PaperBLAST – Find papers about a protein or its homologs

 

PaperBLAST

PaperBLAST Hits for SwissProt::Q5XDV5 Probable ABC transporter ATP-binding protein M6_Spy0273 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) (256 a.a., MSILEINNLH...)

Other sequence analysis tools:

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Found 280 similar proteins in the literature:

Y273_STRP6 / Q5XDV5 Probable ABC transporter ATP-binding protein M6_Spy0273 from Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)
Spy49_0242 Iron-sulfur cluster assembly ATPase protein SufC from Streptococcus pyogenes NZ131
SPy0285 putative ABC transporter (ATP-binding protein) from Streptococcus pyogenes M1 GAS
100% identity, 100% coverage

spyM18_0273 putative ABC transporter (ATP-binding protein) from Streptococcus pyogenes MGAS8232
100% identity, 100% coverage

WP_000114500 Fe-S cluster assembly ATPase SufC from Streptococcus agalactiae GB00640
89% identity, 100% coverage

SPD_0762 FeS assembly ATPase SufC from Streptococcus pneumoniae D39
86% identity, 100% coverage

SSA_1956 ABC-type Fe-S cluster assembly transporter, ATPase component, putative from Streptococcus sanguinis SK36
86% identity, 100% coverage

T303_02075 Fe-S cluster assembly ATPase SufC from Streptococcus thermophilus ASCC 1275
85% identity, 100% coverage

stu0164 ABC transporter ATP binding protein from Streptococcus thermophilus LMG 18311
85% identity, 96% coverage

EF2394 ABC transporter, ATP-binding protein from Enterococcus faecalis V583
EF_2394, OG1RF_11829 Fe-S cluster assembly ATPase SufC from Enterococcus faecalis V583
81% identity, 100% coverage

LLKF_1966 SUF system FeS cluster assembly protein ATP-dependent transporter SufC from Lactococcus lactis subsp. lactis KF147
78% identity, 100% coverage

CG42_RS12665 Fe-S cluster assembly ATPase SufC from Listeria monocytogenes
lmo2415 similar to ABC transporter, ATP-binding protein from Listeria monocytogenes EGD-e
74% identity, 94% coverage

SERP0496 FeS assembly ATPase SufC from Staphylococcus epidermidis RP62A
72% identity, 97% coverage

OENOO_57011 ABC transporter, ATP-binding protein from Oenococcus oeni ATCC BAA-1163
72% identity, 98% coverage

BSU32710 sulfur mobilizing ABC protein, ATPase from Bacillus subtilis subsp. subtilis str. 168
P80866 Vegetative protein 296 from Bacillus subtilis (strain 168)
72% identity, 96% coverage

SAOUHSC_00847 ABC transporter, ATP-binding protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
Q2FZY7 ABC transporter, ATP-binding protein, putative from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SA0774 hypothetical protein from Staphylococcus aureus subsp. aureus N315
NP_371366, SAV0842 ABC transporter ATP-binding protein homolog from Staphylococcus aureus subsp. aureus Mu50
SAUSA300_0818 FeS assembly ATPase SufC from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL0914 FeS assembly ATPase SufC from Staphylococcus aureus subsp. aureus COL
71% identity, 97% coverage

BC4983 ABC transporter ATP-binding protein from Bacillus cereus ATCC 14579
71% identity, 96% coverage

lp_1468 ABC transporter, ATP-binding protein from Lactobacillus plantarum WCFS1
69% identity, 95% coverage

Dgeo_0474 FeS assembly ATPase SufC from Deinococcus geothermalis DSM 11300
60% identity, 95% coverage

DR2107 ABC transporter, ATP-binding protein, Ycf16 family from Deinococcus radiodurans R1
59% identity, 95% coverage

TTHA1838 SufC protein (ATP-binding protein) from Thermus thermophilus HB8
61% identity, 97% coverage

2d2fA / Q5SH92 Crystal structure of atypical cytoplasmic abc-atpase sufc from thermus thermophilus hb8 (see paper)
61% identity, 96% coverage

PG0258 ABC transporter, ATP-binding protein from Porphyromonas gingivalis W83
55% identity, 96% coverage

PGN_0358 putative ABC transporter ATP-binding protein from Porphyromonas gingivalis ATCC 33277
55% identity, 96% coverage

AMUC_RS02675 Fe-S cluster assembly ATPase SufC from Akkermansia muciniphila ATCC BAA-835
57% identity, 93% coverage

cg1762 Iron-regulated ABC transporter ATPase subunit from Corynebacterium glutamicum ATCC 13032
55% identity, 94% coverage

FTL_1229 ABC transporter, ATP-binding protein from Francisella tularensis subsp. holarctica
FTH_1206 ABC superfamily ATP binding cassette transporter, ABC protein from Francisella tularensis subsp. holarctica OSU18
56% identity, 95% coverage

CE_RS08390 Fe-S cluster assembly ATPase SufC from Corynebacterium efficiens YS-314
55% identity, 94% coverage

MAB_2747c Probable conserved ABC transporter, ATP-binding protein from Mycobacterium abscessus ATCC 19977
55% identity, 97% coverage

Bd0187 Iron-regulated ABC transporter ATPase subunit SufC from Bdellovibrio bacteriovorus HD100
55% identity, 94% coverage

XAC2936 ABC transporter ATP-binding protein from Xanthomonas axonopodis pv. citri str. 306
57% identity, 93% coverage

DIP1293 Putative ABC transport system, ATP-binding subunit from Corynebacterium diphtheriae NCTC 13129
54% identity, 94% coverage

A9WT29 FeS assembly ATPase from Renibacterium salmoninarum (strain ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235)
56% identity, 94% coverage

P51241 Probable ATP-dependent transporter ycf16 from Porphyra purpurea
55% identity, 95% coverage

