PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for BRENDA::Q9Z4X8 4-hydroxymandelate oxidase (EC 1.1.3.46) (Streptomyces coelicolor) (377 a.a., MREPLTLDDF...)

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Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Found 225 similar proteins in the literature:

Q9Z4X8 4-hydroxymandelate oxidase (EC 1.1.3.46) from Streptomyces coelicolor (see paper)
SCO3228 glycolate oxidase from Streptomyces coelicolor A3(2)
100% identity, 100% coverage

5zzqA / O52792 The crystal structure of mandelate oxidase with (s)-4-hydroxymandelic acid (see paper)
48% identity, 90% coverage

HMO_AMYOR / O52792 4-hydroxymandelate oxidase; EC 1.1.3.46 from Amycolatopsis orientalis (Nocardia orientalis) (see 3 papers)
O52792 4-hydroxymandelate oxidase (EC 1.1.3.46) from Amycolatopsis orientalis (see 2 papers)
48% identity, 90% coverage

AT4G18360 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
NP_193570 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
O49506 Glycolate oxidase 3 from Arabidopsis thaliana
45% identity, 89% coverage

6a08A / O52792 The crystal structure of mandelate oxidase with benzoyl-formic acid (see paper)
47% identity, 90% coverage

HAOX2_ARATH / Q24JJ8 Peroxisomal (S)-2-hydroxyacid oxidase GLO3; Glycolate oxidase 3; AtGLO3; GOX 3; Short chain alpha-hydroxy acid oxidase GLO3; lHAOX2; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q24JJ8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Arabidopsis thaliana (see paper)
AT3G14150 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
45% identity, 90% coverage

HAOX1_HUMAN / Q9UJM8 2-Hydroxyacid oxidase 1; HAOX1; Glycolate oxidase; GO; GOX; Glyoxylate oxidase; EC 1.1.3.15; EC 1.2.3.5 from Homo sapiens (Human) (see 4 papers)
Q9UJM8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Homo sapiens (see 2 papers)
NP_060015 2-Hydroxyacid oxidase 1 from Homo sapiens
43% identity, 90% coverage

6gmbA / Q9UJM8 Structure of human hydroxyacid oxidase 1 bound with fmn and glycolate
43% identity, 90% coverage

HAOX1_ARATH / Q9LJH5 Peroxisomal (S)-2-hydroxyacid oxidase GLO4; Glycolate oxidase 4; AtGLO4; GOX 4; lHAOX1; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q9LJH5 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Arabidopsis thaliana (see paper)
AT3G14130 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
45% identity, 90% coverage

BN5_0696 alpha-hydroxy acid oxidase from Pseudomonas oleovorans CECT 5344
48% identity, 92% coverage

E1AXT8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Nicotiana benthamiana (see 2 papers)
42% identity, 98% coverage

7r4pA / Q9UJM8 Structure of human hydroxyacid oxidase 1 bound with 6-amino-1-benzyl- 5-(methylamino)pyrimidine-2,4(1h,3h)-dione
44% identity, 90% coverage

XP_006233084 2-Hydroxyacid oxidase 2 isoform X2 from Rattus norvegicus
42% identity, 92% coverage

GLO2_ARATH / Q9LRS0 Glycolate oxidase 2; AtGLO2; GOX2; (S)-2-hydroxy-acid oxidase GLO2; Short chain alpha-hydroxy acid oxidase GLO2; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_188059 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
AT3G14415 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
41% identity, 95% coverage

M1VAT1 Glycolate oxidase, peroxysomal from Cyanidioschyzon merolae (strain NIES-3377 / 10D)
42% identity, 91% coverage

GLO1_ORYSJ / Q10CE4 Glycolate oxidase 1; GOX 1; OsGLO1; Peroxisomal (S)-2-hydroxy-acid oxidase GLO1; Short chain alpha-hydroxy acid oxidase GLO1; EC 1.1.3.15 from Oryza sativa subsp. japonica (Rice) (see 4 papers)
Q10CE4 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Oryza sativa Japonica Group (see paper)
45% identity, 92% coverage

A0A0P0KG57 4-hydroxymandelate oxidase (EC 1.1.3.46) from Streptomyces sp. (see paper)
50% identity, 88% coverage

B0BNF9 2-Hydroxyacid oxidase 1 from Rattus norvegicus
NP_001101250 2-Hydroxyacid oxidase 1 from Rattus norvegicus
42% identity, 90% coverage

LOC100646060 2-Hydroxyacid oxidase 1 from Bombus terrestris
40% identity, 95% coverage

5zbmB / E1AXT8 Structure of glycolate oxidase containing fmn from nicotiana benthamiana (see paper)
43% identity, 91% coverage

HAOX2_RAT / Q07523 2-Hydroxyacid oxidase 2; HAOX2; (S)-2-hydroxy-acid oxidase, peroxisomal; Long chain alpha-hydroxy acid oxidase; Long-chain L-2-hydroxy acid oxidase; LCHAO; EC 1.1.3.15 from Rattus norvegicus (Rat) (see 5 papers)
42% identity, 92% coverage

B9ST74 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Ricinus communis (see paper)
43% identity, 91% coverage

B9S0Y9 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Ricinus communis (see paper)
42% identity, 94% coverage

GOX1_MAIZE / A0A3L6E0R4 Glycolate oxidase 1; GOX; EC 1.1.3.15 from Zea mays (Maize) (see 2 papers)
44% identity, 92% coverage

GLO1_ARATH / Q9LRR9 Glycolate oxidase 1; AtGLO1; GOX1; (S)-2-hydroxy-acid oxidase GLO1; Short chain alpha-hydroxy acid oxidase GLO1; EC 1.1.3.15 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Q9LRR9 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Arabidopsis thaliana (see paper)
AT3G14420 (S)-2-hydroxy-acid oxidase, peroxisomal, putative / glycolate oxidase, putative / short chain alpha-hydroxy acid oxidase, putative from Arabidopsis thaliana
NP_188060 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
42% identity, 94% coverage

HAOX1_MOUSE / Q9WU19 2-Hydroxyacid oxidase 1; HAOX1; Glycolate oxidase; GOX; Glyoxylate oxidase; EC 1.1.3.15; EC 1.2.3.5 from Mus musculus (Mouse) (see paper)
Q9WU19 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Mus musculus (see 3 papers)
NP_034533 2-Hydroxyacid oxidase 1 from Mus musculus
41% identity, 90% coverage

GOX_SPIOL / P05414 Glycolate oxidase; GAO; GOX; Short chain alpha-hydroxy acid oxidase; EC 1.1.3.15 from Spinacia oleracea (Spinach) (see 5 papers)
P05414 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Spinacia oleracea (see paper)
42% identity, 94% coverage

3sgzA / Q07523 High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chiorophenyl) sulfanyl]-1, 2, 3-thiadiazole. (see paper)
42% identity, 92% coverage

Q6YT73 Glycolate oxidase 5 from Oryza sativa subsp. japonica
44% identity, 92% coverage

LOC101764130 peroxisomal (S)-2-hydroxy-acid oxidase GLO4 from Setaria italica
43% identity, 91% coverage

P93260 (S)-2-hydroxy-acid oxidase from Mesembryanthemum crystallinum
42% identity, 92% coverage

Q8H3I4 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Oryza sativa Japonica Group (see paper)
43% identity, 91% coverage

HAOX2_HUMAN / Q9NYQ3 2-Hydroxyacid oxidase 2; HAOX2; (S)-2-hydroxy-acid oxidase, peroxisomal; Cell growth-inhibiting gene 16 protein; Long chain alpha-hydroxy acid oxidase; Long-chain L-2-hydroxy acid oxidase; EC 1.1.3.15 from Homo sapiens (Human) (see paper)
Q9NYQ3 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Homo sapiens (see paper)
44% identity, 91% coverage

XP_015138965 hydroxyacid oxidase 1 isoform X3 from Gallus gallus
45% identity, 82% coverage

G4V4S8 4-hydroxymandelate oxidase (EC 1.1.3.46) from Amycolatopsis orientalis (see 2 papers)
47% identity, 89% coverage

Q7FAS1 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Oryza sativa Japonica Group (see paper)
B8AUI3 Glycolate oxidase 3 from Oryza sativa subsp. indica
42% identity, 90% coverage

Q39640 (S)-2-hydroxy-acid oxidase from Cucurbita hybrid cultivar
41% identity, 97% coverage

GRMZM2G148194 aldolase-type TIM barrel family protein-like from Zea mays
44% identity, 89% coverage

DMB42_RS42735 alpha-hydroxy acid oxidase from Nonomuraea sp. WAC 01424
47% identity, 89% coverage

PAAG_07725 peroxisomal (S)-2-hydroxy-acid oxidase from Paracoccidioides lutzii Pb01
40% identity, 84% coverage

HAOX2_MOUSE / Q9NYQ2 2-Hydroxyacid oxidase 2; HAOX2; (S)-2-hydroxy-acid oxidase, peroxisomal; Medium chain alpha-hydroxy acid oxidase; Medium-chain L-2-hydroxy acid oxidase; EC 1.1.3.15 from Mus musculus (Mouse) (see paper)
Q9NYQ2 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Mus musculus (see paper)
40% identity, 92% coverage

LOX_NOSS1 / Q8Z0C8 L-lactate oxidase; LOX; Glyoxylate oxidase; No-LOX; EC 1.1.3.-; EC 1.2.3.5 from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (see 2 papers)
Q8Z0C8 L-lactate oxidase (EC 1.1.3.2) from Nostoc sp. PCC 7120 = FACHB-418 (see paper)
all0170 glycolate oxidase from Nostoc sp. PCC 7120
43% identity, 93% coverage

RL3578 putative L-lactate dehydrogenase from Rhizobium leguminosarum bv. viciae 3841
40% identity, 89% coverage

XP_502755 Hydroxyacid oxidase 1 from Yarrowia lipolytica
39% identity, 91% coverage

A8MS37 (S)-2-hydroxy-acid oxidase from Arabidopsis thaliana
43% identity, 83% coverage

LOX_CHLRE / F8WQN2 L-lactate oxidase; LOX; Cr-LOX; EC 1.1.3.- from Chlamydomonas reinhardtii (Chlamydomonas smithii) (see paper)
F8WQN2 L-lactate oxidase (EC 1.1.3.2) from Chlamydomonas reinhardtii (see paper)
42% identity, 90% coverage

LOX_LYSSC / B1HZY7 L-lactate oxidase; LOX; (S)-2-hydroxy-acid oxidase; EC 1.1.3.-; EC 1.1.3.15 from Lysinibacillus sphaericus (strain C3-41) (see paper)
39% identity, 87% coverage

LOX_LACJE / A0A5N1I561 L-lactate oxidase; LOX; (S)-2-hydroxy-acid oxidase; EC 1.1.3.-; EC 1.1.3.15 from Lactobacillus jensenii (see paper)
39% identity, 82% coverage

Q9I197 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pseudomonas aeruginosa (see paper)
NP_251072 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
PA14_33860 L-lactate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
PA2382 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
38% identity, 91% coverage

NMA1592 L-lactate dehydrogenase from Neisseria meningitidis Z2491
37% identity, 85% coverage

lldA / AAB09666.1 lactate dehydrogenase from Neisseria meningitidis (see paper)
NMB1377 L-lactate dehydrogenase from Neisseria meningitidis MC58
37% identity, 85% coverage

NGK_1275 putative L-lactate dehydrogenase from Neisseria gonorrhoeae NCCP11945
37% identity, 85% coverage

NGO0639 putative L-lactate dehydrogenase from Neisseria gonorrhoeae FA 1090
37% identity, 85% coverage

CNAG_01080 glycolate oxidase from Cryptococcus neoformans var. grubii H99
40% identity, 90% coverage

CND02080 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
40% identity, 90% coverage

SM_b20850 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Sinorhizobium meliloti 1021
36% identity, 93% coverage

FUB9_FUSO4 / A0A0D2YG00 Oxidase FUB9; Fusaric acid biosynthesis protein 9; EC 1.-.-.- from Fusarium oxysporum f. sp. lycopersici (strain 4287 / CBS 123668 / FGSC 9935 / NRRL 34936) (Fusarium vascular wilt of tomato) (see 8 papers)
38% identity, 89% coverage

FUB9_GIBM7 / W7NCP1 Oxidase FUB9; Fusaric acid biosynthesis protein 9; EC 1.-.-.- from Gibberella moniliformis (strain M3125 / FGSC 7600) (Maize ear and stalk rot fungus) (Fusarium verticillioides) (see 9 papers)
38% identity, 89% coverage

SLG_34570 alpha-hydroxy acid oxidase from Sphingobium sp. SYK-6
42% identity, 91% coverage

LOX_ALIDK / F4G5A4 L-lactate oxidase; LOX; Glycolate oxidase; EC 1.1.3.-; EC 1.1.3.15 from Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601) (see paper)
45% identity, 91% coverage

C9Y9E7 L-lactate dehydrogenase [cytochrome] from Curvibacter symbiont subsp. Hydra magnipapillata
35% identity, 91% coverage

BOV_RS14715 alpha-hydroxy acid oxidase from Brucella ovis ATCC 25840
36% identity, 92% coverage

BAB2_0315 FMN-dependent alpha-hydroxy acid dehydrogenase:FMN/related compound-binding core from Brucella melitensis biovar Abortus 2308
36% identity, 92% coverage

BMEII0377 L-LACTATE DEHYDROGENASE (CYTOCHROME) from Brucella melitensis 16M
36% identity, 92% coverage

AORI_1496 alpha-hydroxy acid oxidase from Amycolatopsis keratiniphila
47% identity, 89% coverage

FTN_0217 L-lactate dehydrogenase from Francisella tularensis subsp. novicida U112
33% identity, 91% coverage

NP_879338 L-lactate dehydrogenase from Bordetella pertussis Tohama I
BP0484 alpha-hydroxy acid oxidase from Bordetella pertussis Tohama I
37% identity, 90% coverage

H1A07_09050 alpha-hydroxy-acid oxidizing protein from Lactobacillus taiwanensis
36% identity, 88% coverage

1huvA / P05414,P20932 Crystal structure of a soluble mutant of the membrane-associated (s)- mandelate dehydrogenase from pseudomonas putida at 2.15a resolution (see paper)
38% identity, 92% coverage

bll6401 L-lactate dehydrogenase from Bradyrhizobium japonicum USDA 110
37% identity, 85% coverage

LJ1826 glycolate oxidase from Lactobacillus johnsonii NCC 533
38% identity, 81% coverage

FUB9_GIBF5 / S0DRI9 Oxidase FUB9; Fusaric acid biosynthesis protein 9; EC 1.-.-.- from Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) (Bakanae and foot rot disease fungus) (Fusarium fujikuroi) (see 8 papers)
37% identity, 92% coverage

STY1444 putative glycolate oxidase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
39% identity, 82% coverage

E0NE46 L-lactate oxidase from Pediococcus acidilactici DSM 20284
37% identity, 92% coverage

STM1620 putative oxidase from Salmonella typhimurium LT2
STM14_1959 lactate oxidase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
38% identity, 81% coverage

SC1616 putative oxidase from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
39% identity, 82% coverage

6r9vA / E0NE46 Crystal structure of pediococcus acidilactici lactate oxidase a94g mutant (see paper)
37% identity, 92% coverage

Q43775 (S)-2-hydroxy-acid oxidase (Fragment) from Solanum lycopersicum
43% identity, 77% coverage

LSA1399 L-Lactate oxidase from Lactobacillus sakei subsp. sakei 23K
37% identity, 93% coverage

G3I6D1 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 from Cricetulus griseus
43% identity, 41% coverage

W1QKE8 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Ogataea angusta (see 2 papers)
36% identity, 61% coverage

QULF_PENCI / P0DUR7 FMN-dependent alpha-hydroxy acid dehydrogenase qulF; Quinolactacin A2 biosynthesis cluster protein F; EC 1.13.12.- from Penicillium citrinum (see paper)
37% identity, 84% coverage

FGSG_03984 hypothetical protein from Fusarium graminearum PH-1
37% identity, 79% coverage

CH_124019 putative FMN dependent dehydrogenase [Aspergillus fumigatus Af293] from Magnaporthe grisea 70-15 (see paper)
39% identity, 78% coverage

A0A099P7X2 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pichia kudriavzevii (see paper)
38% identity, 57% coverage

LOX_LENH9 / C0XIJ3 L-lactate oxidase; LOX; EC 1.1.3.- from Lentilactobacillus hilgardii (strain ATCC 8290 / DSM 20176 / CCUG 30140 / JCM 1155 / KCTC 3500 / NBRC 15886 / NCIMB 8040 / NRRL B-1843 / 9) (see paper)
38% identity, 89% coverage

Bphy_5156 L-lactate dehydrogenase (cytochrome) from Burkholderia phymatum STM815
38% identity, 78% coverage

PAJ_p0276 FMN-dependent L-lactate dehydrogenase LldD from Pantoea ananatis AJ13355
38% identity, 88% coverage

Bphy_5156 alpha-hydroxy acid oxidase from Paraburkholderia phymatum STM815
38% identity, 79% coverage

Ac3H11_1623 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Acidovorax sp. GW101-3H11
35% identity, 89% coverage

lctO / D4YFM2 lactate oxidase monomer (EC 1.1.3.2) from Aerococcus viridans (strain ATCC 11563 / DSM 20340 / CCUG 4311 / JCM 20461 / NBRC 12219 / NCTC 8251 / M1) (see 29 papers)
D4YFM2 L-lactate oxidase (EC 1.1.3.2) from Aerococcus viridans (see 2 papers)
WP_003142047 L-lactate oxidase from Aerococcus viridans
36% identity, 92% coverage

6bfgA / P20932 Crystal structure of monotopic membrane protein (s)-mandelate dehydrogenase (see paper)
35% identity, 92% coverage

mdlB / P20932 (S)-mandelate dehydrogenase (EC 1.1.99.31) from Pseudomonas putida (see 2 papers)
MDLB_PSEPU / P20932 (S)-mandelate dehydrogenase; MDH; L(+)-mandelate dehydrogenase; EC 1.1.99.31 from Pseudomonas putida (Arthrobacter siderocapsulatus) (see 5 papers)
P20932 (S)-mandelate dehydrogenase (EC 1.1.99.31) from Pseudomonas putida (see 5 papers)
35% identity, 88% coverage

H16_B0460 L-Lactate cytochrome reductase from Ralstonia eutropha H16
H16_B0460 alpha-hydroxy acid oxidase from Cupriavidus necator H16
34% identity, 92% coverage

LOX_AERVM / Q44467 L-lactate oxidase; LOD; LOX; Lactate oxidase; EC 1.1.3.- from Aerococcus viridans (strain ATCC 11563 / DSM 20340 / CCUG 4311 / JCM 20461 / NBRC 12219 / NCTC 8251 / M1) (see 11 papers)
Q44467 L-lactate dehydrogenase (EC 1.1.1.27); L-lactate oxidase (EC 1.1.3.2) from Aerococcus viridans (see 18 papers)
2du2A / Q44467 Crystal structure analysis of the l-lactate oxidase (see paper)
36% identity, 92% coverage

SP_0715 lactate oxidase from Streptococcus pneumoniae TIGR4
35% identity, 97% coverage

lp_3586 lactate oxidase from Lactobacillus plantarum WCFS1
38% identity, 89% coverage

CIMG_08907 cytochrome b2 from Coccidioides immitis RS
34% identity, 71% coverage

C0J08_14140 alpha-hydroxy acid oxidase from Marinomonas sp. CT5
37% identity, 84% coverage

SPD_0621 lactate oxidase from Streptococcus pneumoniae D39
spr0627 Lactate oxidase from Streptococcus pneumoniae R6
SPND141_00711 L-lactate oxidase from Streptococcus pneumoniae
35% identity, 97% coverage

Snov_0680 alpha-hydroxy acid oxidase from Ancylobacter novellus DSM 506
35% identity, 91% coverage

E6SCX5 (S)-2-hydroxy-acid oxidase from Intrasporangium calvum (strain ATCC 23552 / DSM 43043 / JCM 3097 / NBRC 12989 / NCIMB 10167 / NRRL B-3866 / 7 KIP)
38% identity, 86% coverage

LOX_STRIN / O33655 L-lactate oxidase; LOX; EC 1.1.3.- from Streptococcus iniae (Streptococcus shiloi) (see paper)
O33655 L-lactate oxidase (EC 1.1.3.2) from Streptococcus iniae (see paper)
35% identity, 89% coverage

2j6xH / Q44467 The crystal structure of lactate oxidase (see paper)
34% identity, 92% coverage

VDAG_08961 cytochrome b2 from Verticillium dahliae VdLs.17
34% identity, 69% coverage

CNAG_05169 L-lactate dehydrogenase (cytochrome) from Cryptococcus neoformans var. grubii H99
38% identity, 65% coverage

W6W585 (S)-2-hydroxy-acid oxidase from Rhizobium sp. (strain CF080)
36% identity, 82% coverage

CNL04570 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
38% identity, 65% coverage

A9QH69 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15); L-lactate oxidase (EC 1.1.3.2) from Streptococcus iniae (see paper)
34% identity, 92% coverage

BPSS1800 putative dehydrogenase from Burkholderia pseudomallei K96243
36% identity, 86% coverage

RL0444 putative lactate dehydrogenase from Rhizobium leguminosarum bv. viciae 3841
37% identity, 90% coverage

6m73A / I6SYK8 Crystal structure of enterococcus hirae l-lactate oxidase in complex with d-lactate form ligand
35% identity, 90% coverage

Q9CG58 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Lactococcus lactis (see 2 papers)
38% identity, 83% coverage

R7SNP0 Glyoxylate dehydrogenase from Dichomitus squalens (strain LYAD-421)
35% identity, 69% coverage

LLKF_1317 L-lactate oxidase from Lactococcus lactis subsp. lactis KF147
38% identity, 83% coverage

Q87G18 L-lactate dehydrogenase from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
VPA1499 L-lactate dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
35% identity, 90% coverage

WU75_03655 FMN-dependent L-lactate dehydrogenase LldD from Vibrio parahaemolyticus
35% identity, 90% coverage

HD0084 L-lactate dehydrogenase from Haemophilus ducreyi 35000HP
35% identity, 90% coverage

LOX_LACRM / C2K1F0 L-lactate oxidase; LOX; EC 1.1.3.- from Lacticaseibacillus rhamnosus (strain LMS2-1) (see paper)
39% identity, 86% coverage

An04g01450 uncharacterized protein from Aspergillus niger
35% identity, 81% coverage

AFUA_4G03120 mitochondrial cytochrome b2, putative from Aspergillus fumigatus Af293
34% identity, 70% coverage

CND03480 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
34% identity, 64% coverage

A4TKI4 L-lactate dehydrogenase from Yersinia pestis (strain Pestoides F)
36% identity, 90% coverage

SPy0414, SPy_0414 putative lactate oxidase from Streptococcus pyogenes M1 GAS
35% identity, 85% coverage

M5005_RS01875 L-lactate oxidase from Streptococcus pyogenes MGAS5005
M5005_Spy_0340 L-lactate oxidase from Streptococcus pyogenes MGAS5005
35% identity, 85% coverage

C645_RS09865 FMN-dependent L-lactate dehydrogenase LldD from Haemophilus influenzae 2019
34% identity, 90% coverage

Swit_1643 FMN-dependent alpha-hydroxy acid dehydrogenase from Sphingomonas wittichii RW1
39% identity, 89% coverage

YKN3_SCHPO / Q9HDX2 FMN-dependent alpha-hydroxy acid dehydrogenase PB1A11.03; EC 1.13.12.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
SPAPB1A11.03 FMN dependent dehydrogenase from Schizosaccharomyces pombe
36% identity, 77% coverage

FOXG_11687 L-lactate dehydrogenase (cytochrome) from Fusarium oxysporum f. sp. lycopersici 4287
37% identity, 71% coverage

P09437 L-lactate dehydrogenase (cytochrome) from Wickerhamomyces anomalus
33% identity, 61% coverage

ML2046 L-lactate dehydrogenase from Mycobacterium leprae TN
35% identity, 83% coverage

Q9HV37 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pseudomonas aeruginosa (see paper)
PA4771 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
NP_253459 L-lactate dehydrogenase from Pseudomonas aeruginosa PAO1
36% identity, 90% coverage

6dvhA / P21795 Lactate monooxygenase from mycobacterium smegmatis - c203a mutant (see paper)
36% identity, 89% coverage

CE2762 putative L-lactate dehydrogenase from Corynebacterium efficiens YS-314
36% identity, 84% coverage

HI1739.1 L-lactate dehydrogenase (lctD) from Haemophilus influenzae Rd KW20
P46454 L-lactate dehydrogenase from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
34% identity, 90% coverage

LMO_MYCSM / P21795 L-lactate 2-monooxygenase; LMO; Lactate monooxygenase; EC 1.13.12.4 from Mycolicibacterium smegmatis (Mycobacterium smegmatis) (see 2 papers)
MSMEG_3962 lactate 2-monooxygenase from Mycobacterium smegmatis str. MC2 155
36% identity, 89% coverage

PA14_63090 L-lactate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
36% identity, 90% coverage

AO090023000871 No description from Aspergillus oryzae RIB40
35% identity, 89% coverage

NTHI2049 L-lactate dehydrogenase from Haemophilus influenzae 86-028NP
34% identity, 90% coverage

WP_005545672 FMN-dependent L-lactate dehydrogenase LldD from Aggregatibacter actinomycetemcomitans
33% identity, 90% coverage

An11g03500 uncharacterized protein from Aspergillus niger
35% identity, 90% coverage

A9QH71 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Streptococcus iniae (see paper)
33% identity, 88% coverage

WP_011728393 lactate 2-monooxygenase from Mycolicibacterium smegmatis MC2 155
38% identity, 88% coverage

HELO_1220 FMN-dependent L-lactate dehydrogenase LldD from Halomonas elongata DSM 2581
34% identity, 89% coverage

NCgl2817 quinone-dependent L-lactate dehydrogenase from Corynebacterium glutamicum ATCC 13032
cg3227 putative L-lactate dehydrogenase from Corynebacterium glutamicum ATCC 13032
35% identity, 82% coverage

LOX_ROSS0 / B7RR92 L-lactate oxidase; LOX; (S)-2-hydroxy-acid oxidase; EC 1.1.3.-; EC 1.1.3.15 from Roseobacter sp. (strain GAI101) (see paper)
40% identity, 92% coverage

VCA0984 L-lactate dehydrogenase from Vibrio cholerae O1 biovar eltor str. N16961
35% identity, 90% coverage

CNAG_01229 L-mandelate dehydrogenase from Cryptococcus neoformans var. grubii H99
33% identity, 64% coverage

LGG_02356 L-lactate dehydrogenase (FMN-dependent) related alpha-hydroxy acid dehydrogenase from Lactobacillus rhamnosus GG
LGG_02356 lactate oxidase from Lacticaseibacillus rhamnosus GG
36% identity, 91% coverage

Q6DAY3 L-lactate dehydrogenase from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
35% identity, 89% coverage

APL_1849 L-lactate dehydrogenase (cytochrome) from Actinobacillus pleuropneumoniae L20
APPSER1_RS10140 FMN-dependent L-lactate dehydrogenase LldD from Actinobacillus pleuropneumoniae serovar 1 str. 4074
33% identity, 90% coverage

PMPD1_1350 FMN-dependent L-lactate dehydrogenase LldD from Paramixta manurensis
35% identity, 91% coverage

Rv1872c POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD2 from Mycobacterium tuberculosis H37Rv
35% identity, 83% coverage

SMLT_RS13830 FMN-dependent L-lactate dehydrogenase LldD from Stenotrophomonas maltophilia K279a
36% identity, 90% coverage

Mb1903c POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD2 from Mycobacterium bovis AF2122/97
BCG_1908c putative L-lactate dehydrogenase (cytochrome) lldD2 from Mycobacterium bovis BCG str. Pasteur 1173P2
35% identity, 83% coverage

B8MMC0 Oxidoreductase, putative from Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006)
34% identity, 68% coverage

MAP1585c LldD2 from Mycobacterium avium subsp. paratuberculosis str. k10
34% identity, 87% coverage

H16_B1817 alpha-hydroxy acid oxidase from Cupriavidus necator H16
37% identity, 83% coverage

PP4736, PP_4736 L-lactate dehydrogenase from Pseudomonas putida KT2440
36% identity, 90% coverage

CYB2 / P00175 L-lactate dehydrogenase subunit (EC 1.1.2.3) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 2 papers)
CYB2_YEAST / P00175 L-lactate dehydrogenase (cytochrome); Cytochrome b2; Flavocytochrome b2; FCB2; L-lactate ferricytochrome c oxidoreductase; L-LCR; EC 1.1.2.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 8 papers)
P00175 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Saccharomyces cerevisiae (see 9 papers)
NP_013658 L-lactate dehydrogenase (cytochrome) from Saccharomyces cerevisiae S288C
YML054C Cyb2p from Saccharomyces cerevisiae
33% identity, 59% coverage

Z5032 L-lactate dehydrogenase from Escherichia coli O157:H7 EDL933
35% identity, 86% coverage

Lct / b3605 L-lactate dehydrogenase from Escherichia coli K-12 substr. MG1655 (see 7 papers)
lldD / P33232 L-lactate dehydrogenase from Escherichia coli (strain K12) (see 6 papers)
LLDD_ECOLI / P33232 L-lactate dehydrogenase; EC 1.1.-.- from Escherichia coli (strain K12) (see 2 papers)
lldD L-lactate dehydrogenase [cytochrome]; EC 1.1.2.3 from Escherichia coli K12 (see paper)
lctD / AAA03585.1 L-lactate dehydrogenase from Escherichia coli (see paper)
NP_418062 L-lactate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
b3605 L-lactate dehydrogenase, FMN-linked from Escherichia coli str. K-12 substr. MG1655
35% identity, 86% coverage

1kbiA / P00175 Crystallographic study of the recombinant flavin-binding domain of baker's yeast flavocytochrome b2: comparison with the intact wild- type enzyme (see paper)
33% identity, 69% coverage

PFLU4305 L-lactate dehydrogenase from Pseudomonas fluorescens SBW25
35% identity, 89% coverage

ABUW_3812 FMN-dependent L-lactate dehydrogenase LldD from Acinetobacter baumannii
34% identity, 90% coverage

ABTJ_03740 FMN-dependent L-lactate dehydrogenase LldD from Acinetobacter baumannii MDR-TJ
34% identity, 90% coverage

ACIAD0108 L-lactate dehydrogenase, FMN linked from Acinetobacter sp. ADP1
32% identity, 91% coverage

PS417_19130 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) from Pseudomonas simiae WCS417
35% identity, 91% coverage

DW68_005145 FMN-dependent L-lactate dehydrogenase LldD from Pseudomonas mendocina S5.2
36% identity, 90% coverage

AN479_RS14060 FMN-dependent L-lactate dehydrogenase LldD from Serratia marcescens
34% identity, 90% coverage

CNH01230 cytochrome b2, mitochondrial precursor from Cryptococcus neoformans var. neoformans JEC21
34% identity, 59% coverage

H16_B1817 L-Lactate cytochrome c reductase from Ralstonia eutropha H16
37% identity, 91% coverage

LKW31_15200 FMN-dependent L-lactate dehydrogenase LldD from Pantoea agglomerans
34% identity, 91% coverage

BP1669 lactate dehydrogenase from Bordetella pertussis Tohama I
33% identity, 88% coverage

KP13_00216 FMN-dependent L-lactate dehydrogenase LldD from Klebsiella pneumoniae subsp. pneumoniae Kp13
A6TFK0 L-lactate dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
KPN_03949 L-lactate dehydrogenase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
34% identity, 88% coverage

6dviD / P21795 Wild-type lactate monooxygenase from mycobacterium smegmatis (see paper)
35% identity, 93% coverage

2nliB / Q44467 Crystal structure of the complex between l-lactate oxidase and a substrate analogue at 1.59 angstrom resolution (see paper)
32% identity, 92% coverage

1ldcB / P00175 X-ray structure of two complexes of the y143f flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl-lactate (see paper)
32% identity, 91% coverage

STY4102 putative L-lactate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
Q8Z2E5 L-lactate dehydrogenase from Salmonella typhi
35% identity, 86% coverage

SPO0598 alpha-hydroxy acid oxidase from Ruegeria pomeroyi DSS-3
SPO0598, YP_165858 FMN-dependent alpha-hydroxy acid dehydrogenase family protein from Silicibacter pomeroyi DSS-3
35% identity, 88% coverage

SPC_3776 putative L-lactate dehydrogenase from Salmonella enterica subsp. enterica serovar Paratyphi C strain RKS4594
35% identity, 86% coverage

slcD / A3SN06 sulfolactate dehydrogenase from Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM) (see paper)
34% identity, 92% coverage

MAP3486 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
34% identity, 91% coverage

CNAG_05318 L-mandelate dehydrogenase from Cryptococcus neoformans var. grubii H99
33% identity, 65% coverage

MAP2959c hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
36% identity, 90% coverage

B7QEL2 Glycolate oxidase, putative (Fragment) from Ixodes scapularis
42% identity, 71% coverage

NCU11278 hypothetical protein from Neurospora crassa OR74A
34% identity, 79% coverage

CCNA_01462 lactate 2-monooxygenase from Caulobacter crescentus NA1000
CC_1396 L-lactate 2-monooxygenase from Caulobacter crescentus CB15
36% identity, 81% coverage

BMAA1565 dehydrogenase, FMN-dependent family from Burkholderia mallei ATCC 23344
35% identity, 86% coverage

Afu4g07050 L-lactate dehydrogenase from Aspergillus fumigatus Af293
33% identity, 81% coverage

AO090023000884 No description from Aspergillus oryzae RIB40
32% identity, 74% coverage

CNAG_03663 L-lactate dehydrogenase from Cryptococcus neoformans var. grubii H99
31% identity, 58% coverage

CNB01620 L-lactate dehydrogenase (cytochrome) from Cryptococcus neoformans var. neoformans JEC21
31% identity, 58% coverage

R1E6X7 Putative fmn-dependent dehydrogenase protein from Botryosphaeria parva (strain UCR-NP2)
35% identity, 85% coverage

B7FUG8 (S)-2-hydroxy-acid oxidase (EC 1.1.3.15) from Phaeodactylum tricornutum (see paper)
31% identity, 77% coverage

SPO1172 alpha-hydroxy acid oxidase from Ruegeria pomeroyi DSS-3
35% identity, 89% coverage

CYB2_TALSN / B8MKR3 L-lactate dehydrogenase (cytochrome); EC 1.1.2.3 from Talaromyces stipitatus (strain ATCC 10500 / CBS 375.48 / QM 6759 / NRRL 1006) (Penicillium stipitatum) (see paper)
33% identity, 70% coverage

SPO1172, YP_166419 FMN-dependent alpha-hydroxy acid dehydrogenase family protein from Silicibacter pomeroyi DSS-3
35% identity, 90% coverage

FGSG_01531 hypothetical protein from Fusarium graminearum PH-1
33% identity, 86% coverage

Afu8g06000 FMN dependent dehydrogenase, putative from Aspergillus fumigatus Af293
35% identity, 88% coverage

A0A1P8B993 Aldolase-type TIM barrel family protein from Arabidopsis thaliana
37% identity, 61% coverage

Afu4g07020 mitochondrial cytochrome b2-like, putative from Aspergillus fumigatus Af293
32% identity, 66% coverage

CYBL_RHOGR / P32953 (S)-mandelate dehydrogenase, mitochondrial; Flavocytochrome b; L(+)-mandelate dehydrogenase; L-MDH; EC 1.1.99.31 from Rhodotorula graminis (Yeast) (see 2 papers)
CAA04758.1 L-mandelate dehydrogenase from Rhodotorula graminis (see paper)
32% identity, 61% coverage

mftD / A0PM50 pre-mycofactocin synthase (EC 1.4.3.26) from Mycobacterium ulcerans (strain Agy99) (see paper)
MFTD_MYCUA / A0PM50 Pre-mycofactocin synthase; PMFT synthase; EC 1.4.3.26 from Mycobacterium ulcerans (strain Agy99) (see paper)
A0PM50 pre-mycofactocin synthase (EC 1.4.3.26) from Mycobacterium ulcerans (see paper)
MUL_0774 L-lactate dehydrogenase (cytochrome) LldD1 from Mycobacterium ulcerans Agy99
33% identity, 87% coverage

VDAG_07114 cytochrome b2 from Verticillium dahliae VdLs.17
33% identity, 85% coverage

RF|XP_001522874.1 putative cytochrome b2, mitochondrial precursor [Cryptococcus neoformans] from Magnaporthe grisea 70-15 (see paper)
33% identity, 85% coverage

MSMEG_1424, MSMEI_1389 pre-mycofactocin synthase MftD from Mycolicibacterium smegmatis MC2 155
32% identity, 86% coverage

MFTD_MYCS2 / A0QSB9 Pre-mycofactocin synthase; PMFT synthase; EC 1.4.3.26 from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see 3 papers)
A0QSB9 pre-mycofactocin synthase (EC 1.4.3.26) from Mycolicibacterium smegmatis (see 2 papers)
MSMEG_1424 FMN-dependent dehydrogenase from Mycobacterium smegmatis str. MC2 155
32% identity, 85% coverage

MAP_RS21325 pre-mycofactocin synthase MftD from Mycobacterium avium subsp. paratuberculosis K-10
MAP4154 LldD1 from Mycobacterium avium subsp. paratuberculosis str. k10
32% identity, 86% coverage

MT0721 FMN-dependent alpha-hydroxy acid dehydrogenase family protein from Mycobacterium tuberculosis CDC1551
32% identity, 84% coverage

P9WND7 pre-mycofactocin synthase (EC 1.4.3.26) from Mycobacterium tuberculosis (see paper)
BCG_0743 putative L-lactate dehydrogenase (cytochrome) lldD1 from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv0694 POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD1 from Mycobacterium tuberculosis H37Rv
Mb0713 POSSIBLE L-LACTATE DEHYDROGENASE (CYTOCHROME) LLDD1 from Mycobacterium bovis AF2122/97
33% identity, 86% coverage

MAB_3834c Possible L-lactate dehydrogenase (cytochrome) LldD1 from Mycobacterium abscessus ATCC 19977
32% identity, 87% coverage

M4EEX7 FMN hydroxy acid dehydrogenase domain-containing protein from Brassica campestris
31% identity, 51% coverage

CD1263 putative FMN-dependent dehydrogenase from Clostridium difficile 630
31% identity, 80% coverage

LOC114303062 peroxisomal (S)-2-hydroxy-acid oxidase GLO4-like from Camellia sinensis
35% identity, 56% coverage

Dret_0157 FMN-dependent alpha-hydroxy acid dehydrogenase from Desulfohalobium retbaense DSM 5692
47% identity, 36% coverage

Dde_0750 L-lactate dehydrogenase (lldD) from Desulfovibrio desulfuricans G20
52% identity, 32% coverage

DVU2784 dehydrogenase, FMN-dependent family from Desulfovibrio vulgaris Hildenborough
49% identity, 32% coverage

CACET_c16820 alpha-hydroxy-acid oxidizing protein from Clostridium aceticum
49% identity, 36% coverage

WP_005721074 FMN-dependent dehydrogenase from Lactobacillus crispatus
26% identity, 83% coverage

AF0807 L-lactate dehydrogenase, cytochrome-type (lldD) from Archaeoglobus fulgidus DSM 4304
41% identity, 36% coverage

AF_0807 alpha-hydroxy acid oxidase from Archaeoglobus fulgidus DSM 4304
41% identity, 37% coverage

TP0291 T. pallidum predicted coding region TP0291 from Treponema pallidum subsp. pallidum str. Nichols
TPASS_0291 hypothetical protein from Treponema pallidum subsp. pallidum SS14
37% identity, 29% coverage

mgsC / D7R621 N-methyl-L-glutamate synthase γ subunit (EC 2.1.1.21) from Methyloversatilis universalis (see 2 papers)
33% identity, 25% coverage

New Search

For advice on how to use these tools together, see Interactive tools for functional annotation of bacterial genomes.

Statistics

The PaperBLAST database links 784,739 different protein sequences to 1,253,012 scientific articles. Searches against EuropePMC were last performed on November 25 2024.

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:

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:

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.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory