 alcohol dehydrogenase / acetaldehyde dehydrogenase from Chlamydomonas reinhardtii (28% identity, 39% coverage) (see 2 papers)
XP_001703585 dual function alcohol dehydrogenase / acetaldehyde dehydrogenase from Chlamydomonas reinhardtii

I3VU69 Iron-containing alcohol dehydrogenase from Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485) (28% identity, 91% coverage)

BL1575 Adh2 (NCBI) from Bifidobacterium longum NCC2705 (30% identity, 37% coverage)

Asuc_0591 iron-containing alcohol dehydrogenase (RefSeq) from Actinobacillus succinogenes 130Z (32% identity, 32% coverage)

Kole_0742 iron-containing alcohol dehydrogenase (RefSeq) from Thermotogales bacterium TBF 19.5.1 (29% identity, 92% coverage)
Kole_0742 alcohol dehydrogenase from Kosmotoga olearia TBF 19.5.1

Tpet_0563 iron-containing alcohol dehydrogenase (RefSeq) from Thermotoga petrophila RKU-1 (30% identity, 90% coverage)

PA1146 probable iron-containing alcohol dehydrogenase (NCBI) from Pseudomonas aeruginosa PAO1 (30% identity, 97% coverage)

PF0608 alcohol dehydrogenase (NCBI ptt file) from Pyrococcus furiosus DSM 3638 (30% identity, 97% coverage)

T260_01930 NAD-dependent alcohol dehydrogenase from Geobacillus sp. MAS1 (33% identity, 81% coverage)

AF0024 alcohol dehydrogenase, iron-containing (NCBI ptt file) from Archaeoglobus fulgidus DSM 4304 (28% identity, 88% coverage)

YP_193379 alcohol-acetaldehyde dehydrogenase (RefSeq) from Lactobacillus acidophilus NCFM (29% identity, 40% coverage)

GL50803_93358 Alcohol dehydrogenase from Giardia lamblia ATCC 50803 (27% identity, 38% coverage)

gbd / PRF|2104199G 4-hydroxybutyrate dehydrogenase; EC 1.1.1.61 from Cupriavidus necator (32% identity, 92% coverage) (see paper)

SMU_148 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Streptococcus mutans UA159 (27% identity, 38% coverage)

Mvan_0443 iron-containing alcohol dehydrogenase (NCBI) from Mycobacterium vanbaalenii PYR-1 (31% identity, 41% coverage)

AF0339 alcohol dehydrogenase, iron-containing (NCBI ptt file) from Archaeoglobus fulgidus DSM 4304 (28% identity, 94% coverage)

Entcl_1745 iron-containing alcohol dehydrogenase from Enterobacter lignolyticus SCF1 (30% identity, 95% coverage)

PF0075 alcohol dehydrogenase (NCBI ptt file) from Pyrococcus furiosus DSM 3638 (28% identity, 96% coverage)

NCDO2118_2257 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Lactococcus lactis subsp. lactis NCDO 2118 (27% identity, 37% coverage)

Dhaf_0588 iron-containing alcohol dehydrogenase (RefSeq) from Desulfitobacterium hafniense DCB-2 (28% identity, 75% coverage)

Q9XDN0 propanol dehydrogenase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (30% identity, 83% coverage) (see paper)
NP_460997 propanediol utilization protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

llmg_2432 alcohol-acetaldehyde dehydrogenase (NCBI) from Lactococcus lactis subsp. cremoris MG1363 (27% identity, 37% coverage)

lmo1166 similar to NADPH-dependent butanol dehydrogenase (NCBI ptt file) from Listeria monocytogenes EGD-e (27% identity, 96% coverage)

L21SP2_0358 hypothetical protein from Salinispira pacifica (28% identity, 82% coverage)

LSA0258 Putative iron-containing alcohol dehydrogenase (oxidoreductase) (NCBI) from Lactobacillus sakei subsp. sakei 23K (30% identity, 71% coverage)

Csac_0622 iron-containing alcohol dehydrogenase (RefSeq) from Caldicellulosiruptor saccharolyticus DSM 8903 (27% identity, 92% coverage)

TCEL_00064 alcohol dehydrogenase from Thermobrachium celere DSM 8682 (30% identity, 79% coverage)