SMc00531 PUTATIVE ABC TRANSPORTER ATP-BINDING PROTEIN from Sinorhizobium meliloti 1021
55% identity, 95% coverage

Teth39_0116 FeS assembly ATPase SufC from Thermoanaerobacter ethanolicus ATCC 33223
55% identity, 94% coverage

Q82UN3 Iron-regulated ABC transporter ATPase subunit SufC from Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)
54% identity, 92% coverage

slr0075 ABC transporter subunit from Synechocystis sp. PCC 6803
56% identity, 94% coverage

MAE_RS10060 Fe-S cluster assembly ATPase SufC from Microcystis aeruginosa NIES-843
56% identity, 93% coverage

RLV_4846 Fe-S cluster assembly ATPase SufC from Rhizobium leguminosarum bv. viciae
55% identity, 95% coverage

SYNW0320 ABC transporter, ATP-binding component from Synechococcus sp. WH 8102
51% identity, 82% coverage

AFA2_00636 Fe-S cluster assembly ATPase SufC from Alcaligenes faecalis subsp. faecalis NBRC 13111
52% identity, 97% coverage

Mb1498 PROBABLE CONSERVED ATP-BINDING PROTEIN ABC TRANSPORTER from Mycobacterium bovis AF2122/97
Rv1463 PROBABLE CONSERVED ATP-BINDING PROTEIN ABC TRANSPORTER from Mycobacterium tuberculosis H37Rv
54% identity, 91% coverage

LIMLP_14580 Fe-S cluster assembly ATPase SufC from Leptospira interrogans serovar Manilae
54% identity, 95% coverage

XF1475 ABC transporter ATP-binding protein from Xylella fastidiosa 9a5c
53% identity, 87% coverage

MLUT_RS17270 Fe-S cluster assembly ATPase SufC from Micrococcus luteus NCTC 2665
C5CBR0 Iron-regulated ABC transporter ATPase subunit SufC from Micrococcus luteus (strain ATCC 4698 / DSM 20030 / JCM 1464 / CCM 169 / CCUG 5858 / IAM 1056 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230)
55% identity, 95% coverage

RERY_39460 Fe-S cluster assembly ATPase SufC from Rhodococcus erythropolis
52% identity, 92% coverage

YPTB2312 putative ATP-dependent transporter from Yersinia pseudotuberculosis IP 32953
52% identity, 95% coverage

MSMEG_3124 FeS assembly ATPase SufC from Mycobacterium smegmatis str. MC2 155
MSMEG_3124 Fe-S cluster assembly ATPase SufC from Mycolicibacterium smegmatis MC2 155
53% identity, 96% coverage

SEN1674 putative ABC transport ATP-binding subunit from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
52% identity, 95% coverage

A0T0E5 Iron-sulfur cluster formation ABC transporter ATP-binding subunit from Phaeodactylum tricornutum (strain CCAP 1055/1)
52% identity, 93% coverage

STM1371 putative ABC superfamily (atp_bind) transport protein from Salmonella typhimurium LT2
52% identity, 95% coverage

DW34_RS14455 Fe-S cluster assembly ATPase SufC from Yersinia pestis YN1683
YPO2402 putative ATP-dependent transporter from Yersinia pestis CO92
y1936 cysteine desulfurase ATPase component from Yersinia pestis KIM
52% identity, 95% coverage

KPNJ2_02281 Fe-S cluster assembly ATPase SufC from Klebsiella pneumoniae 30684/NJST258_2
52% identity, 95% coverage

A7MF61 ABC transporter domain-containing protein from Cronobacter sakazakii (strain ATCC BAA-894)
51% identity, 95% coverage

FRAAL4560 Transport protein associated with Fe-S cluster assembly; ATP-binding component from Frankia alni ACN14a
54% identity, 92% coverage

AM1_1223 FeS assembly ATPase SufC from Acaryochloris marina MBIC11017
50% identity, 94% coverage

Atu1823 ABC transporter, nucleotide binding/ATPase protein from Agrobacterium tumefaciens str. C58 (Cereon)
54% identity, 95% coverage

PMM0072 ABC transporter, ATP binding component from Prochlorococcus marinus sp. MED4
53% identity, 92% coverage

Bbr_0909 Fe-S cluster assembly ATPase SufC from Bifidobacterium breve UCC2003
53% identity, 93% coverage

MAP1189 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
51% identity, 95% coverage

CCNA_01938 ATP-dependent transporter sufC from Caulobacter crescentus NA1000
CC_1862 ABC transporter, ATP-binding protein from Caulobacter crescentus CB15
56% identity, 93% coverage

ECs2389 putative ATP-binding component of a transport system from Escherichia coli O157:H7 str. Sakai
52% identity, 95% coverage

ML0595 putative ABC transporter ATP-binding protein from Mycobacterium leprae TN
51% identity, 95% coverage

BL0870 probable ATP binding protein of ABC transporter from Bifidobacterium longum NCC2705
53% identity, 93% coverage

YnhD / b1682 Fe-S cluster scaffold complex subunit SufC from Escherichia coli K-12 substr. MG1655 (see 25 papers)
SUFC_ECOLI / P77499 Probable ATP-dependent transporter SufC from Escherichia coli (strain K12) (see 3 papers)
NP_416197 Fe-S cluster scaffold complex subunit SufC from Escherichia coli str. K-12 substr. MG1655
b1682 cysteine desulfurase ATPase component from Escherichia coli str. K-12 substr. MG1655
WP_000948863 Fe-S cluster assembly ATPase SufC from Escherichia coli
52% identity, 95% coverage

BMEI1041 ABC TRANSPORTER ATP-BINDING PROTEIN from Brucella melitensis 16M
53% identity, 86% coverage

BAB1_0949 ATP/GTP-binding site motif A (P-loop):ABC transporter:AAA ATPase from Brucella melitensis biovar Abortus 2308
53% identity, 95% coverage

BR0932 ABC transporter, ATP-binding protein from Brucella suis 1330
53% identity, 95% coverage

GM298_13625 Fe-S cluster assembly ATPase SufC from Enterobacter sp. HSTU-ASh6
50% identity, 95% coverage

HVO_0859 FeS assembly ATPase SufC from Haloferax volcanii DS2
D4GUK6 Fe-S cluster assembly complex ATPase SufC from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
46% identity, 82% coverage

DJ66_RS00825 Fe-S cluster assembly ATPase SufC from Candidatus Liberibacter solanacearum
52% identity, 96% coverage

RSP_0437 Suf C, ATPase from Rhodobacter sphaeroides 2.4.1
55% identity, 95% coverage

Hlac_0176 FeS assembly ATPase SufC from Halorubrum lacusprofundi ATCC 49239
47% identity, 81% coverage

O83620 ABC transporter, ATP-binding protein from Treponema pallidum (strain Nichols)
TP0611 ABC transporter, ATP-binding protein from Treponema pallidum subsp. pallidum str. Nichols
52% identity, 94% coverage

ZMO0425 FeS assembly ATPase SufC from Zymomonas mobilis subsp. mobilis ZM4
52% identity, 93% coverage

CAC3288 Iron-regulated ABC transporter ATPase subunit (SufC), VEG296 B.subtilis ortholog from Clostridium acetobutylicum ATCC 824
50% identity, 94% coverage

HQ_RS03630 ABC transporter ATP-binding protein from Haloquadratum walsbyi DSM 16790
44% identity, 80% coverage

CD16_RS04765, CLIBASIA_RS04720 Fe-S cluster assembly ATPase SufC from Candidatus Liberibacter asiaticus
CLIBASIA_04810 ABC transporter, nucleotide binding/ATPase protein from Candidatus Liberibacter asiaticus str. psy62
50% identity, 96% coverage

X276_17610 Fe-S cluster assembly ATPase SufC from Clostridium beijerinckii NRRL B-598
49% identity, 97% coverage

Cbei_1848 FeS assembly ATPase SufC from Clostridium beijerincki NCIMB 8052
49% identity, 97% coverage

AB6I_ARATH / Q9CAF5 ABC transporter I family member 6, chloroplastic; ABC transporter ABCI.6; AtABCI6; ABC transporter ATPase; Non-intrinsic ABC protein 7; AtNAP7; Plastid SufC-like protein from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G10670 non-intrinsic ABC protein 7 from Arabidopsis thaliana
49% identity, 72% coverage

Bfl360 probable ATP-dependent transporter sufC from Candidatus Blochmannia floridanus
49% identity, 95% coverage

SAR11_0740 FeS assembly ATPase SufC from Candidatus Pelagibacter ubique HTCC1062
52% identity, 95% coverage

SUFC_PLAF7 / Q8ILW0 Iron-sulfur cluster assembly protein SufC; PfSufC; EC 3.6.1.- from Plasmodium falciparum (isolate 3D7) (see 4 papers)
PF3D7_1413500, XP_001348306 FeS assembly ATPase SufC from Plasmodium falciparum 3D7
45% identity, 71% coverage

SUFC_PLABA / A0A509AN56 Iron-sulfur cluster assembly protein SufC; EC 3.6.1.- from Plasmodium berghei (strain Anka) (see paper)
PBANKA_102920 ABC transporter I family member 1 from Plasmodium berghei ANKA
43% identity, 68% coverage

ST1201 248aa long hypothetical ABC transporter ATP-binding protein from Sulfolobus tokodaii str. 7
45% identity, 96% coverage

TGME49_025800 iron-sulfur assembly ATPase from Toxoplasma gondii ME49
46% identity, 47% coverage

TM1368 ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
48% identity, 94% coverage

CTLon_0054 ABC transporter ATP-binding protein from Chlamydia trachomatis L2b/UCH-1/proctitis
41% identity, 93% coverage

PAP_02345 Fe-S cluster assembly ATPase SufC from Palaeococcus pacificus DY20341
44% identity, 97% coverage

PF1287 putative ABC transporter (ATP-binding protein) from Pyrococcus furiosus DSM 3638
40% identity, 96% coverage

TON_0530 ABC-type transport system involved in Fe-S cluster assembly, ATPase component from Thermococcus onnurineus NA1
45% identity, 97% coverage

BP1026B_I0955 Fe-S cluster assembly ATPase SufC from Burkholderia pseudomallei 1026b
38% identity, 94% coverage

CAB052 Fe-S cluster assembly ATPase SufC from Chlamydia abortus S26/3
39% identity, 93% coverage

MTBMA_c15330 Fe-S cluster assembly ATPase SufC from Methanothermobacter marburgensis str. Marburg
38% identity, 97% coverage

MTH1149 ABC transporter subunit Ycf16 from Methanothermobacter thermautotrophicus str. Delta H
37% identity, 97% coverage

MJ0035 ABC transporter subunit from Methanocaldococcus jannaschii DSM 2661
37% identity, 89% coverage

MMP1168 ABC transporter ATP-binding protein from Methanococcus maripaludis S2
36% identity, 93% coverage

D7DT53 ABC transporter related protein from Methanococcus voltae (strain ATCC BAA-1334 / A3)
34% identity, 93% coverage

TM1417 ABC transporter, ATP-binding protein from Thermotoga maritima MSB8
34% identity, 90% coverage

SSO0925 ABC transporter from Sulfolobus solfataricus P2
44% identity, 59% coverage

H375_1050 LPS export ABC transporter ATP-binding protein from Rickettsia prowazekii str. Breinl
32% identity, 95% coverage

CLP_2159 ABC transporter ATP-binding protein from Clostridium butyricum E4 str. BoNT E BL5262
36% identity, 81% coverage

Avin_12800 LPS transport protein LptB from Azotobacter vinelandii AvOP
29% identity, 95% coverage

PP0953 ABC transporter, ATP-binding protein, putative from Pseudomonas putida KT2440
29% identity, 95% coverage

NGO1605 putative ABC transporter, ATP-binding protein from Neisseria gonorrhoeae FA 1090
30% identity, 89% coverage

LOAG_00381 hypothetical protein from Loa loa
35% identity, 15% coverage

E6MYT4 ABC-type lipopolysaccharide transporter (EC 7.5.2.5) from Neisseria meningitidis serogroup B / serotype 15 (see 2 papers)
NMB0356 ABC transporter, ATP-binding protein from Neisseria meningitidis MC58
30% identity, 89% coverage

ELZ14_04750 LPS export ABC transporter ATP-binding protein from Pseudomonas brassicacearum
28% identity, 95% coverage

Q0PAK5 ABC-transporter ATP-binding protein from Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Cj0669 ABC-transporter ATP-binding protein from Campylobacter jejuni subsp. jejuni NCTC 11168
32% identity, 99% coverage

A0A071L2Z5 ABC-type lipopolysaccharide transporter (EC 7.5.2.5) from Pseudomonas aeruginosa (see paper)
TC 3.A.1.152.1 / Q9HVV6 Probable ATP-binding component of ABC transporter, component of LPS export system, LptF (M), LptG (M) and LptB (C) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA4461 probable ATP-binding component of ABC transporter from Pseudomonas aeruginosa PAO1
28% identity, 95% coverage

LHK_02024 probable ABC transporter, ATP-binding protein from Laribacter hongkongensis HLHK9
30% identity, 90% coverage

BCAL0814 ABC transporter ATP-binding protein from Burkholderia cenocepacia J2315
32% identity, 88% coverage

PSPTO_4452 ABC transporter, ATP-binding protein from Pseudomonas syringae pv. tomato str. DC3000
27% identity, 95% coverage

PPUBIRD1_3895 ABC transporter ATP-binding protein from Pseudomonas putida BIRD-1
32% identity, 70% coverage

NP_879529 ABC transporter from Bordetella pertussis Tohama I
BP0697 LPS export ABC transporter ATP-binding protein from Bordetella pertussis Tohama I
30% identity, 84% coverage

HI1148 ABC transporter, ATP-binding protein from Haemophilus influenzae Rd KW20
31% identity, 80% coverage

H16_A0388 ABC-type transporter, ATPase component: HAAT family from Ralstonia eutropha H16
29% identity, 85% coverage

SYNW1112 possible ABC transporter, ATP-binding component from Synechococcus sp. WH 8102
29% identity, 89% coverage

Q3Y5V5 MDR efflux pump ABC3 from Pyricularia grisea
31% identity, 17% coverage

AMK58_21070 LPS export ABC transporter ATP-binding protein from Azospirillum brasilense
30% identity, 79% coverage

BPSL0534 ABC transporter system, ATP-binding protein from Burkholderia pseudomallei K96243
32% identity, 88% coverage

SO0742 iron(III) ABC transporter, ATP-binding protein from Shewanella oneidensis MR-1
29% identity, 66% coverage

SP_RS04030 amino acid ABC transporter ATP-binding protein from Streptococcus pneumoniae TIGR4
31% identity, 89% coverage

CIBE_5584 ABC transporter ATP-binding protein from Clostridium beijerinckii
35% identity, 62% coverage

LBJ_RS07965 LPS export ABC transporter ATP-binding protein from Leptospira borgpetersenii serovar Hardjo-bovis str. JB197
29% identity, 89% coverage

TP0786 ABC transporter, ATP-binding protein, putative from Treponema pallidum subsp. pallidum str. Nichols
TPANIC_0786 LPS export ABC transporter ATP-binding protein from Treponema pallidum subsp. pallidum str. Nichols
28% identity, 89% coverage

BC343_09585 LPS export ABC transporter ATP-binding protein from Mucilaginibacter pedocola
29% identity, 88% coverage

SPD_0720 amino acid ABC transporter, ATP-binding protein from Streptococcus pneumoniae D39
DQM66_RS03875 amino acid ABC transporter ATP-binding protein from Streptococcus pneumoniae
30% identity, 89% coverage

RA0C_1993 LPS export ABC transporter ATP-binding protein from Riemerella anatipestifer ATCC 11845 = DSM 15868
30% identity, 88% coverage

mll3197 ABC transporter ATP-binding protein (in rpoN upstream) from Mesorhizobium loti MAFF303099
29% identity, 81% coverage

lmo0848 similar to amino acid ABC transporter, ATP-binding protein from Listeria monocytogenes EGD-e
LMRG_02271 glutamine ABC transporter, ATP-binding protein from Listeria monocytogenes 10403S
31% identity, 90% coverage

HZ99_RS26135 ABC transporter ATP-binding protein from Pseudomonas fluorescens
29% identity, 70% coverage

AL01_00410 ABC transporter ATP-binding protein from Bombella intestini
31% identity, 85% coverage

AO090009000651 No description from Aspergillus oryzae RIB40
32% identity, 16% coverage

An17g01770 uncharacterized protein from Aspergillus niger
29% identity, 19% coverage

Dtur_1053 ABC transporter related from Dictyoglomus turgidum DSM 6724
32% identity, 79% coverage

MDR2_TRIRC / F2T1C4 ABC multidrug transporter MDR2; Multidrug resistance protein 2 from Trichophyton rubrum (strain ATCC MYA-4607 / CBS 118892) (Athlete's foot fungus) (see 3 papers)
TERG_08613 uncharacterized protein from Trichophyton rubrum CBS 118892
31% identity, 17% coverage

RSP_2696 ABC transporter, fused ATPase and inner membrane subunits from Rhodobacter sphaeroides 2.4.1
32% identity, 37% coverage

gbs0120 Unknown from Streptococcus agalactiae NEM316
30% identity, 81% coverage

LGAS_1844 Cytochrome bd biosynthesis ABC-type transporter, ATPase and permease component from Lactobacillus gasseri ATCC 33323
29% identity, 39% coverage

C4R9D9 Multidrug resistance protein from Komagataella phaffii (strain GS115 / ATCC 20864)
F2QQK6 Plasma membrane ATP-binding cassette transporter required for the export of a-factor from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1)
33% identity, 16% coverage

LIC10580 ABC transporter, atp-binding protein from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
32% identity, 36% coverage

XP_623564 multidrug resistance protein homolog 49 isoform X1 from Apis mellifera
30% identity, 18% coverage

SP_0709 amino acid ABC transporter, ATP-binding protein from Streptococcus pneumoniae TIGR4
30% identity, 89% coverage

ATRD_EMENI / Q5BAY0 ABC multidrug transporter atrD from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see 2 papers)
31% identity, 17% coverage

ATRD_EMEND / Q9Y8G1 ABC multidrug transporter atrD from Emericella nidulans (Aspergillus nidulans) (see 2 papers)
atrD ABC-transporter from Emericella nidulans (see paper)
31% identity, 17% coverage

LSA0272 Putative multidrug ABC exporter, ATP-binding and membrane-spanning/permease subunits from Lactobacillus sakei subsp. sakei 23K
29% identity, 36% coverage

BB0466 ABC transporter, ATP-binding protein from Borrelia burgdorferi B31
28% identity, 79% coverage

YP_001168064 ABC transporter related from Rhodobacter sphaeroides ATCC 17025
31% identity, 37% coverage

DOFOFD_07020 LPS export ABC transporter ATP-binding protein from Sorlinia euscelidii
30% identity, 83% coverage

AL01_00180 LPS export ABC transporter ATP-binding protein from Bombella intestini
30% identity, 85% coverage

MGYG_04329 leptomycin B resistance protein pmd1 from Nannizzia gypsea CBS 118893
31% identity, 17% coverage

B488_13000 LPS export ABC transporter ATP-binding protein from Liberibacter crescens BT-1
29% identity, 86% coverage

PXO_02228 ABC transporter ATP-binding protein from Xanthomonas oryzae pv. oryzae PXO99A
29% identity, 83% coverage

Clocel_4224 peptidase domain-containing ABC transporter from Clostridium cellulovorans 743B
27% identity, 32% coverage

CpecA_0283, CpecF_0282 LPS export ABC transporter ATP-binding protein from Chlamydia pecorum DBDeUG
27% identity, 95% coverage

TTHERM_00240450 ABC transporter family protein from Tetrahymena thermophila SB210
31% identity, 16% coverage

MDR2_TRIIM / A0A059JJ46 ABC multidrug transporter MDR2; Multidrug resistance protein 2 from Trichophyton interdigitale (strain MR816) (see 4 papers)
30% identity, 17% coverage

AKL23_RS07400 amino acid ABC transporter ATP-binding protein from Streptococcus thermophilus
31% identity, 79% coverage

FN0695 ABC transporter ATP-binding protein from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
27% identity, 89% coverage

TC 3.A.1.201.20 / I7LXH0 12 TMS multidrug resistance transprter of 1318 aas, AbcB15 (Xiong et al. 2010) is the probable exporter of dichlorodiphenyltrichloroethane (DDT). Expression is induced by treatment with DDT, and this transporter appears to be responsible for DDT tolerance by pumping it out of the cell from Tetrahymena thermophila (strain SB210)
31% identity, 16% coverage

ABCB5_HUMAN / Q2M3G0 ATP-binding cassette sub-family B member 5; ABCB5 P-gp; P-glycoprotein ABCB5; EC 7.6.2.2 from Homo sapiens (Human) (see 11 papers)
Q2M3G0 ABC-type xenobiotic transporter (EC 7.6.2.2) from Homo sapiens (see 2 papers)
NP_001157413 ATP-binding cassette sub-family B member 5 isoform 1 from Homo sapiens
31% identity, 16% coverage

TC 3.A.1.201.13 / Q2M3G0 Plasma membrane AbcB5, of 812 aas and 6 TMSs, mediates resistance of tumor cells to doxorubicin and other drugs including taxanes and anthracyclines (Kawanobe et al. 2012) by catalyzing efflux of these drugs from Homo sapiens (see 8 papers)
31% identity, 25% coverage

MDR2_TRIEC / F2PRR1 ABC multidrug transporter MDR2; Multidrug resistance protein 2 from Trichophyton equinum (strain ATCC MYA-4606 / CBS 127.97) (Horse ringworm fungus) (see paper)
MDR2_TRIT1 / F2RP52 ABC multidrug transporter MDR2; Multidrug resistance protein 2 from Trichophyton tonsurans (strain CBS 112818) (Scalp ringworm fungus) (see paper)
30% identity, 17% coverage

lp_3040 ABC transporter, ATP-binding protein from Lactobacillus plantarum WCFS1
29% identity, 38% coverage

SACOL1915 amino acid ABC transporter, ATP-binding protein from Staphylococcus aureus subsp. aureus COL
SA1674 glutamate ABC transporter ATP-binding protein from Staphylococcus aureus subsp. aureus N315
SAOUHSC_01990 amino acid ABC transporter, ATP-binding protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1807 amino acid ABC transporter, ATP-binding protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1749 glutamine transport ATP-binding protein from Staphylococcus aureus subsp. aureus str. Newman
31% identity, 89% coverage

PSPTO_3882 polyamine ABC transporter, ATP-binding protein, putative from Pseudomonas syringae pv. tomato str. DC3000
29% identity, 70% coverage

4ymuJ / Q8RCC2 Crystal structure of an amino acid abc transporter complex with arginines and atps (see paper)
Q8RCC2 ABC-type polar amino acid transport system, ATPase component from Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)
30% identity, 87% coverage

SPD_0616 amino acid ABC transporter, ATP-binding protein from Streptococcus pneumoniae D39
DQM66_RS03315 amino acid ABC transporter ATP-binding protein from Streptococcus pneumoniae
29% identity, 89% coverage

plu4040 Probable ABC transporter ATP-binding protein yhbG from Photorhabdus luminescens subsp. laumondii TTO1
28% identity, 80% coverage

Atu3744 ABC transporter, nucleotide binding/ATPase protein from Agrobacterium tumefaciens str. C58 (Cereon)
A9CFL3 ABC transporter, nucleotide binding/ATPase protein from Agrobacterium fabrum (strain C58 / ATCC 33970)
30% identity, 36% coverage

NGR_c00180 LPS export ABC transporter ATP-binding protein from Sinorhizobium fredii NGR234
29% identity, 81% coverage

XP_008260013 ATP-dependent translocase ABCB1 isoform X3 from Oryctolagus cuniculus
30% identity, 16% coverage

NGR_c00180 predicted ABC transporter, ATP-binding protein from Rhizobium sp. NGR234
29% identity, 80% coverage

MDR1_ASPFU / Q4WTT9 ABC multidrug transporter mdr1 from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (Neosartorya fumigata) (see 5 papers)
AFUA_5G06070 ABC multidrug transporter Mdr1 from Aspergillus fumigatus Af293
31% identity, 16% coverage

TC 3.A.1.201.10 / B0Y3B6 Mdr1; resistance to Cilofungin and other drugs from Aspergillus fumigatus (strain CEA10 / CBS 144.89 / FGSC A1163) (see paper)
31% identity, 16% coverage

XAC2971 ABC transporter ATP-binding protein from Xanthomonas axonopodis pv. citri str. 306
29% identity, 83% coverage

PF1654 similar to ABC transporter (ATP-binding protein) from Pyrococcus furiosus DSM 3638
32% identity, 37% coverage

lptB / O25417 lipopolysaccharide transport system ATP-binding protein LptB (EC 7.5.2.5) from Helicobacter pylori (strain ATCC 700392 / 26695) (see paper)
HPG27_671 ABC transporter. ATP-binding protein from Helicobacter pylori G27
HP0715 ABC transporter, ATP-binding protein from Helicobacter pylori 26695
HPG27_RS03465, HPYLSS1_00622 LPS export ABC transporter ATP-binding protein from Helicobacter pylori G27
29% identity, 90% coverage

XP_004079446 ATP-binding cassette sub-family B member 8, mitochondrial from Oryzias latipes
32% identity, 33% coverage

7qkrA / F2QQK6 Cryo-em structure of abc transporter ste6-2p from pichia pastoris with verapamil at 3.2 a resolution (see paper)
33% identity, 18% coverage

XP_006779228 multidrug resistance protein 1 from Myotis davidii
32% identity, 18% coverage

Q835Z8 Spermidine/putrescine ABC transporter, ATP-binding protein from Enterococcus faecalis (strain ATCC 700802 / V583)
27% identity, 73% coverage

lptB / Q2YP14 lipopolysaccharide transport system ATP-binding protein (EC 7.5.2.5) from Brucella abortus (strain 2308) (see paper)
BCAN_A0162 Probable ABC transporter ATP-binding protein in ntrA/rpoN 5'region from Brucella canis ATCC 23365
BMEI1790 ABC TRANSPORTER ATP-BINDING PROTEIN from Brucella melitensis 16M
28% identity, 79% coverage

TC 3.A.1.201.12 / B2WTH9 California mussel ABCB/MDR multixenobiotic resistance efflux pump from Mytilus californianus (see paper)
30% identity, 17% coverage

LLNZ_01800 ABC transporter ATP-binding protein from Lactococcus cremoris subsp. cremoris NZ9000
31% identity, 43% coverage

ZMO0275 ABC transporter related protein from Zymomonas mobilis subsp. mobilis ZM4
28% identity, 87% coverage

BOV_0152 ABC transporter, ATP-binding protein from Brucella ovis ATCC 25840
28% identity, 86% coverage

Athe_1109 ABC transporter related from Anaerocellum thermophilum DSM 6725
Athe_1109 ABC transporter ATP-binding protein from Caldicellulosiruptor bescii DSM 6725
31% identity, 66% coverage

cg2939 ABC-type dipeptide/oligopeptide/nickel transport system, fused permease and ATPase components from Corynebacterium glutamicum ATCC 13032
28% identity, 34% coverage

V089_02512 SAV1866 family putative multidrug efflux ABC transporter from Staphylococcus aureus GD2010-115
31% identity, 40% coverage

HP1171 glutamine ABC transporter, ATP-binding protein (glnQ) from Helicobacter pylori 26695
28% identity, 84% coverage

W475_02351 SAV1866 family putative multidrug efflux ABC transporter from Staphylococcus aureus VET0166R
31% identity, 39% coverage

Ssal_01465 ABC transporter ATP-binding protein from Streptococcus salivarius 57.I
32% identity, 68% coverage

YEJF_AGRFC / A9CKL2 Peptidoglycan transport ATP-binding protein YejF; EC 7.4.2.- from Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58)) (see paper)
Atu0190 ABC transporter, nucleotide binding/ATPase protein (peptide) from Agrobacterium tumefaciens str. C58 (Cereon)
27% identity, 40% coverage

BL105A_0547 amino acid ABC transporter ATP-binding protein from Bifidobacterium longum
29% identity, 77% coverage

W538_02582 SAV1866 family putative multidrug efflux ABC transporter from Staphylococcus aureus VET0261R
31% identity, 38% coverage

Y1866_STAAM / Q99T13 Putative multidrug export ATP-binding/permease protein SAV1866; EC 7.6.2.- from Staphylococcus aureus (strain Mu50 / ATCC 700699) (see paper)
Q99T13 ABC-type xenobiotic transporter (EC 7.6.2.2) from Staphylococcus aureus (see paper)
TC 3.A.1.106.2 / Q2G2M9 The homodimeric Sav1866 multidrug exporter (transports doxorubicin, verapamil, ethidium, tetraphenylphosphonium, vinblastine and the fluorescent dye, Hoechst 33342; 3-D structure known at 3 Å resolution; Dawson and Locher, 2006; Velamakanni et al., 2008) The empty site opens by rotation of the nucleotide-binding domain whereas the ATP-bound site remains occluded (Jones and George, 2011). Conformational changes induced by ATP-binding and hydrolysis have been proposed (Becker et al. 2010; Oliveira et al., 2011). The alternating access mechanism and the flippase activity of this ABC exporter has been shown to be lipid-dependent (Becker et al. 2010; Oliveira et al., 2011). The alternating access mechanism and the flippase activity of this ABC exporter has been shown to be lipid-dependent from Staphylococcus aureus (strain NCTC 8325)
2hydA / Q99T13 Multidrug abc transporter sav1866 (see paper)
SAOUHSC_02003 ABC transporter, ATP-binding/permease protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAAV_1916 toxin exporting ABC transporter, permease from Staphylococcus aureus subsp. aureus ED98
SAV1866 ABC transporter homolog from Staphylococcus aureus subsp. aureus Mu50
NWMN_1758 ABC transporter ATP-binding protein from Staphylococcus aureus subsp. aureus str. Newman
SACOL1924 toxin exporting ABC transporter, permease/ATP-binding protein, putative from Staphylococcus aureus subsp. aureus COL
31% identity, 38% coverage

DVU0105 glutamine ABC transporter, ATP-binding protein from Desulfovibrio vulgaris Hildenborough
28% identity, 79% coverage

azo2266 probable glutamine transport ATP-binding protein from Azoarcus sp. BH72
29% identity, 89% coverage

SO_3665 ABC transporter, ATP-binding/permease protein, putative from Shewanella oneidensis MR-1
32% identity, 37% coverage

bgla_2g29570 ABC transporter ATP-binding protein from Burkholderia gladioli BSR3
31% identity, 41% coverage

WP_124781844 SAV1866 family putative multidrug efflux ABC transporter from Staphylococcus aureus
32% identity, 38% coverage

EAMY_0863 putative ABC transport system, ATP-binding component from Erwinia amylovora CFBP1430
31% identity, 90% coverage

Q7RVS1 Multidrug resistance protein MDR from Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
NCU07546 multidrug resistance protein MDR from Neurospora crassa OR74A
29% identity, 17% coverage

TON_0243 ABC-type cobalt transport system, ATPase component from Thermococcus onnurineus NA1
29% identity, 85% coverage

HMPREF1014_04858 peptidase domain-containing ABC transporter from Bacillus sp. 7_6_55CFAA_CT2
30% identity, 29% coverage

IRTA_MYCT3 / G7CBF5 Mycobactin import ATP-binding/permease protein IrtA; EC 7.2.2.- from Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316) (Mycobacterium thermoresistibile) (see paper)
30% identity, 24% coverage

ECs0887 ATP-binding component of glutamine high-affinity transport system from Escherichia coli O157:H7 str. Sakai
29% identity, 90% coverage

SAK_RS04085 ATP-binding cassette domain-containing protein from Streptococcus agalactiae A909
30% identity, 79% coverage

LJ1813 ABC transporter ATPase and permease components from Lactobacillus johnsonii NCC 533
30% identity, 37% coverage

LOC100810510 ABC transporter B family member 25 from Glycine max
31% identity, 33% coverage

Amuc_0672 ABC transporter related from Akkermansia muciniphila ATCC BAA-835
29% identity, 80% coverage

SE1540 glutamate ABC transporter ATP-binding protein from Staphylococcus epidermidis ATCC 12228
31% identity, 89% coverage

lptB / Q7CPN9 LPS export ABC transporter ATP-binding protein (EC 7.5.2.5) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see 9 papers)
28% identity, 80% coverage

SMc02357 PUTATIVE HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING ABC TRANSPORTER PROTEIN from Sinorhizobium meliloti 1021
31% identity, 89% coverage

ECH_0085 ABC transporter, ATP-binding protein from Ehrlichia chaffeensis str. Arkansas
29% identity, 88% coverage

G1XU57 ABC transporter domain-containing protein from Arthrobotrys oligospora (strain ATCC 24927 / CBS 115.81 / DSM 1491)
29% identity, 22% coverage

DA471_RS01675 amino acid ABC transporter ATP-binding protein from Staphylococcus aureus
31% identity, 88% coverage

ZP_03149641 ABC transporter-related protein from Geobacillus sp. G11MC16
31% identity, 30% coverage

TAGA_DICDI / Q9GTN7 Serine protease/ABC transporter B family protein tagA; EC 3.4.21.- from Dictyostelium discoideum (Social amoeba) (see 3 papers)
DDB_G0293002 ABC transporter B family protein from Dictyostelium discoideum AX4
28% identity, 12% coverage

PSCT_04355 phosphate ABC transporter ATP-binding protein from Pseudomonas sp. SCT
28% identity, 80% coverage

YP_001126158 Lantibiotic mersacidin transporter system from Geobacillus thermodenitrificans NG80-2
GTNG_2061 peptidase domain-containing ABC transporter from Geobacillus thermodenitrificans NG80-2
31% identity, 30% coverage

HD0586 putative ABC transporter ATP-binding protein from Haemophilus ducreyi 35000HP
27% identity, 80% coverage

W903_RS03765 ATP-binding cassette domain-containing protein from Streptococcus agalactiae CNCTC 10/84
30% identity, 79% coverage

A9497_03790 amino acid ABC transporter ATP-binding protein from Streptococcus thermophilus
32% identity, 79% coverage

Bbr_0166 dipeptide/oligopeptide/nickel ABC transporter permease/ATP-binding protein from Bifidobacterium breve UCC2003
28% identity, 34% coverage

AAA66477.1 SMDR2 from Schistosoma mansoni (see paper)
31% identity, 17% coverage

XF1409 ABC transporter ATP-binding protein from Xylella fastidiosa 9a5c
29% identity, 75% coverage

TC 3.A.1.3.25 / Q9CES4 Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity from Lactococcus lactis subsp. lactis (strain IL1403)
30% identity, 78% coverage

BOV_A0500 ABC transporter ATP-binding protein from Brucella ovis ATCC 25840
29% identity, 66% coverage

VVMO6_04162 ABC transporter ATP-binding protein from Vibrio vulnificus MO6-24/O
31% identity, 39% coverage

GlnQ / b0809 L-glutamine ABC transporter ATP binding subunit (EC 7.4.2.1) from Escherichia coli K-12 substr. MG1655 (see 2 papers)
GlnQ / P10346 L-glutamine ABC transporter ATP binding subunit (EC 7.4.2.1) from Escherichia coli (strain K12) (see paper)
GLNQ_ECOLI / P10346 Glutamine transport ATP-binding protein GlnQ from Escherichia coli (strain K12) (see paper)
TC 3.A.1.3.2 / P10346 GlnQ aka B0809, component of Three component ABC L-glutamine porter. The basal ATPase activity (ATP hydrolysis in the absence of substrate) is mainly caused by the docking of the closed-unliganded state of GlnH onto the transporter domain of GlnPQ. Unlike glutamine, arginine binds both GlnH domains, but does not trigger their closing. Comparison of the ATPase activity in nanodiscs with glutamine transport in proteoliposomes suggested that the stoichiometry of ATP per substrate is close to two from Escherichia coli (see 5 papers)
glnQ / GB|ABB65374.1 glutamine ABC transporter, ATP-binding protein GlnQ from Escherichia coli K12 (see 5 papers)
b0809 glutamine ABC transporter ATP-binding protein from Escherichia coli str. K-12 substr. MG1655
NP_415330 L-glutamine ABC transporter ATP binding subunit from Escherichia coli str. K-12 substr. MG1655
30% identity, 79% coverage

jhp0653 putative abc transporter, ATP-binding protein from Helicobacter pylori J99
28% identity, 90% coverage

GBAA_1933 ABC transporter ATP-binding protein from Bacillus anthracis str. 'Ames Ancestor'
27% identity, 92% coverage

JHW33_RS01275 glutamine ABC transporter ATP-binding protein GlnQ from Rahnella aceris
28% identity, 89% coverage

RL3547 putative ATP-binding component of ABC transporter protein from Rhizobium leguminosarum bv. viciae 3841
30% identity, 70% coverage

BCAL3101 ABC transporter ATP-binding protein from Burkholderia cenocepacia J2315
29% identity, 80% coverage

NP_001265699 ATP-dependent translocase ABCB1 from Cavia porcellus
31% identity, 18% coverage

CT653 ABC Transporter ATPase from Chlamydia trachomatis D/UW-3/CX
27% identity, 95% coverage

PGP1_CAEEL / P34712 Multidrug resistance protein pgp-1; P-glycoprotein A; P-glycoprotein-related protein 1; EC 7.6.2.2 from Caenorhabditis elegans (see paper)
P34712 ABC-type xenobiotic transporter (EC 7.6.2.2) from Caenorhabditis elegans (see paper)
TC 3.A.1.201.14 / P34712 P-glycoprotein-1 MDR exporter from Caenorhabditis elegans
30% identity, 16% coverage

ABCB1 / P08183 ATP-dependent translocase ABCB1 (EC 7.6.2.2) from Homo sapiens (see 39 papers)
MDR1_HUMAN / P08183 ATP-dependent translocase ABCB1; ATP-binding cassette sub-family B member 1; Multidrug resistance protein 1; P-glycoprotein 1; Phospholipid transporter ABCB1; CD243 antigen; EC 7.6.2.2; EC 7.6.2.1 from Homo sapiens (Human) (see 8 papers)
P08183 ABC-type xenobiotic transporter (EC 7.6.2.2); ABC-type glutathione-S-conjugate transporter (EC 7.6.2.3) from Homo sapiens (see 10 papers)
TC 3.A.1.201.1 / P08183 Broad specificity multidrug resistance (MDR1; MDR-1; Pgp; P-gp; ABCB1; P-glycoprotein) efflux pump. It exports organic cations and amphiphilic compounds of unrelated chemical structure from Homo sapiens (Human) (see 19 papers)
NP_000918 ATP-dependent translocase ABCB1 isoform 2 from Homo sapiens
33% identity, 18% coverage

O46605 Multidrug resistance p-glycoprotein from Canis lupus familiaris
33% identity, 18% coverage

SGO_0983 amino acid transport protein SP0709 from Streptococcus gordonii str. Challis substr. CH1
29% identity, 89% coverage

ABCB1 / RF|NP_000918.2 multidrug resistance protein 1 from Homo sapiens
33% identity, 18% coverage

Q9X196 Spermidine/putrescine import ATP-binding protein PotA from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
35% identity, 47% coverage

FPV33_RS17200 glutamine ABC transporter ATP-binding protein GlnQ from Klebsiella aerogenes
29% identity, 91% coverage

TC_RS00120 LPS export ABC transporter ATP-binding protein from Chlamydia muridarum str. Nigg
TC0023 ABC transporter, ATP-binding protein from Chlamydia muridarum Nigg
27% identity, 95% coverage

4f4cA / P34712 The crystal structure of the multi-drug transporter (see paper)
30% identity, 17% coverage

XP_005806663 ATP-binding cassette sub-family B member 9 from Xiphophorus maculatus
30% identity, 27% 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