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PaperBLAST

PaperBLAST Hits for reanno::Btheta:353284 N-succinylornithine aminotransferase (EC 2.6.1.81) (Bacteroides thetaiotaomicron VPI-5482) (373 a.a., MKLFDVYPLY...)

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Found 250 similar proteins in the literature:

BT3758 N-succinylornithine aminotransferase (EC 2.6.1.81) from Bacteroides thetaiotaomicron VPI-5482
BT3758 acetylornithine aminotransferase from Bacteroides thetaiotaomicron VPI-5482
100% identity, 100% coverage

Echvi_3848 N-succinylornithine aminotransferase (EC 2.6.1.81) from Echinicola vietnamensis KMM 6221, DSM 17526
55% identity, 98% coverage

BSU11220 acetylornithine aminotransferase from Bacillus subtilis subsp. subtilis str. 168
P36839 Acetylornithine aminotransferase from Bacillus subtilis (strain 168)
40% identity, 96% coverage

UAI_00297 acetylornithine transaminase from Enterococcus malodoratus ATCC 43197
42% identity, 95% coverage

TTHA1755 acetylornithine/acetyl-lysine aminotransferase from Thermus thermophilus HB8
38% identity, 93% coverage

lysJ / Q93R93 L-2-aminoadipate semialdehyde transaminase monomer (EC 2.6.1.118) from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see 2 papers)
LYSJ_THET2 / Q93R93 [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.118 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27) (see 2 papers)
Q93R93 [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) from Thermus thermophilus (see 2 papers)
TTC1393 No description from Thermus thermophilus HB27
38% identity, 93% coverage

1vefA / Q5SHH5 Acetylornithine aminotransferase from thermus thermophilus hb8
38% identity, 95% coverage

ATE50_RS13990 acetylornithine transaminase from Bacillus velezensis
40% identity, 93% coverage

BPP2543 acetylornithine aminotransferase from Bordetella parapertussis 12822
39% identity, 93% coverage

Pchl3084_2275 aspartate aminotransferase family protein from Pseudomonas chlororaphis subsp. aureofaciens 30-84
38% identity, 91% coverage

GL331_10540 acetylornithine transaminase from Bacillus velezensis
40% identity, 93% coverage

TSC_c03550 [LysW]-aminoadipate semialdehyde transaminase LysJ from Thermus scotoductus SA-01
38% identity, 93% coverage

STH2881 N-acetylornithine aminotransferase from Symbiobacterium thermophilum IAM 14863
38% identity, 90% coverage

CYA_1537 acetylornithine transaminase from Synechococcus sp. JA-3-3Ab
39% identity, 89% coverage

lpg2968 N-acetylornithine aminotransferase ArgD from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
38% identity, 96% coverage

Teth39_0226 acetylornithine and succinylornithine aminotransferase from Thermoanaerobacter ethanolicus ATCC 33223
40% identity, 92% coverage

CYB_1419 acetylornithine transaminase from Synechococcus sp. JA-2-3B'a(2-13)
38% identity, 85% coverage

DET1258 acetylornithine aminotransferase from Dehalococcoides ethenogenes 195
39% identity, 91% coverage

Dgeo_1416 acetylornithine and succinylornithine aminotransferases from Deinococcus geothermalis DSM 11300
36% identity, 89% coverage

DR0794, DR_0794 acetylornithine aminotransferase from Deinococcus radiodurans R1
36% identity, 79% coverage

Deima_2454 aspartate aminotransferase family protein from Deinococcus maricopensis DSM 21211
37% identity, 89% coverage

ACIAD1231 acetylornithine aminotransferase from Acinetobacter sp. ADP1
38% identity, 91% coverage

Atu0428 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein from Agrobacterium tumefaciens str. C58 (Cereon)
Q8UI71 Acetylornithine aminotransferase from Agrobacterium fabrum (strain C58 / ATCC 33970)
39% identity, 92% coverage

KO21_RS08195 acetylornithine transaminase from Listeria monocytogenes
38% identity, 96% coverage

2ordA / Q9X2A5 Crystal structure of acetylornithine aminotransferase (ec 2.6.1.11) (acoat) (tm1785) from thermotoga maritima at 1.40 a resolution
36% identity, 95% coverage

TM1785 acetylornithine aminotransferase from Thermotoga maritima MSB8
36% identity, 97% coverage

Q71Z79 Acetylornithine aminotransferase from Listeria monocytogenes serotype 4b (strain F2365)
38% identity, 96% coverage

D4I307 Acetylornithine/succinyldiaminopimelate aminotransferase from Erwinia amylovora (strain CFBP1430)
EAMY_3415 bifunctional acetylornithine delta-aminotransferase / N-succinyldiaminopimelate aminotransferase from Erwinia amylovora CFBP1430
36% identity, 91% coverage

B1XNF8 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) from Synechococcus sp. PCC 7002 (see paper)
SYNPCC7002_A0326 acetylornithine aminotransferase from Synechococcus sp. PCC 7002
35% identity, 88% coverage

Deide_16910 putative bifunctional protein: acetylornithine transaminase/acetyl-lysine aminotransferase from Deinococcus deserti VCD115
35% identity, 89% coverage

PMI_RS13935 aspartate aminotransferase family protein from Proteus mirabilis HI4320
PMI2821 acetylornithine/succinyldiaminopimelate aminotransferase from Proteus mirabilis HI4320
37% identity, 92% coverage

GSU0151 acetylornithine aminotransferase from Geobacter sulfurreducens PCA
36% identity, 93% coverage

VC2618 acetylornithine aminotransferase from Vibrio cholerae O1 biovar eltor str. N16961
36% identity, 89% coverage

SPISAL_06590 acetylornithine transaminase from Spiribacter salinus M19-40
38% identity, 93% coverage

2eh6A / O66442 Crystal structure of acetylornithine aminotransferase from aquifex aeolicus vf5
36% identity, 99% coverage

Cthe_1866 acetylornithine aminotransferase from Clostridium thermocellum ATCC 27405
38% identity, 89% coverage

PBPRA0289 putative acetylornithine aminotransferase from Photobacterium profundum SS9
36% identity, 92% coverage

lmo1588 highly similar to N-acetylornithine aminotransferase from Listeria monocytogenes EGD-e
38% identity, 96% coverage

8ht4B / Q59282 Crystal structure of acetylornithine aminotransferase complex with plp from corynebacterium glutamicum (see paper)
37% identity, 92% coverage

cg1583 acetylornithine aminotransferase from Corynebacterium glutamicum ATCC 13032
NCgl1343 acetylornithine transaminase from Corynebacterium glutamicum ATCC 13032
37% identity, 92% coverage

BL1061 acetylornithine aminotransferase from Bifidobacterium longum NCC2705
36% identity, 83% coverage

UTI89_C3862 acetylornithine aminotransferase from Escherichia coli UTI89
35% identity, 91% coverage

HMPREF0010_00392 aspartate aminotransferase family protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
37% identity, 91% coverage

Sant_0398 aspartate aminotransferase family protein from Sodalis praecaptivus
36% identity, 91% coverage

tlr1328 N-acetylornithine aminotransferase from Thermosynechococcus elongatus BP-1
37% identity, 90% coverage

ECs4210 acetylornithine delta-aminotransferase from Escherichia coli O157:H7 str. Sakai
Z4720 acetylornithine delta-aminotransferase from Escherichia coli O157:H7 EDL933
35% identity, 91% coverage

HP15_3042 acetylornithine aminotransferase (EC 2.6.1.11); succinylornithine aminotransferase (EC 2.6.1.81) from Marinobacter adhaerens HP15
36% identity, 91% coverage

Tter_0321 acetylornithine and succinylornithine aminotransferase from Thermobaculum terrenum ATCC BAA-798
36% identity, 95% coverage

Dtu / b3359 N-acetylornithine aminotransferase / N-succinyldiaminopimelate aminotransferase (EC 2.6.1.11; EC 2.6.1.17) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
argD / P18335 N-acetylornithine aminotransferase / N-succinyldiaminopimelate aminotransferase (EC 2.6.1.11; EC 2.6.1.17) from Escherichia coli (strain K12) (see 12 papers)
ARGD_ECOLI / P18335 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 from Escherichia coli (strain K12) (see paper)
b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase from Escherichia coli str. K-12 substr. MG1655
NP_417818 N-acetylornithine aminotransferase/N-succinyldiaminopimelate aminotransferase from Escherichia coli str. K-12 substr. MG1655
34% identity, 91% coverage

ACICU_01135 ornithine/acetylornithine aminotransferase from Acinetobacter baumannii ACICU
37% identity, 87% coverage

Ava_3730 Acetylornithine and succinylornithine aminotransferase from Anabaena variabilis ATCC 29413
35% identity, 87% coverage

BAU10_13850 aspartate aminotransferase family protein from Vibrio alginolyticus
36% identity, 92% coverage

alr1080 N-acetylornithine aminotransferase from Nostoc sp. PCC 7120
35% identity, 87% coverage

BAB1_0331 Acetylornithine and succinylornithine aminotransferase:Aminotransferase class-III from Brucella melitensis biovar Abortus 2308
BMEI1621 aspartate aminotransferase family protein from Brucella melitensis bv. 1 str. 16M
37% identity, 90% coverage

ECA4065 aspartate aminotransferase family protein from Pectobacterium atrosepticum SCRI1043
36% identity, 91% coverage

C6AZH0 Acetylornithine aminotransferase from Rhizobium leguminosarum bv. trifolii (strain WSM1325)
36% identity, 93% coverage

CC0584 succinylornithine transaminase, putative from Caulobacter crescentus CB15
37% identity, 94% coverage

STM14_4175 aspartate aminotransferase family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
34% identity, 92% coverage

SGO_1566 Acetylornithine aminotransferase (ACOAT) from Streptococcus gordonii str. Challis substr. CH1
36% identity, 98% coverage

SEN3295 acetylornithine aminotransferase from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
34% identity, 92% coverage

SLUN_RS38465 acetylornithine transaminase from Streptomyces lunaelactis
37% identity, 89% coverage

ACIAD1284 succinylornithine transaminase (also has acetylornitine transaminase activity, PLP-dependent) (carbon starvation protein C) from Acinetobacter sp. ADP1
36% identity, 89% coverage

VpaChn25_2721 aspartate aminotransferase family protein from Vibrio parahaemolyticus
36% identity, 92% coverage

HVO_0043 acetylornithine aminotransferase from Haloferax volcanii DS2
35% identity, 96% coverage

ARGD_SALTY / P40732 Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
STM3468 acetylornithine transaminase (NAcOATase and DapATase) from Salmonella typhimurium LT2
34% identity, 92% coverage

lysJ / Q4JAP8 [amino group carrier protein]-C-terminal-L-glutamyl-γ-L-lysine aminotransferase (EC 2.6.1.118; EC 2.6.1.124) from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (see 2 papers)
Saci_0755 acetylornithine aminotransferase from Sulfolobus acidocaldarius DSM 639
Q4JAP8 [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
36% identity, 95% coverage

DDA3937_RS19450 aspartate aminotransferase family protein from Dickeya dadantii 3937
35% identity, 91% coverage

BB341_RS23960, SCLAV_0798 acetylornithine transaminase from Streptomyces clavuligerus
35% identity, 92% coverage

4jevB / P40732 N-acetylornithine aminotransferase from s. Typhimurium complexed with gabaculine
34% identity, 92% coverage

KP1_2498 putative succinylornithine transaminase from Klebsiella pneumoniae NTUH-K2044
37% identity, 90% coverage

CA_C2388, CEA_G2403 aspartate aminotransferase family protein from Clostridium acetobutylicum ATCC 824
CAC2388 N-acetylornithine aminotransferase from Clostridium acetobutylicum ATCC 824
36% identity, 95% coverage

Synpcc7942_0943 acetylornithine and succinylornithine aminotransferases from Synechococcus elongatus PCC 7942
36% identity, 88% coverage

NGO_0646 aspartate aminotransferase family protein from Neisseria gonorrhoeae FA 1090
36% identity, 90% coverage

MSMEG_3773 acetylornithine aminotransferase from Mycobacterium smegmatis str. MC2 155
MSMEG_3773 acetylornithine transaminase from Mycolicibacterium smegmatis MC2 155
35% identity, 95% coverage

Deide_09040 putative 4-aminobutyrate aminotransferase, aminotransferase class-III from Deinococcus deserti VCD115
36% identity, 78% coverage

T303_03440 acetylornithine transaminase from Streptococcus thermophilus ASCC 1275
36% identity, 99% coverage

SCO1577 acetylornithine aminotransferase from Streptomyces coelicolor A3(2)
36% identity, 92% coverage

DRA0029, DR_A0029 4-aminobutyrate aminotransferase from Deinococcus radiodurans R1
36% identity, 76% coverage

CwatDRAFT_5161 Acetylornithine and succinylornithine aminotransferase from Crocosphaera watsonii WH 8501
34% identity, 88% coverage

SSA_0760 Acetylornithine aminotransferase, putative from Streptococcus sanguinis SK36
35% identity, 98% coverage

A7ME32 Acetylornithine/succinyldiaminopimelate aminotransferase from Cronobacter sakazakii (strain ATCC BAA-894)
34% identity, 89% coverage

ARGD_ARATH / Q9M8M7 Acetylornithine aminotransferase, chloroplastic/mitochondrial; ACOAT; Acetylornithine transaminase; AOTA; Protein HOPW1-1-INTERACTING 1; EC 2.6.1.11 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_178175 HOPW1-1-interacting 1 from Arabidopsis thaliana
AT1G80600 WIN1 (HOPW1-1-INTERACTING 1); N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase/ catalytic/ pyridoxal phosphate binding / transaminase from Arabidopsis thaliana
36% identity, 78% coverage

BCG_1694 putative Acetylornithine aminotransferase argD from Mycobacterium bovis BCG str. Pasteur 1173P2
NP_216171 acetylornithine aminotransferase from Mycobacterium tuberculosis H37Rv
Rv1655 acetylornithine aminotransferase from Mycobacterium tuberculosis H37Rv
36% identity, 93% coverage

7nn4A / P9WPZ7 Crystal structure of mycobacterium tuberculosis argd with prosthetic group pyridoxal 5'-phosphate and 3-hydroxy-2-naphthoic acid.
36% identity, 95% coverage

PF1685 acetylornithine aminotransferase from Pyrococcus furiosus DSM 3638
37% identity, 95% coverage

AWY96_RS23480 aspartate aminotransferase family protein from Serratia plymuthica
35% identity, 92% coverage

GBAA4352 acetylornithine aminotransferase from Bacillus anthracis str. 'Ames Ancestor'
36% identity, 96% coverage

Dgeo_0989 aminotransferase class-III from Deinococcus geothermalis DSM 11300
38% identity, 78% coverage

WPa_0783 aspartate aminotransferase family protein from Wolbachia endosymbiont of Culex quinquefasciatus Pel
37% identity, 93% coverage

PAB2440 acetylornithine aminotransferase from Pyrococcus abyssi GE5
38% identity, 95% coverage

PH1716 acetylornithine aminotransferase from Pyrococcus horikoshii OT3
38% identity, 94% coverage

Q5JFW3 Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
TK0275 N2-acetyl-lysine aminotransferase from Thermococcus kodakaraensis KOD1
37% identity, 95% coverage

ARG8 / P18544 acetylornithine transaminase (EC 2.6.1.11) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 9 papers)
ARGD_YEAST / P18544 Acetylornithine aminotransferase, mitochondrial; ACOAT; EC 2.6.1.11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 3 papers)
YOL140W Acetylornithine aminotransferase, catalyzes the fourth step in the biosynthesis of the arginine precursor ornithine from Saccharomyces cerevisiae
36% identity, 86% coverage

aruC / O30508 succinylornithine transaminase subunit (EC 2.6.1.13; EC 2.6.1.11; EC 2.6.1.81) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
ARUC_PSEAE / O30508 Succinylornithine transaminase/acetylornithine aminotransferase; ACOAT; SOAT; Succinylornithine aminotransferase; EC 2.6.1.11; EC 2.6.1.81 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
O30508 succinylornithine transaminase (EC 2.6.1.81) from Pseudomonas aeruginosa (see paper)
PA0895 N-succinylglutamate 5-semialdehyde dehydrogenase from Pseudomonas aeruginosa PAO1
35% identity, 88% coverage

PA14_52720 N-succinylglutamate 5-semialdehyde dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
35% identity, 88% coverage

OKIT_0630 acetylornithine transaminase from Oenococcus kitaharae DSM 17330
37% identity, 92% coverage

bglu_1g10100 Succinylornithine transaminase from Burkholderia glumae BGR1
35% identity, 88% coverage

Q688Q8 acetylornithine transaminase from Oryza sativa subsp. japonica
36% identity, 77% coverage

ECH_0886 acetylornithine/succinyldiaminopimelate aminotransferase from Ehrlichia chaffeensis str. Arkansas
ECH_RS03645 aspartate aminotransferase family protein from Ehrlichia chaffeensis str. Arkansas
37% identity, 95% coverage

W6QU95 Acetylornithine aminotransferase from Pseudomonas pseudoalcaligenes (strain CECT 5344)
34% identity, 90% coverage

BPSL2390 succinylornithine transaminase from Burkholderia pseudomallei K96243
36% identity, 87% coverage

B8CGH5 acetylornithine transaminase from Thalassiosira pseudonana
THAPSDRAFT_270136 n-acetylornithine aminotransferase from Thalassiosira pseudonana CCMP1335
35% identity, 77% coverage

PGA1_c24230 aspartate aminotransferase family protein from Phaeobacter inhibens DSM 17395
37% identity, 93% coverage

glr3849 4-aminobutyrate aminotransferase from Gloeobacter violaceus PCC 7421
35% identity, 80% coverage

AZOBR_RS19025 aspartate aminotransferase family protein from Azospirillum baldaniorum
36% identity, 93% coverage

AZOBR_RS19025 acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] from Azospirillum brasilense Sp245
36% identity, 93% coverage

MAP_RS06930 acetylornithine transaminase from Mycobacterium avium subsp. paratuberculosis K-10
35% identity, 90% coverage

BWI76_RS11670 Succinylornithine transaminase (EC 2.6.1.81) from Klebsiella michiganensis M5al
34% identity, 88% coverage

Sant_1573 putrescine aminotransferase from Sodalis praecaptivus
35% identity, 77% coverage

PMT9312_1397 acetylornithine and succinylornithine aminotransferases from Prochlorococcus marinus str. MIT 9312
35% identity, 89% coverage

NJ7G_0260 aspartate aminotransferase family protein from Natrinema sp. J7-2
33% identity, 92% coverage

XF1427 succinylornithine aminotransferase from Xylella fastidiosa 9a5c
Q9PDF2 Acetylornithine aminotransferase from Xylella fastidiosa (strain 9a5c)
XF_RS06015 acetylornithine transaminase from Xylella fastidiosa 9a5c
35% identity, 90% coverage

WP_034270149 aspartate aminotransferase family protein from Actinospica robiniae DSM 44927
33% identity, 79% coverage

BBIF_1100 acetylornithine transaminase from Bifidobacterium bifidum S17
36% identity, 83% coverage

PS417_21710 Succinylornithine transaminase (EC 2.6.1.81) from Pseudomonas simiae WCS417
35% identity, 88% coverage

Ava_0214 Aminotransferase class-III from Anabaena variabilis ATCC 29413
33% identity, 84% coverage

BCAL1059 succinylornithine transaminase from Burkholderia cenocepacia J2315
35% identity, 90% coverage

HMPREF0389_01570 aspartate aminotransferase family protein from Filifactor alocis ATCC 35896
34% identity, 92% coverage

dat / B0VCM6 diaminobutyrate—2-oxoglutarate transaminase monomer (EC 2.6.1.76) from Acinetobacter baumannii (strain AYE) (see 2 papers)
AB57_2881 diaminobutyrate--2-oxoglutarate aminotransferase from Acinetobacter baumannii AB0057
35% identity, 79% coverage

PP_4481 aspartate aminotransferase family protein from Pseudomonas putida KT2440
PP4481 acetylornithine aminotransferase from Pseudomonas putida KT2440
34% identity, 88% coverage

H16_B0981 4-aminobutyrate--2-oxoglutarate transaminase from Cupriavidus necator H16
34% identity, 87% coverage

gabT / Q0K2K2 4-aminobutyrate aminotransferase monomer (EC 2.6.1.19) from Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) (see paper)
Q0K2K2 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) from Cupriavidus necator (see paper)
H16_B0981 4-Aminobutyrate aminotransferase from Ralstonia eutropha H16
34% identity, 86% coverage

alr2398 4-aminobutyrate aminotransferase from Nostoc sp. PCC 7120
34% identity, 82% coverage

AFUA_2G12470, Afu2g12470 acetylornithine aminotransferase from Aspergillus fumigatus Af293
36% identity, 71% coverage

Pro1375 Ornithine/acetylornithine aminotransferase from Prochlorococcus marinus str. SS120
34% identity, 93% coverage

YP_001847319 4-aminobutyrate aminotransferase from Acinetobacter baumannii ACICU
35% identity, 79% coverage

A1S_2454 diaminobutyrate--2-oxoglutarate aminotransferase from Acinetobacter baumannii ATCC 17978
35% identity, 83% coverage

ACIAD1210 diaminobutyrate--2-oxoglutarate aminotransferase (L-diaminobutyric acid transaminase) (Diaminobutyrate transaminase) (DABA aminotransferase) (DABA-AT) (L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase) from Acinetobacter sp. ADP1
35% identity, 79% coverage

SAR11_0502 Acetylornithine aminotransferase from Candidatus Pelagibacter ubique HTCC1062
36% identity, 91% coverage

YPTB1959 succinylornithine aminotransferase from Yersinia pseudotuberculosis IP 32953
34% identity, 89% coverage

PD0654 succinylornithine aminotransferase from Xylella fastidiosa Temecula1
35% identity, 90% coverage

An15g02360 uncharacterized protein from Aspergillus niger
35% identity, 76% coverage

A0A140N9B6 succinylornithine transaminase (EC 2.6.1.81) from Escherichia coli (see paper)
35% identity, 87% coverage

ECs2454 acetylornithine delta-aminotransferase from Escherichia coli O157:H7 str. Sakai
Z2780 acetylornithine delta-aminotransferase from Escherichia coli O157:H7 EDL933
35% identity, 87% coverage

YPO1962 succinylornithine aminotransferase from Yersinia pestis CO92
34% identity, 88% coverage

AstC / b1748 succinylornithine transaminase (EC 2.6.1.81; EC 2.6.1.11) from Escherichia coli K-12 substr. MG1655 (see 8 papers)
astC / P77581 succinylornithine transaminase (EC 2.6.1.81; EC 2.6.1.11) from Escherichia coli (strain K12) (see 6 papers)
ASTC_ECOLI / P77581 Succinylornithine transaminase; SOAT; Carbon starvation protein C; Succinylornithine aminotransferase; EC 2.6.1.81 from Escherichia coli (strain K12) (see paper)
astC / RF|NP_416262.1 succinylornithine transaminase; EC 2.6.1.81 from Escherichia coli K12 (see 5 papers)
A7ZML6 Succinylornithine transaminase from Escherichia coli O139:H28 (strain E24377A / ETEC)
b1748 succinylornithine transaminase, PLP-dependent from Escherichia coli str. K-12 substr. MG1655
35% identity, 87% coverage

SAUSA300_0187 ornithine--oxo-acid transaminase from Staphylococcus aureus subsp. aureus USA300_FPR3757
33% identity, 93% coverage

A8A0U0 Succinylornithine transaminase from Escherichia coli O9:H4 (strain HS)
34% identity, 87% coverage

4adbB / P77581 Structural and functional study of succinyl-ornithine transaminase from e. Coli (see paper)
35% identity, 89% coverage

YPTS_2011 succinylornithine transaminase family protein from Yersinia pseudotuberculosis PB1/+
YPK_2229 succinylornithine transaminase family protein from Yersinia pseudotuberculosis YPIII
34% identity, 82% coverage

SA0179 ornithine aminotransferase from Staphylococcus aureus subsp. aureus N315
33% identity, 93% coverage

PSHAa0194 acetylornithine transaminase (NAcOATase and DapATase), PLP-dependent from Pseudoalteromonas haloplanktis TAC125
34% identity, 90% coverage

slr1022 / P73133 bifunctional acetylornithine transaminase/4-aminobutyrate—2-oxoglutarate transaminase (EC 2.6.1.19; EC 2.6.1.11) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see 4 papers)
ARGD_SYNY3 / P73133 Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (see 2 papers)
P73133 acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) from Synechococcus sp. PCC 6803 (see paper)
slr1022 N-acetylornithine aminotransferase from Synechocystis sp. PCC 6803
34% identity, 84% coverage

NWMN_0129 ornithine aminotransferase from Staphylococcus aureus subsp. aureus str. Newman
33% identity, 93% coverage

KPHS_46340 putrescine aminotransferase from Klebsiella pneumoniae subsp. pneumoniae HS11286
36% identity, 74% coverage

PMT0331 Acetylornithine and succinylornithine aminotransferases from Prochlorococcus marinus str. MIT 9313
34% identity, 88% coverage

t1182 succinylornithine transaminase from Salmonella enterica subsp. enterica serovar Typhi Ty2
36% identity, 87% coverage

ASTC_SALTY / Q8ZPV2 Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
STM14_1582 aspartate aminotransferase family protein from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM1303 succinylornithine transaminase, also has acetylornitine transaminase activity from Salmonella typhimurium LT2
36% identity, 87% coverage

A0A0E1X760 Ornithine aminotransferase from Staphylococcus aureus subsp. aureus MN8
34% identity, 90% coverage

ECs3523 4-aminobutyrate aminotransferase activity from Escherichia coli O157:H7 str. Sakai
37% identity, 80% coverage

WP_000069444 4-aminobutyrate--2-oxoglutarate transaminase from Shigella dysenteriae
37% identity, 80% coverage

SSPN_RS0106580 aspartate aminotransferase family protein from Saccharopolyspora spinosa NRRL 18395
34% identity, 82% coverage

3q8nC / A0QQ04 Crystal structure of 4-aminobutyrate transaminase from mycobacterium smegmatis (see paper)
36% identity, 82% coverage

YE2469 succinylornithine aminotransferase from Yersinia enterocolitica subsp. enterocolitica 8081
33% identity, 88% coverage

SXYL_00238 ornithine--oxo-acid transaminase from Staphylococcus xylosus
33% identity, 93% coverage

PatA / b3073 putrescine aminotransferase (EC 2.6.1.29) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
patA / P42588 putrescine aminotransferase (EC 2.6.1.82; EC 2.6.1.29) from Escherichia coli (strain K12) (see 15 papers)
PAT_ECOLI / P42588 Putrescine aminotransferase; PAT; PATase; Cadaverine transaminase; Diamine transaminase; Putrescine transaminase; Putrescine--2-oxoglutaric acid transaminase; Putrescine:2-OG aminotransferase; EC 2.6.1.82; EC 2.6.1.29 from Escherichia coli (strain K12) (see 8 papers)
P42588 putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) from Escherichia coli (see 4 papers)
b3073 putrescine:2-oxoglutaric acid aminotransferase, PLP-dependent from Escherichia coli str. K-12 substr. MG1655
NP_417544 putrescine aminotransferase from Escherichia coli str. K-12 substr. MG1655
ETEC_3343 putrescine aminotransferase from Escherichia coli ETEC H10407
34% identity, 76% coverage

DA471_RS02540 ornithine--oxo-acid transaminase from Staphylococcus aureus
34% identity, 91% coverage

Igni_0944 N2-acetyl-L-lysine aminotransferase from Ignicoccus hospitalis KIN4/I
34% identity, 96% coverage

AGT22_ARATH / Q94AL9 Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G38400 AGT3 (ALANINE:GLYOXYLATE AMINOTRANSFERASE 3); alanine-glyoxylate transaminase/ catalytic/ pyridoxal phosphate binding / transaminase from Arabidopsis thaliana
34% identity, 74% coverage

ECs3955 putrescine--2-oxoglutarate aminotransferase from Escherichia coli O157:H7 str. Sakai
34% identity, 75% coverage

KR75_05020 putrescine aminotransferase from Klebsiella variicola
35% identity, 74% coverage

argD / CAB82482.1 acetylornithine aminotransferase from Streptomyces clavuligerus (see 3 papers)
34% identity, 91% coverage

8r2pD / P38507,P42588 Yzwideal x16 a scaffold for cryo-em of small proteins of interest crystallizing in space group 19 (p 21 21 21)
34% identity, 69% coverage

GabT / b2662 4-aminobutyrate aminotransferase GabT (EC 2.6.1.19; EC 2.6.1.48; EC 2.6.1.11) from Escherichia coli K-12 substr. MG1655 (see 29 papers)
gabT / P22256 4-aminobutyrate aminotransferase GabT (EC 2.6.1.19; EC 2.6.1.48; EC 2.6.1.11) from Escherichia coli (strain K12) (see 28 papers)
GABT_ECOLI / P22256 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 from Escherichia coli (strain K12) (see 6 papers)
NP_417148 4-aminobutyrate aminotransferase GabT from Escherichia coli str. K-12 substr. MG1655
b2662 4-aminobutyrate aminotransferase from Escherichia coli str. K-12 substr. MG1655
37% identity, 80% coverage

1sf2A / P22256 Structure of e. Coli gamma-aminobutyrate aminotransferase (see paper)
37% identity, 80% coverage

Z3960 4-aminobutyrate aminotransferase activity from Escherichia coli O157:H7 EDL933
37% identity, 80% coverage

STY3396 putrescine--2-oxoglutarate aminotransferase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
34% identity, 75% coverage

B7GEJ6 acetylornithine transaminase from Phaeodactylum tricornutum (strain CCAP 1055/1)
34% identity, 78% coverage

AM326 acetylornithine aminotransferase from Anaplasma marginale str. St. Maries
35% identity, 94% coverage

ESA_01203 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
34% identity, 78% coverage

FUT48_13600 4-aminobutyrate--2-oxoglutarate transaminase from Pseudomonas sp. JG-B
33% identity, 85% coverage

Q18040 Probable ornithine aminotransferase, mitochondrial from Caenorhabditis elegans
30% identity, 85% coverage

PSHAb0428 putative acetylornithine transaminase from Pseudoalteromonas haloplanktis TAC125
33% identity, 90% coverage

SA0818 ornithine--oxo-acid transaminase from Staphylococcus aureus subsp. aureus N315
Q6GAW9 Ornithine aminotransferase 2 from Staphylococcus aureus (strain MSSA476)
SAV0957 ornithine--oxo-acid transaminase from Staphylococcus aureus subsp. aureus Mu50
SAOUHSC_00894 ornithine aminotransferase, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0860 Ornithine aminotransferase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL0960 ornithine aminotransferase from Staphylococcus aureus subsp. aureus COL
CH51_RS04860 ornithine--oxo-acid transaminase from Staphylococcus aureus
34% identity, 91% coverage

PODANS_3_9430 uncharacterized protein from Podospora anserina S mat+
35% identity, 82% coverage

Q8ZLX7 Putrescine aminotransferase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
34% identity, 76% coverage

STM3218 putrescine--2-oxoglutarate aminotransferase from Salmonella typhimurium LT2
34% identity, 75% coverage

WP_042715413 putrescine aminotransferase from Enterobacter mori
35% identity, 74% coverage

PMN2A_0867 Aminotransferase class-III pyridoxal-phosphate:Acetylornithin... from Prochlorococcus marinus str. NATL2A
35% identity, 89% coverage

NCU05410 acetylornithine aminotransferase from Neurospora crassa OR74A
38% identity, 76% coverage

davT / Q9I6M4 5-aminovalerate aminotransferase (EC 2.6.1.48) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 2 papers)
DAVT_PSEAE / Q9I6M4 5-aminovalerate aminotransferase DavT; 5-aminovalerate transaminase; Delta-aminovalerate aminotransferase; EC 2.6.1.48 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
Q9I6M4 5-aminovalerate transaminase (EC 2.6.1.48) from Pseudomonas aeruginosa (see paper)
PA0266 4-aminobutyrate aminotransferase from Pseudomonas aeruginosa PAO1
34% identity, 83% coverage

OAT_BACSU / P38021 Ornithine aminotransferase; OAT; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 from Bacillus subtilis (strain 168) (see 2 papers)
BSU40340 ornithine--oxo-acid transaminase from Bacillus subtilis subsp. subtilis str. 168
34% identity, 92% coverage

PMM1301 Acetylornithine and succinylornithine aminotransferases from Prochlorococcus marinus sp. MED4
33% identity, 88% coverage

SYNW1634 putative N-acetylornithine aminotransferase from Synechococcus sp. WH 8102
33% identity, 88% coverage

PA14_03450 4-aminobutyrate aminotransferase from Pseudomonas aeruginosa UCBPP-PA14
34% identity, 83% coverage

LOC100576186 alanine--glyoxylate aminotransferase 2, mitochondrial from Apis mellifera
33% identity, 71% coverage

VpaChn25_1376 4-aminobutyrate--2-oxoglutarate transaminase from Vibrio parahaemolyticus
32% identity, 87% coverage

HD73_0366 4-aminobutyrate--2-oxoglutarate transaminase from Bacillus thuringiensis serovar kurstaki str. HD73
35% identity, 77% coverage

SXYL_01965 ornithine--oxo-acid transaminase from Staphylococcus xylosus
33% identity, 91% coverage

STM2792 4-aminobutyrate aminotransferase from Salmonella typhimurium LT2
STM14_3368 4-aminobutyrate--2-oxoglutarate transaminase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
35% identity, 81% coverage

Syncc9605_0858 acetylornithine and succinylornithine aminotransferases from Synechococcus sp. CC9605
34% identity, 85% coverage

BC0355 4-aminobutyrate aminotransferase from Bacillus cereus ATCC 14579
35% identity, 73% coverage

t2687 4-aminobutyrate aminotransferase from Salmonella enterica subsp. enterica serovar Typhi Ty2
35% identity, 81% coverage

Smp_000660 ornithine--oxo-acid transaminase from Schistosoma mansoni
31% identity, 83% coverage

VP1771 4-aminobutyrate aminotransferase from Vibrio parahaemolyticus RIMD 2210633
32% identity, 87% coverage

dat / P56744 L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase monomer (EC 2.6.1.76) from Acinetobacter baumannii (see 2 papers)
P56744 diaminobutyrate decarboxylase (EC 4.1.1.86) from Acinetobacter baumannii (see paper)
dat / GB|BAA21844.1 diaminobutyrate--2-oxoglutarate transaminase; EC 2.6.1.76 from Acinetobacter baumannii (see paper)
34% identity, 81% coverage

WP_038545752 aspartate aminotransferase family protein from Synechococcus sp. KORDI-100
34% identity, 93% coverage

FGSG_01573 acetylornithine aminotransferase from Fusarium graminearum PH-1
36% identity, 79% coverage

SCO6769 probable aminotransferase from Streptomyces coelicolor A3(2)
33% identity, 79% coverage

YP_003564524 4-aminobutyrate transaminase from Bacillus megaterium QM B1551
32% identity, 79% coverage

Tmar_2123 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme from Thermaerobacter marianensis DSM 12885
34% identity, 37% coverage

PODANS_7_10880 uncharacterized protein from Podospora anserina S mat+
30% identity, 79% coverage

WH7805_05656 acetylornithine aminotransferase from Synechococcus sp. WH 7805
33% identity, 91% coverage

Pf1N1B4_3440 Succinylornithine transaminase (EC 2.6.1.81) from Pseudomonas fluorescens FW300-N1B4
35% identity, 88% coverage

Rru_A3466 Ornithine aminotransferase from Rhodospirillum rubrum ATCC 11170
32% identity, 88% coverage

TTC0553 No description from Thermus thermophilus HB27
34% identity, 86% coverage

J7QVE2 ornithine aminotransferase from Methylocystis sp. (strain SC2)
31% identity, 82% coverage

CAC0368 4 animobutyrate aminotransferase from Clostridium acetobutylicum ATCC 824
33% identity, 82% coverage

SERP0545 ornithine aminotransferase from Staphylococcus epidermidis RP62A
33% identity, 91% coverage

PAB0086 Pyridoxal phosphate-dependent aminotransferase from Pyrococcus abyssi GE5
32% identity, 77% coverage

XP_010494787 ornithine aminotransferase, mitochondrial from Camelina sativa
34% identity, 78% coverage

T643_RS11485 4-aminobutyrate--2-oxoglutarate transaminase from Klebsiella pneumoniae MRSN 1319
35% identity, 86% coverage

XP_006398303 ornithine aminotransferase, mitochondrial from Eutrema salsugineum
34% identity, 72% coverage

blr3010 blr3010 from Bradyrhizobium japonicum USDA 110
34% identity, 76% coverage

PAAG_06217 acetylornithine aminotransferase from Paracoccidioides lutzii Pb01
35% identity, 73% coverage

XP_006280404 ornithine aminotransferase, mitochondrial from Capsella rubella
33% identity, 78% coverage

CG8745 uncharacterized protein from Drosophila melanogaster
33% identity, 73% coverage

ThesuDRAFT_00745 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme from Thermaerobacter subterraneus DSM 13965
33% identity, 41% coverage

A8J933 acetylornithine transaminase (EC 2.6.1.11) from Chlamydomonas reinhardtii (see paper)
XP_001698091 uncharacterized protein from Chlamydomonas reinhardtii
32% identity, 78% coverage

Cj0227 acetylornithine aminotransferase from Campylobacter jejuni subsp. jejuni NCTC 11168
35% identity, 93% coverage

ArtHe_01125 aspartate aminotransferase family protein from Arthrobacter sp. Helios
33% identity, 80% coverage

MSMEG_6685 4-aminobutyrate transaminase from Mycobacterium smegmatis str. MC2 155
A0R6V5 4-aminobutyrate transaminase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_6685, MSMEI_6505 4-aminobutyrate--2-oxoglutarate transaminase from Mycolicibacterium smegmatis MC2 155
35% identity, 74% coverage

VK055_1960 aspartate aminotransferase family protein from Klebsiella pneumoniae subsp. pneumoniae
31% identity, 81% coverage

SPISAL_02400 aspartate aminotransferase family protein from Spiribacter salinus M19-40
32% identity, 84% coverage

LOC101890114 alanine--glyoxylate aminotransferase 2-like from Musca domestica
33% identity, 73% coverage

3nx3A / Q9PIR7 Crystal structure of acetylornithine aminotransferase (argd) from campylobacter jejuni
35% identity, 95% coverage

BCAL2701 aminotransferase class-III from Burkholderia cenocepacia J2315
34% identity, 92% coverage

PflSS101_0208 4-aminobutyrate--2-oxoglutarate transaminase from Pseudomonas lactis
35% identity, 81% coverage

Pf6N2E2_4013 5-aminovalerate transaminase (EC 2.6.1.48) from Pseudomonas fluorescens FW300-N2E2
34% identity, 81% coverage

ELJP6_14505 diaminobutyrate--2-oxoglutarate transaminase from Enterobacter ludwigii
32% identity, 79% coverage

TW652 4-aminobutyrate aminotransferase from Tropheryma whipplei TW08/27
34% identity, 83% coverage

TWT633 4-aminobutyrate aminotransferase from Tropheryma whipplei str. Twist
34% identity, 83% coverage

AO353_11510 5-aminovalerate transaminase (EC 2.6.1.48) from Pseudomonas fluorescens FW300-N2E3
34% identity, 81% coverage

bll2855 ornithine aminotransferase from Bradyrhizobium japonicum USDA 110
31% identity, 91% coverage

Q9SR86 beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) from Arabidopsis thaliana (see paper)
AT3G08860 alanine--glyoxylate aminotransferase, putative / beta-alanine-pyruvate aminotransferase, putative / AGT, putative from Arabidopsis thaliana
33% identity, 73% coverage

RS9917_02041 Acetylornithine and succinylornithine aminotransferase from Synechococcus sp. RS9917
32% identity, 92% coverage

Cabys_3334 ornithine--oxo-acid transaminase from Caldithrix abyssi DSM 13497
32% identity, 92% coverage

An04g04130 uncharacterized protein from Aspergillus niger
30% identity, 80% coverage

OAT_KLULA / Q6CWC1 Ornithine aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (Yeast) (Candida sphaerica) (see paper)
32% identity, 79% coverage

gabT / Q4KKA1 4-aminobutyrate transaminase subunit (EC 2.6.1.19) from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (see paper)
34% identity, 81% coverage

LOC21404820 alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial from Morus notabilis
34% identity, 73% coverage

Amir_1996 aminotransferase class-III from Actinosynnema mirum DSM 43827
31% identity, 85% coverage

EAM_2305 4-aminobutyrate aminotransferase from Erwinia amylovora ATCC 49946
37% identity, 83% coverage

arg1 / RF|NP_588255.1 acetylornithine aminotransferase; EC 2.6.1.11 from Schizosaccharomyces pombe (see paper)
O74548 Probable acetylornithine aminotransferase, mitochondrial from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
SPCC777.09c acetylornithine aminotransferase from Schizosaccharomyces pombe
33% identity, 83% coverage

APL_1974 Diaminobutyrate--2-oxoglutarate aminotransferase from Actinobacillus pleuropneumoniae L20
33% identity, 83% coverage

CJJ81176_0252 acetylornithine aminotransferase from Campylobacter jejuni subsp. jejuni 81-176
34% identity, 94% coverage

LLKF_1589 putrescine/ornithine aminotransferase from Lactococcus lactis subsp. lactis KF147
35% identity, 76% coverage

δ-OAT / Q9FNK4 ornithine-δ-aminotransferase (EC 2.6.1.13) from Arabidopsis thaliana (see 2 papers)
OAT_ARATH / Q9FNK4 Ornithine aminotransferase, mitochondrial; Ornithine delta-aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 from Arabidopsis thaliana (Mouse-ear cress) (see 4 papers)
Q9FNK4 ornithine aminotransferase (EC 2.6.1.13) from Arabidopsis thaliana (see paper)
NP_199430 ornithine-delta-aminotransferase from Arabidopsis thaliana
AT5G46180 delta-OAT; ornithine-oxo-acid transaminase from Arabidopsis thaliana
34% identity, 73% coverage

XP_017641965 ornithine aminotransferase, mitochondrial isoform X1 from Gossypium arboreum
34% identity, 73% coverage

OAT / P04181 Ornithine aminotransferase (EC 2.6.1.13) from Homo sapiens (see 3 papers)
OAT_HUMAN / P04181 Ornithine aminotransferase, mitochondrial; Ornithine delta-aminotransferase; Ornithine--oxo-acid aminotransferase; EC 2.6.1.13 from Homo sapiens (Human) (see 8 papers)
NP_000265 ornithine aminotransferase, mitochondrial isoform 1 precursor from Homo sapiens
NP_001309894 ornithine aminotransferase, mitochondrial isoform 1 precursor from Homo sapiens
31% identity, 82% 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 789,361 different protein sequences to 1,256,019 scientific articles. Searches against EuropePMC were last performed on January 10 2025.

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