Ethha_2239 alcohol dehydrogenase from Ethanoligenens harbinense YUAN-3 (26% identity, 79% coverage)

I3VXI1 Iron-containing alcohol dehydrogenase from Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485) (26% identity, 97% coverage)

Ethha_1164 alcohol dehydrogenase from Ethanoligenens harbinense YUAN-3 (29% identity, 97% coverage)

ATO21_04225 NAD-dependent alcohol dehydrogenase from Pediococcus acidilactici (28% identity, 82% coverage)

TK1569 iron-containing alcohol dehydrogenase (NCBI) from Thermococcus kodakaraensis KOD1 (29% identity, 86% coverage)

TON_0544 alcohol dehydrogenase (RefSeq) from Thermococcus onnurineus NA1 (28% identity, 91% coverage)

NP_996969 hydroxyacid-oxoacid transhydrogenase, mitochondrial from Danio rerio (26% identity, 79% coverage)

XP_849448 hydroxyacid-oxoacid transhydrogenase, mitochondrial isoform X4 from Canis lupus familiaris (27% identity, 80% coverage)

ADHA_THEET / Q9F282 Long-chain primary alcohol dehydrogenase AdhA; EC 1.1.1.2 from Thermoanaerobacter ethanolicus (Clostridium thermohydrosulfuricum) (28% identity, 93% coverage) (see paper)
Teth514_0564 iron-containing alcohol dehydrogenase (RefSeq) from Thermoanaerobacter ethanolicus X514

I3VS20 Iron-containing alcohol dehydrogenase from Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485) (28% identity, 92% coverage)

Q9U2M4 Hydroxyacid-oxoacid transhydrogenase, mitochondrial from Caenorhabditis elegans (25% identity, 81% coverage)
NP_496764 Hydroxyacid-oxoacid transhydrogenase, mitochondrial from Caenorhabditis elegans

Teth39_0220 iron-containing alcohol dehydrogenase (RefSeq) from Thermoanaerobacter ethanolicus ATCC 33223 (28% identity, 92% coverage)

NP_477209 type III alcohol dehydrogenase from Drosophila melanogaster (27% identity, 80% coverage)

TM0920 alcohol dehydrogenase, iron-containing (NCBI ptt file) from Thermotoga maritima MSB8 (27% identity, 78% coverage)

CTN_1655 Iron-containing alcohol dehydrogenase (RefSeq) from Thermotoga neapolitana DSM 4359 (26% identity, 99% coverage)

I3VX46 Iron-containing alcohol dehydrogenase from Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485) (27% identity, 93% coverage)

Teth514_0654 iron-containing alcohol dehydrogenase (RefSeq) from Thermoanaerobacter ethanolicus X514 (27% identity, 92% coverage)

Pcar_1095 NADH-dependent butanol dehydrogenase II (NCBI) from Pelobacter carbinolicus str. DSM 2380 (29% identity, 88% coverage)

HOT_HUMAN / Q8IWW8 Hydroxyacid-oxoacid transhydrogenase, mitochondrial; HOT; EC 1.1.99.24; Alcohol dehydrogenase iron-containing protein 1; ADHFe1; Fe-containing alcohol dehydrogenase from Homo sapiens (Human) (28% identity, 73% coverage) (see 2 papers)
NP_653251 hydroxyacid-oxoacid transhydrogenase, mitochondrial from Homo sapiens

Tpet_0007 iron-containing alcohol dehydrogenase (RefSeq) from Thermotoga petrophila RKU-1 (27% identity, 78% coverage)

TK1008 Fe-containing alcohol dehydrogenase (NCBI) from Thermococcus kodakaraensis KOD1 (27% identity, 91% coverage)

Teth39_1597 iron-containing alcohol dehydrogenase (RefSeq) from Thermoanaerobacter ethanolicus ATCC 33223 (26% identity, 90% coverage)

TTE0313 NADH-dependent alcohol dehydrogenase from Caldanaerobacter subterraneus subsp. tengcongensis MB4 (29% identity, 75% coverage)
TTE0313 uncharacterized oxidoreductases, Fe-dependent alcohol dehydrogenase family (NCBI ptt file) from Thermoanaerobacter tengcongensis MB4

TTE0696 Alcohol dehydrogenase IV (NCBI ptt file) from Thermoanaerobacter tengcongensis MB4 (28% identity, 86% coverage)

HOT_RAT / Q4QQW3 Hydroxyacid-oxoacid transhydrogenase, mitochondrial; HOT; EC 1.1.99.24; Alcohol dehydrogenase iron-containing protein 1; ADHFe1 from Rattus norvegicus (Rat) (26% identity, 80% coverage) (see paper)
NP_001020594 hydroxyacid-oxoacid transhydrogenase, mitochondrial from Rattus norvegicus

Tagg_0471 alcohol dehydrogenase from Thermosphaera aggregans DSM 11486 (27% identity, 84% coverage)

ADHE_CLOAB / P33744 Aldehyde-alcohol dehydrogenase; AAD from Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (26% identity, 40% coverage) (see paper)
P33744 alcohol/aldehyde dehydrogenase from Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787) (see 3 papers)
aad / GB|AAD04638.1 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 from Clostridium acetobutylicum ATCC 824 (see paper)
CA_P0162 bifunctional acetaldehyde-CoA/alcohol dehydrogenase from Clostridium acetobutylicum ATCC 824
CAP0162 Aldehyde dehydrogenase (NAD+) (NCBI ptt file) from Clostridium acetobutylicum ATCC 824

NP_989277 hydroxyacid-oxoacid transhydrogenase, mitochondrial from Xenopus tropicalis (28% identity, 74% coverage)

Teth39_1979 iron-containing alcohol dehydrogenase (RefSeq) from Thermoanaerobacter ethanolicus ATCC 33223 (25% identity, 90% coverage)

XP_017168188 hydroxyacid-oxoacid transhydrogenase, mitochondrial isoform X2 from Mus musculus (26% identity, 89% coverage)

HOT_MOUSE / Q8R0N6 Hydroxyacid-oxoacid transhydrogenase, mitochondrial; HOT; EC 1.1.99.24; Alcohol dehydrogenase iron-containing protein 1; ADHFe1 from Mus musculus (Mouse) (26% identity, 80% coverage) (see paper)
NP_780445 hydroxyacid-oxoacid transhydrogenase, mitochondrial from Mus musculus

Csac_1500 iron-containing alcohol dehydrogenase (RefSeq) from Caldicellulosiruptor saccharolyticus DSM 8903 (26% identity, 72% coverage)

TKV_c02600 NADH-dependent alcohol dehydrogenase from Thermoanaerobacter kivui (25% identity, 92% coverage)

Athe_0928 alcohol dehydrogenase from Caldicellulosiruptor bescii DSM 6725 (26% identity, 73% coverage)
Athe_0928 iron-containing alcohol dehydrogenase (RefSeq) from Anaerocellum thermophilum DSM 6725

Cbei_2421 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium beijerincki NCIMB 8052 (27% identity, 97% coverage)

XP_749583 Fe-containing alcohol dehydrogenase from Aspergillus fumigatus Af293 (25% identity, 69% coverage)

ADH2_GEOTN / A4ISB9 Long-chain-alcohol dehydrogenase 2; EC 1.1.1.192; Alcohol dehydrogenase 2; ADH2; Fatty alcohol oxidoreductase 2 from Geobacillus thermodenitrificans (strain NG80-2) (25% identity, 91% coverage) (see paper)
GTNG_2878 NADH-dependent butanol dehydrogenase A (RefSeq) from Geobacillus thermodenitrificans NG80-2

EHI_166490 alcohol dehydrogenase, putative from Entamoeba histolytica HM-1:IMSS (29% identity, 71% coverage)

CTN_1756 Iron-containing alcohol dehydrogenase (RefSeq) from Thermotoga neapolitana DSM 4359 (25% identity, 88% coverage)

CPE0858 NADH-dependent butanol dehydrogenase (NCBI ptt file) from Clostridium perfringens str. 13 (26% identity, 97% coverage)

Cthe_0101 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium thermocellum ATCC 27405 (26% identity, 75% coverage)

Atu2528 maleylacetate reductase (RefSeq) from Agrobacterium tumefaciens str. C58 (Cereon) (28% identity, 94% coverage)

D7PC19 phophonoacetaldehyde reductase from Streptomyces luridus (31% identity, 66% coverage) (see paper)

C8J_1329 hypothetical protein (RefSeq) from Campylobacter jejuni subsp. jejuni 81116 (28% identity, 72% coverage)

bdhA / GI|15026377 NADH-dependent butanol dehydrogenase A from Clostridium acetobutylicum ATCC 824 (23% identity, 90% coverage) (see paper)
bdhA NADH-dependent butanol dehydrogenase A; EC 1.1.1.- from Clostridium acetobutylicum (see paper)
CA_C3299 NADH-dependent butanol dehydrogenase from Clostridium acetobutylicum ATCC 824
CAC3299 NADH-dependent butanol dehydrogenase A (BDH I) (NCBI ptt file) from Clostridium acetobutylicum ATCC 824

SMB_G3335 NADH-dependent butanol dehydrogenase B from Clostridium acetobutylicum DSM 1731 (28% identity, 73% coverage)
CA_C3298 NADH-dependent butanol dehydrogenase from Clostridium acetobutylicum ATCC 824
CAC3298 NADH-dependent butanol dehydrogenase B (BDH II) (NCBI ptt file) from Clostridium acetobutylicum ATCC 824

Q45072 maleylacetate reductase from Burkholderia cepacia (28% identity, 83% coverage) (see paper)
tftE / GB|AAC43333.1 maleylacetate reductase; EC 1.3.1.32 from Burkholderia cepacia (see paper)
Q45072 Maleylacetate reductase from Burkholderia cepacia

Ccel_3337 NADH-dependent alcohol dehydrogenase from [Clostridium] cellulolyticum H10 (25% identity, 90% coverage)
Ccel_3337 iron-containing alcohol dehydrogenase (RefSeq) from Clostridium cellulolyticum H10

Swit_4891 iron-containing alcohol dehydrogenase (RefSeq) from Sphingomonas wittichii RW1 (26% identity, 81% coverage)

A1IIX4 maleylacetate reductase from Rhizobium sp. MTP-10005 (26% identity, 93% coverage) (see paper)

TM0820 NADH-dependent butanol dehydrogenase, putative (NCBI ptt file) from Thermotoga maritima MSB8 (25% identity, 88% coverage)

Q471H8 maleylacetate reductase from Cupriavidus necator (strain JMP 134 / LMG 1197) (28% identity, 78% coverage) (see paper)
Reut_A1589 Iron-containing alcohol dehydrogenase (NCBI) from Ralstonia eutropha JMP134

CBO1407 NADH-dependent butanol dehydrogenase (RefSeq) from Clostridium botulinum A str. ATCC 3502 (24% identity, 90% coverage)

Q5W9E3 maleylacetate reductase from Sphingobium japonicum (28% identity, 77% coverage) (see paper)

Tpet_0107 iron-containing alcohol dehydrogenase (RefSeq) from Thermotoga petrophila RKU-1 (25% identity, 88% coverage)

SOV_2c03040 NAD-dependent alcohol dehydrogenase from Sporomusa ovata DSM 2662 (31% identity, 66% coverage)

Fitness Blast Results

Query Sequence

>VIMSS3615187 iron-containing alcohol dehydrogenase
MSHDLSQLRKFVSPEIIFGAGSRHNVGNYAKTFGARKVLIVSDPGVVAAGWAGDVEASLQ
AQGIDYCLYTGVSPNPRVEEVMTGAELYRSEGCNVIVAVGGGSPMDCAKGIGIVVAHGRN
ILEFEGVDTLRVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAVVPDVSLID
PETTLSMDPFLSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINGNLVQMIANPAD
IALREKIMLGSMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYSAA
PERFKVIAETLGIDCRGLTHTQIRQRLVEHLIAFKHAVGFRETLGLHGVGTSDIPFLSSH
AMDDPCILTNPRESTQRDVEVVYGEAL

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Statistics

The PaperBLAST database links 357,933 different protein sequences to 875,526 scientific articles. Searches against EuropePMC were last performed on December 29 2017.

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, Swiss-Prot, CAZy (as made available by dbCAN), CharProtDB, MetaCyc, EcoCyc, REBASE, and the Fitness Browser. 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 links between protein sequences and articles:

Except for GeneRIF, the curated entries include a short curated description of the protein's function. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. Also note some changes since the paper was written:

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

Some important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles) 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 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.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory