PaperBLAST
PaperBLAST Hits for IAI46_19690 (86 a.a., MLAVATQTPS...)
Show query sequence
>IAI46_19690
MLAVATQTPSTLSPVPVDYTPRDRFIRLPEVLYTTGLSRSTVYEMMARRQFPAQISLGGK
TVAWLESEIENWMAERIANRHQGATA
Running BLASTp...
Found 46 similar proteins in the literature:
ESA_00625 helix-turn-helix transcriptional regulator from Cronobacter sakazakii ATCC BAA-894
58% identity, 97% coverage
NP_042041 excisionase and transcriptional regulator from Enterobacteria phage P4
NP_042041 transcriptional regulator from Enterobacteria phage P4
48% identity, 93% coverage
t2651 hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
56% identity, 84% coverage
- Genotyping of Salmonella enterica serovar Typhi strains isolated from 1959 to 2006 in China and analysis of genetic diversity by genomic microarray
Zhang, Croatian medical journal 2011 - “...divergent genes but only 9 were absent. It was surprising that genes t2648, t2649, t2650, t2651, and t2652 were all absent from ST890 and ST892. Table 3 The absent and divergent genes in two novel sequence types (ST) of S. Typhi compared to S. Typhi Ty2...”
- “...t2651, t2652, t2653, t2654, t2655, t2656 t1134, t1135, t1137, t1141, t1151, t1691, t2648, t2649, t2650, t2651, t2652, t4259, t4260, t4261, t4263, t4264, t4265, t4266, t4268, t4269, t4270, t4271, t4273, t4274, t4275, t4281, t4282, t4283, t4284, t4286, t4289, nucD, nucE, t4317, t4318, t4319, t4320, t4321 Variably present...”
- Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18
Deng, Journal of bacteriology 2003 - “...University of California, Berkeley t1446 t2647 t2648 t2649 t2650 t2651 t2652 t2653 t2654 t2655 t2656 t2718 t2720 t2722 t2724 t2947 t2948 t2949 t2950 t2951 t2952...”
t4525 phage DNA binding protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
61% identity, 60% coverage
- Genotyping of Salmonella enterica serovar Typhi strains isolated from 1959 to 2006 in China and analysis of genetic diversity by genomic microarray
Zhang, Croatian medical journal 2011 - “...t2647, t2648, t2656, t4521, t4528 t0869, t0871, t2647, t2648 t2647, t2648, t2656, t4518, t4522, t4523, t4525, t4527 Discussion We used MLST to analyze 40 S. Typhi isolates from 5 Chinese provinces and found two novel sequence types, ST890 and ST892. In ST890, the housekeeping gene hisD...”
ESA_00625 hypothetical protein from Enterobacter sakazakii ATCC BAA-894
63% identity, 70% coverage
BHW77_22420 helix-turn-helix transcriptional regulator from Escherichia coli
58% identity, 74% coverage
- Comparative genomics reveals structural and functional features specific to the genome of a foodborne Escherichia coli O157:H7
Sharma, BMC genomics 2019 - “...cdtI 48.2 22 3,709,5953,757,796 BHW77_19495 and BHW77_19800 50.11 NC_009514 18/Enterobacteria phage SfI 26.1 6 4,330,9604,357,158 BHW77_22420 and BHW77_22605 45.57 NC_027339 19/Acidianus tailed spindle virus 10.1 1 4,801,5734,811,702 BHW77_24685 and BHW77_24755 46.57 NC_029316 a Genes flanking the phage insertion sites are represented as locus-tags in the annotated...”
VFA_000468 helix-turn-helix transcriptional regulator from Vibrio furnissii CIP 102972
53% identity, 69% coverage
VV2261 predicted transcriptional regulator from Vibrio vulnificus YJ016
55% identity, 70% coverage
ASA_2928 probable prophage regulatory protein from Aeromonas salmonicida subsp. salmonicida A449
52% identity, 74% coverage
A55_2025 transcriptional regulator, putative from Vibrio cholerae 1587
53% identity, 67% coverage
VC1809 transcriptional regulator, putative from Vibrio cholerae O1 biovar eltor str. N16961
53% identity, 67% coverage
- Emergence of multidrug resistant, ctx negative seventh pandemic Vibrio cholerae O1 El Tor sequence type (ST) 69 in coastal water of Kerala, India
Ayyappan, Scientific reports 2024 - “...island 1 (VC0819, VC0827, and VC0847), pathogenicity Island 2 (VC1873, VC 1776, VC1758, VC1790, VC1765, VC1809, VC1760) and pandemic island 1 (VC0175, VC0178, VC0180, VC0183, VC0185) were shown 100% identity with V. cholerae strain N16961 strain (Accession No: AE003852.1). However, VC0180 gene of pandemic island 1...”
- Non-O1/Non-O139 Vibrio cholerae-An Underestimated Foodborne Pathogen? An Overview of Its Virulence Genes and Regulatory Systems Involved in Pathogenesis
Zhang, Microorganisms 2024 - “...III [ 85 ]. 3.3. Vibrio Pathogenicity Island 2 (VPI-2) VPI-2 (located between vc1758 and vc1809) was identified in O1/O139 V. cholerae and NOVCs. However, Jermyn and Boyd (2005), Haley et al. (2014), and Takahashi et al. (2021) studied the genetic variation of VPI-2 in NOVCs...”
- The Response Regulator VC1795 of Vibrio Pathogenicity Island-2 Contributes to Intestinal Colonization by Vibrio cholerae
Yan, International journal of molecular sciences 2023 - “...has aroused global concern. The Vibrio Pathogenicity Island-2 (VPI-2) is a 57.3 kb region, VC1758 VC1809 , which is present in choleragenic V. cholerae . At present, little is known about the function of VC1795 in the VPI-2 of V. cholerae . In this study, the...”
- “...of V. cholerae N16961 was mapped, and it was found to stretch from VC1758 to VC1809 , including a P4-like integrase ( VC1758 ), a restriction-modification system ( VC1765 VC1769 ), a sialic acid metabolism region ( VC1773 VC1784 ), and a Mu phage-like region (...”
- Virulence of Cholera Toxin Gene-Positive Vibrio cholerae Non-O1/non-O139 Strains Isolated From Environmental Water in Kolkata, India
Takahashi, Frontiers in microbiology 2021 - “...N.D. 100.00% (10504/10504) VC1804VC1807 92.8% (2348/2529) 97.4% (2463/2529) 100.0% (2529/2529) VC1808 N.D. N.D. 100.0% (846/846) VC1809 97.0% (195/201) 97.0% (195/201) 100% (201/201) N.D., Not detected DNA fragment whose sequence was homologous to that of the reference gene. Broken, Base sequence of the gene is disrupted by...”
- Virulence Regulation and Innate Host Response in the Pathogenicity of Vibrio cholerae
Ramamurthy, Frontiers in cellular and infection microbiology 2020 - “...the secretory response by binding and penetration of the toxin to enterocytes. Loci VC1758 to VC1809 ( nan-nag gene cluster) present in the VPI-2 was identified to be involved in the transport and catabolism of sialic acid (Almagro-Moreno and Boyd, 2009 ). During the infection process,...”
- Pathogenomics of Virulence Traits of Plesiomonas shigelloides That Were Deemed Inconclusive by Traditional Experimental Approaches
Ekundayo, Frontiers in microbiology 2018 - “...per, Escherichia stcE, Streptococcus neuB, Campylobacter ptmA LS1 4 2.99 Vibrio hsdR, Salmonella rhuM, Vibrio VC1809, Vibrio hsdM GN7 15 11.19 Escherichia z1204, Yersinia gmd, Yersinia manC, Escherichia intl, Escherichia ibeB, Pseudomonas fliR, Escherichia z1203, Escherichia orf72, Escherichia z1216, Escherichia orf51, Yersinia manB, Vibrio radC, Legionella...”
- “...were specific to strain 302-73. Exclusive to strain LS1 were ORF homologous/orthologous to Vibrio hsdR, VC1809 , and hsdM ; and Salmonella rhuM . In addition, 15 virulence genes related to Escherichia z1204, intl, ibeB, z1203, orf72, z1216, orf51 , and orf86 ; Pseudomonas fliR ;...”
- CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules
Carpenter, Journal of bacteriology 2017 - “...GTPase (VC1806) Hypothetical protein Hypothetical protein VefB (VC1809) Homologue accession no. NP_230494 CAG76582 Identity (%) 97 38 N16961 N16961 N16961...”
- Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome
Carpenter, Journal of bacteriology 2015 - “...pBAintV1 intV2 strain harboring pBAintV2 N16961 VC1785 Smr N16961 VC1809 Smr N16961 VC0497 Smr vefA VC1809 Smr vefA vefB VC0497 Smr vefA vefB vefC VC0817 Smr...”
- “...nonpolar deletions of VC0497 (vefC), VC1785 (vefA), and VC1809 (vefB) in V. cholerae N16961 and examined excision using the attB2 excision assay. A wild-type...”
- More
VCB_002857, VCG_002259, VIF_000799 helix-turn-helix transcriptional regulator from Vibrio cholerae TMA 21
53% identity, 67% coverage
- Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA
Almagro-Moreno, BMC microbiology 2010 - “...Vibrio cholerae N16961* VC1758 VC1785/VC1809 Vibrio cholerae TM 11079-80 VIF_001175 VIF_000799 Vibrio cholerae TMA21 VCB_002798 VCB_002857 Vibrio cholerae 12129(1) VCG_002315 VCG_002259 Vibrio cholerae V51 VCV51_1204 VCV51_0550 Vibrio cholerae 1587 A55_1986 A55_2025 Vibrio cholerae CT 5369-93 VIH_002346 VIH_002364 Vibrio cholerae RC385 VCRC385_0574 VCRC385_3603 Vibrio cholerae TMA 21...”
- “...Vibrio cholerae TM 11079-80 VIF_001175 VIF_000799 Vibrio cholerae TMA21 VCB_002798 VCB_002857 Vibrio cholerae 12129(1) VCG_002315 VCG_002259 Vibrio cholerae V51 VCV51_1204 VCV51_0550 Vibrio cholerae 1587 A55_1986 A55_2025 Vibrio cholerae CT 5369-93 VIH_002346 VIH_002364 Vibrio cholerae RC385 VCRC385_0574 VCRC385_3603 Vibrio cholerae TMA 21 VCB_000212 VCB_000197 Vibrio cholerae MZO-3...”
- “...Strain Locus tag Locus tag Vibrio cholerae N16961* VC1758 VC1785/VC1809 Vibrio cholerae TM 11079-80 VIF_001175 VIF_000799 Vibrio cholerae TMA21 VCB_002798 VCB_002857 Vibrio cholerae 12129(1) VCG_002315 VCG_002259 Vibrio cholerae V51 VCV51_1204 VCV51_0550 Vibrio cholerae 1587 A55_1986 A55_2025 Vibrio cholerae CT 5369-93 VIH_002346 VIH_002364 Vibrio cholerae RC385 VCRC385_0574...”
MED222_15529 predicted transcriptional regulator from Vibrio sp. MED222
51% identity, 66% coverage
Reut_A2193 Prophage CP4-57 regulatory from Ralstonia eutropha JMP134
53% identity, 67% coverage
VCJ_000314 AlpA family transcriptional regulator from Vibrio metoecus
53% identity, 69% coverage
G5B91_27730 helix-turn-helix transcriptional regulator from Pseudomonas nitroreducens
53% identity, 69% coverage
VV0515 predicted transcriptional regulator from Vibrio vulnificus YJ016
52% identity, 69% coverage
VCB_000197, VC_0497 AlpA family transcriptional regulator from Vibrio cholerae TMA 21
A51_B0476 transcriptional regulator from Vibrio cholerae MZO-3
VC0497 transcriptional regulator from Vibrio cholerae O1 biovar eltor str. N16961
52% identity, 69% coverage
- Genomic epidemiology of Vibrio cholerae during a mass vaccination campaign of displaced communities in Bangladesh
Taylor-Brown, Nature communications 2023 - “...majority of isolates ( n =155) carried type 4/type D (lacking orthologues of VC_0493 to VC_0497 and VC_00503, in addition to those lost from type 3), while the remaining two carried type 3/type C (Supplementary Fig. S7 ). All 51 Clade 3 isolate genomes possessed VSP-II...”
- Vibrio cholerae circulating throughout a mass vaccination campaign in the Forcibly Displaced Myanmar National population in Cox’s Bazar, Bangladesh
Taylor-Brown, 2022 - Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA
Almagro-Moreno, BMC microbiology 2010 - “...cholerae CT 5369-93 VIH_002346 VIH_002364 Vibrio cholerae RC385 VCRC385_0574 VCRC385_3603 Vibrio cholerae TMA 21 VCB_000212 VCB_000197 Vibrio cholerae MZO-3 A51_B0496 A51_B0476 Vibrio cholerae 12129(1) VCG_003155 VCG_003160 Vibrio cholerae N16961* VC0516 VC0497 Vibrio cholerae MZO-3 A51_B0965 A51_B0948 Vibrio vulnificus YJO16* VV2262 VV2261 Vibrio vulnificus YJ016* VV0817 VV0810...”
- Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA
Almagro-Moreno, BMC microbiology 2010 - “...Vibrio cholerae RC385 VCRC385_0574 VCRC385_3603 Vibrio cholerae TMA 21 VCB_000212 VCB_000197 Vibrio cholerae MZO-3 A51_B0496 A51_B0476 Vibrio cholerae 12129(1) VCG_003155 VCG_003160 Vibrio cholerae N16961* VC0516 VC0497 Vibrio cholerae MZO-3 A51_B0965 A51_B0948 Vibrio vulnificus YJO16* VV2262 VV2261 Vibrio vulnificus YJ016* VV0817 VV0810 Vibrio vulnificus YJO16* VV0560 VV0515...”
- Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China
Luo, Microbiology spectrum 2023 - “...found in most L3 isolates (77.9%, 46/59). Various combinations of genes VC0494 , VC0496 , VC0497 , VC0498 , VC0499 , VC0504 , VC0505 , VC0506 , VC0508 , VC0509, and VC0510 were present in 48 of the 59 (81.3%) L3 isolates (Table S3). Vibrio pathogenic...”
- Vibrio cholerae's mysterious Seventh Pandemic island (VSP-II) encodes novel Zur-regulated zinc starvation genes involved in chemotaxis and cell congregation
Murphy, PLoS genetics 2021 - “...vc0503 , [ 27 ]). The remaining uncharacterized genes are predicted to encode transcriptional regulators (VC0497, VC0513), ribonuclease H (VC0498), a type IV pilin (VC0502), a DNA repair protein (VC0510), methyl-accepting chemotaxis proteins (VC0512, VC0514), a cyclic di-GMP phosphodiesterase (VC0515), and hypothetical proteins [ 23 ]....”
- Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome
Carpenter, Journal of bacteriology 2015 - “...harboring pBAintV2 N16961 VC1785 Smr N16961 VC1809 Smr N16961 VC0497 Smr vefA VC1809 Smr vefA vefB VC0497 Smr vefA vefB vefC VC0817 Smr vefA vefB vefC strain...”
- “...by University of California, Berkeley bp. The vefC strain (VC0497) has 171 bp deleted and a 30-bp truncated vefC gene. Excision assays. In order to observe...”
- The population structure of Vibrio cholerae from the Chandigarh Region of Northern India
Abd, PLoS neglected tropical diseases 2014 - “...1 that has a similar structure to N16961 with a deletion in the loci VC0496, VC0497 and VC0498 ( Figure 3 ). Isolates from both of the clades found in Chandigarh harboured cholera toxin phages that are highly related to phages in other wave-3 V. cholerae...”
- Genome Sequence of Non-O1 Vibrio cholerae PS15
Kumar, Genome announcements 2013 - “...region ( 10 ). Further, PS15 harbors genes of Vibrio seventh pandemic island-II (VC0494 to VC0497). The whole-genome sequence of V.cholerae PS15 will help our future studies to determine the differences in virulence gene composition and the molecular bases for differences in the physiology of substrate...”
- Discovery of novel Vibrio cholerae VSP-II genomic islands using comparative genomic analysis
Taviani, FEMS microbiology letters 2010 - “..., 2002 ). VSP-II was originally identified as a 7.5-kb island, spanning genes VC0490 to VC0497 in V. cholerae O1 El Tor N16961 ( Dziejman et al. , 2002 ), and, subsequently, found to include a larger 26.9-kb region, spanning from VC0490 to VC0516 ( OShea...”
- “...55 92 92 92 VC0496 529739 530338 600,+ hypothetical protein 100 n/a 98 99 98 VC0497 530402 530602 201,+ Transcriptional regulator 100 n/a 98 99 99 VC0498 530684 531124 441,+ Ribonuclease HI, Vibrioparalog 100 n/a 97 76 97 VC0499a 531411 531205 207, transposaseOrfAB, subunit B 100...”
- Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA
Almagro-Moreno, BMC microbiology 2010 - “...as queries [ 57 ]. The most significant BLAST result in these searches was ORF VC0497, which is annotated as a transcriptional regulator, and is encoded within Vibrio Seventh Pandemic island-II (VSP-II). VSP-II also encodes a tyrosine recombinase integrase at ORF VC0516 (IntV3) [ 58 ]....”
- “...initial search for RDFs within one V. cholerae genome (strain N16961) yielded three putative RDFs (VC0497, VC1785, and VC1809), we decided to investigate further the occurrence of RDFs among Vibrio species whose genome sequence is available in the database. We performed BLAST searches against the 20...”
- Three pathogenicity islands of Vibrio cholerae can excise from the chromosome and form circular intermediates
Murphy, Journal of bacteriology 2008 - “...identified as a 7.5-kb region encompassing ORFs VC0490 to VC0497 and was found exclusively in the V. cholerae El Tor O1 and O139 serogroup isolates (4)....”
- “...in both VPI-2 (VC1785 and VC1809) and VSP-II (VC0497), proteins related to AlpA from E. coli that activate transcription of prophage CP4-57 integrase,...”
- More
VV0810 predicted transcriptional regulator from Vibrio vulnificus YJ016
44% identity, 69% coverage
VIC_001987 helix-turn-helix transcriptional regulator from Vibrio coralliilyticus ATCC BAA-450
48% identity, 71% coverage
A1Q_2003 conserved domain protein from Vibrio harveyi HY01
48% identity, 69% coverage
V12B01_05053 predicted transcriptional regulator from Vibrio splendidus 12B01
49% identity, 66% coverage
AL066_26360 helix-turn-helix transcriptional regulator from Pseudomonas nunensis
47% identity, 69% coverage
- Transcriptomic profiling of microbe-microbe interactions reveals the specific response of the biocontrol strain P. fluorescens In5 to the phytopathogen Rhizoctonia solani
Hennessy, BMC research notes 2017 - “...encoding an Mbth-like protein (AL066_04890) and a downregulated gene encoding a putative AlpA transcriptional regulator (AL066_26360). Interestingly, no transcripts were upregulated more than twofold in R. solani and downregulated more than twofold in P. aphanidermatum or vice versa (Additional file 2 ). Fig.1 Gene expression2log plot...”
- “...1.0 AL066_27880 Cytochrome b 3.5 1.2 AL066_11190 Oxidoreductase 3.0 2.0 AL066_11490 Hypothetical protein 3.0 1.2 AL066_26360 AlpA family transcriptional regulator 3.5 3.3 AL066_11195 Sulfite reductase 3.5 2.0 AL066_13155 NIPSNAP domain containing protein 4.1 1.3 AL066_11200 Cytochrome C oxidase Cbb3 4.3 2.6 AL066_11050 (FeS)-binding protein 4.6 1.7...”
VEA_004310 phage transcriptional regulator AlpA from Vibrio sp. Ex25
54% identity, 58% coverage
XF1786 phage-related protein from Xylella fastidiosa 9a5c
39% identity, 83% coverage
VCG_003160 AlpA family transcriptional regulator from Vibrio cholerae 12129(1)
48% identity, 58% coverage
SEN1998 putative phage regulatory protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SEN_RS10410 helix-turn-helix transcriptional regulator from Salmonella enterica subsp. enterica serovar Enteritidis str.
43% identity, 70% coverage
- SEN1990 is a predicted winged helix-turn-helix protein involved in the pathogenicity of Salmonella enterica serovar Enteritidis and the expression of the gene oafB in the SPI-17
Hoppe-Elsholz, Frontiers in microbiology 2023 - “...(10 8 10 2 total chromosomes), as it naturally lacks ROD21. The copy number of SEN1998 was calculated using a standard curve of the plasmid pET15b- SEN1998 (10 8 10 2 total plasmid copies). Island excision was calculated by the relation: % Excision=100 attB / rpoD...”
- “...in each sample. The relative copy number of ROD21 was calculated by the ratio of SEN1998 copies/ rpoD copies. The relative number of episomal ROD21 copies was calculated by normalizing the Ct of attP to rpoD within a sample and then to the WT strain (control...”
- Bioinformatic and experimental characterization of SEN1998: a conserved gene carried by the Enterobacteriaceae-associated ROD21-like family of genomic islands
Piña-Iturbe, Scientific reports 2022 - “...2045-2322 Nature Publishing Group UK London 8844411 6183 10.1038/s41598-022-06183-x Article Bioinformatic and experimental characterization of SEN1998 : a conserved gene carried by the Enterobacteriaceae -associated ROD21-like family of genomic islands Pia-Iturbe Alejandro 1 Hoppe-Elsholz Guillermo 1 Fernndez Paulina A. 2 Santiviago Carlos A. 2 Gonzlez Pablo...”
- “...-associated ROD21-like family of GIs. Using bioinformatic and experimental approaches, we characterized the conserved gene SEN1998 , showing that it encodes a protein with the features of an RDF that binds to the regulatory regions involved in the excision of ROD21. While deletion or overexpression of...”
- Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands
Piña-Iturbe, Genes 2020 - “...]. The excision process is likely promoted by the products of the genes SEN1970 and SEN1998 , which are predicted to encode a tyrosine recombinase and a putative recombination directionality factor, respectively. Indeed, compared with the wildtype strain, the fraction of bacteria with the excised island...”
- Pathogenicity island excision during an infection by Salmonella enterica serovar Enteritidis is required for crossing the intestinal epithelial barrier in mice to cause systemic infection
Pardo-Roa, PLoS pathogens 2019 - “..., SEN1975 , SEN1976 , SEN1976 , SEN1980 , SEN1982 , SEN1993 , SEN1994 and SEN1998) [ 35 ]. Significant differences were observed in the transcription of genes within ROD21 between strains unable to excise ROD21 and between S . Enteritidis-WT and S . Enteritidis-ROD21::ROD21. As...”
- “...Similar results were obtained in the strain lacking SEN1970 and a RDF coding gene ( SEN1998 ). Unfortunately, we were not able to measure the transcription of ROD21 genes in vivo at 48 or 144hpi on mLN and liver, possibly because the mRNA amount of these...”
- Comparative and phylogenetic analysis of a novel family of Enterobacteriaceae-associated genomic islands that share a conserved excision/integration module
Piña-Iturbe, Scientific reports 2018 - “...island. ( a ) Deletion of the integrase ( SEN1970 ) and putative RDF ( SEN1998 ) coding sequences from Salmonella ser. Enteritis results in impairment ofROD21 excision and reduction in expression of ( b ) SEN1975 , ( c ) SEN1980 and ( d )...”
- “...asnT2-SEN1970 )], respectively; while our mutant strain lacksonly the integrase and putative RDF ( SEN1970 SEN1998 ). Therefore, theabsence of SEN1998 may be causing the different outcome. Previous studies on the Vibrio Pathogenicity Islands 1 and 2, which also have their integrase gene located downstream the...”
- Conjugal transfer of the pathogenicity island ROD21 in Salmonella enterica serovar Enteritidis depends on environmental conditions
Salazar-Echegarai, PloS one 2014 - “...chromosome by site-specific recombination, a process catalyzed by the P4 integrase and a putative excisionase (SEN1998), also encoded in this region [6] , [9] . These enzymes are thought to recognize DRSs that flank the pathogenicity island [10] and produce a circular intermediate, which can either...”
- “...a S. Enteritidis strain that excises ROD21 with higher frequency due to over expression of SEN1998, an ORF that encodes for a putative excisionase. We have previously shown that a strain of S. Enteritidis harboring the plasmid pBAD-SEN1998 showed enhanced ROD21 excision due to arabinose-induced SEN1998...”
- Excision of an unstable pathogenicity island in Salmonella enterica serovar Enteritidis is induced during infection of phagocytic cells
Quiroz, PloS one 2011 - “...95 SEN1997 303 20856602085962 Hypothetical protein (S. Gallinarum and S. Enteritidis). Identities: 100%. c2415 95 SEN1998 219 20860322086250 Phage regulatory protein (Salmonella sp.). Identities: 100%. (Domain: Prophage CP4-57 regulatory protein (AlpA)/Predicted transcriptional regulator [Transcription]) - - SEN1999 876 20864012087276 Hypothetical protein (S. Gallinarum and S. Enteritidis)....”
- Comparative genomics identifies distinct lineages of S. Enteritidis from Queensland, Australia
Graham, PloS one 2018 - “...with 8 of the 25 ROD21 genes in P125109 (SEN_RS10280, SEN_RS10310, SEN_RS10315, SEN_RS10335, SEN_RS10400, SEN_RS10405, SEN_RS10410, SEN_RS10415.) ROD21 was found to be absent in S . Enteritidis belonging to the East and West African clades reported in [ 24 ]. ROD9, which contains genes involved in...”
VC1785 transcriptional regulator from Vibrio cholerae O1 biovar eltor str. N16961
48% identity, 58% coverage
- Virulence of Cholera Toxin Gene-Positive Vibrio cholerae Non-O1/non-O139 Strains Isolated From Environmental Water in Kolkata, India
Takahashi, Frontiers in microbiology 2021 - “...Strain No. 1, between VC0817 and VC0818, between VC1772 and VC1773, between VC 1784 and VC1785; Strain No. 2, between VC0817 and VC0818, between VC0824 and VC0825, between VC 1758 and VC1759, between VC1772 and VC1773; Strain No. 3, between VC0837 and VC0838, between VC1788 and...”
- CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules
Carpenter, Journal of bacteriology 2017 - “...hydrolase DUF2628 Domain Hypothetical protein VefA (VC1785) RadC (VC1786) Hypothetical protein Hypothetical protein GTPase (VC1806) Hypothetical protein...”
- Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome
Carpenter, Journal of bacteriology 2015 - “...intV1 strain harboring pBAintV1 intV2 strain harboring pBAintV2 N16961 VC1785 Smr N16961 VC1809 Smr N16961 VC0497 Smr vefA VC1809 Smr vefA vefB VC0497 Smr vefA...”
- “...We constructed in-frame nonpolar deletions of VC0497 (vefC), VC1785 (vefA), and VC1809 (vefB) in V. cholerae N16961 and examined excision using the attB2...”
- Excision dynamics of Vibrio pathogenicity island-2 from Vibrio cholerae: role of a recombination directionality factor VefA
Almagro-Moreno, BMC microbiology 2010 - “...increased expression of three genes, intV2 (VC1758), and two putative recombination directionality factors (RDFs), vefA (VC1785) and vefB (VC1809) encoded within VPI-2. We demonstrate that along with IntV2, the RDF VefA is essential for excision. We constructed a knockout mutant of vefA in V. cholerae N16961,...”
- “.... A . Schematic representation of VPI-2. Small black vertical arrows mark ORFs VC1758 (IntV2), VC1785 (VefA), or VC1809 (VefB). Block arrows represent ORFs and direction of transcription. Black arrows represent core genome ORFs (VC1757 and VC1810) present in all V. cholerae isolates; red arrow indicates...”
- Three pathogenicity islands of Vibrio cholerae can excise from the chromosome and form circular intermediates
Murphy, Journal of bacteriology 2008 - “...Vis, a recombination directional factor, in both VPI-2 (VC1785 and VC1809) and VSP-II (VC0497), proteins related to AlpA from E. coli that activate...”
- Control of SXT integration and excision
Burrus, Journal of bacteriology 2003 - “...genes were close to ml2429 of M. leprae and vc1785 of V. cholerae, the three genes encoding the other three hypothetical Xis-like proteins were each closely...”
- “...with five hypothetical proteins from V.cholerae (VC1785), M.leprae (ML2429), S.meliloti (SMc02201), M.loti (msr5461), and B.melitensis (BMEI1700). Amino acid...”
FTN_0372 regulatory protein, AlpA family from Francisella tularensis subsp. novicida U112
38% identity, 71% coverage
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...tnfn1_pw060419p01q158 FTN_0357 pal peptidoglycan-associated lipoprotein, OmpA family 2 * tnfn1_pw060510p02q122 FTN_0367 phage integrase 4 tnfn1_pw060328p08q132 FTN_0372 regulatory protein, AlpA family 4 tnfn1_pw060323p07q171 FTN_0585 cutC copper homeostasis protein CutC family protein 2 tnfn1_pw060328p06q127 FTN_0713 ostA2 organic solvent tolerance protein OstA 5 # tnfn1_pw060419p01q180 FTN_0713 ostA2 organic solvent...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...tnfn1_pw060419p01q158 FTN_0357 pal peptidoglycan-associated lipoprotein, OmpA family 2 * tnfn1_pw060510p02q122 FTN_0367 phage integrase 4 tnfn1_pw060328p08q132 FTN_0372 regulatory protein, AlpA family 4 tnfn1_pw060323p07q171 FTN_0585 cutC copper homeostasis protein CutC family protein 2 tnfn1_pw060328p06q127 FTN_0713 ostA2 organic solvent tolerance protein OstA 5 # tnfn1_pw060419p01q180 FTN_0713 ostA2 organic solvent...”
ACG06_13180 AlpA family transcriptional regulator from Pseudomonas aeruginosa
39% identity, 80% coverage
- Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853
Cao, BMC genomics 2017 - “...2,677,091 8578 ACG06_12800- ACG06_12845 Mercuric resistance 2,690,535 2,695,956 5421 ACG06_12920- ACG06_12960 - 2,736,058 2,742,733 6675 ACG06_13180- ACG06_13200 Virulence 3,210,856 3,216,077 5221 ACG06_14975- ACG06_15000 Hydrolase 3,217,225 3,221,802 4577 ACG06_15010- ACG06_15040 Hypothetical protein 3,260,302 3,265,059 4757 ACG06_15285- ACG06_15305 Antibiotics biosynthesis 3,271,888 3,278,016 6128 ACG06_15330- ACG06_15350 Monooxygenase and hydrolase...”
WP_019750501 helix-turn-helix transcriptional regulator from Pseudomonas juntendi
45% identity, 64% coverage
VFA_001914 helix-turn-helix transcriptional regulator from Vibrio furnissii CIP 102972
43% identity, 72% coverage
YPO1904 putative transcriptional regulator from Yersinia pestis CO92
40% identity, 67% coverage
- Structural prediction and mutational analysis of the Gifsy-I Xis protein
Flanigan, BMC microbiology 2008 - “...to bottom are as follows: Shigella flexneri Orf41, Shigella flexineri Rox, P4 Vis, Yersinia Pestis YPO1904, E . coli Z112, Salmonella Typhimurium Gifsy-1 Xis, phage lambda Xis, E . coli phage Phi80 Xis, phage e14 Xis, phage P21 Xis, CP4-57 ALPA. Gifsy-1 Xis possesses limited homology...”
- “...other regions. The aligned proteins, Shigella flexneri Orf41, Shigella flexineri Rox, P4 Vis, Yersinia Pestis YPO1904, E . coli Z112, Salmonella Typhimurium Gifsy-1 Xis, phage Phi80 Xis, CP4-57 ALPA, share limited similarity in the putative helix turn helix (H-T-H) motif ( Gifsy-1 Xis residues C18 to...”
- Excision of the Shigella resistance locus pathogenicity island in Shigella flexneri is stimulated by a member of a new subgroup of recombination directionality factors
Luck, Journal of bacteriology 2004 - “...a new subgroup (Fig. 2). Of the new subgroup, Roxshe, YPO1904, and Vis have been shown experimentally to have a role in excision (10, 20; D. Ghisotti, personal...”
- “...encoded by EHEC EDL933 O islands 43 and 48, respectively. YPO1904, Roxshe, Vis, and AlpA are proteins encoded by the HPIs of Y. pestis, the S. flexneri she PAI,...”
KPK_1789 transcriptional regulator, AlpA family from Klebsiella pneumoniae 342
40% identity, 67% coverage
LPC_0208 prophage CP4-57 regulatory protein AlpA from Legionella pneumophila str. Corby
43% identity, 69% coverage
- Legionella pneumophila pangenome reveals strain-specific virulence factors
D'Auria, BMC genomics 2010 - “...integrase (lpa00270, LPC_0202), an htpX protease (lpa00275, LPC_0205), and a prophage regulatory protein alpA (lpa00278, LPC_0208). In the DT2 island, both strains share a putative RNA helicase (lpa00835, LPC_2785), two putative restriction enzymes (LPC_2788, LPC_2790, lpa00832, and lpa_00829) and the set of the tra and trb...”
KPNJ2_RS09325 helix-turn-helix transcriptional regulator from Klebsiella pneumoniae 30684/NJST258_2
37% identity, 63% coverage
AlpA / b2624 CP4-57 prophage; DNA-binding transcriptional activator AlpA from Escherichia coli K-12 substr. MG1655 (see 5 papers)
ALPA_ECOLI / P33997 DNA-binding transcriptional activator AlpA; Prophage CP4-57 regulatory protein AlpA from Escherichia coli (strain K12) (see 2 papers)
AlpA / EW|b2624 CP4-57 prophage; DNA-binding transcriptional activator from Escherichia coli K12 (see paper)
NP_417113 DNA-binding transcriptional activator AlpA from Escherichia coli str. K-12 substr. MG1655
b2624 CP4-57 prophage; DNA-binding transcriptional activator from Escherichia coli str. K-12 substr. MG1655
37% identity, 62% coverage
- function: Positive regulator of the expression of the slpA gene (PubMed:7511582). When overexpressed, leads to suppression of the capsule overproduction and UV sensitivity phenotypes of cells mutant for the Lon ATP-dependent protease (PubMed:7511582). Part of the cryptic P4-like prophage CP4-57 (PubMed:7511583). Overexpression of AlpA leads to excision of the CP4-57 prophage by IntA. This inactivates ssrA (the gene upstream of the prophage) that encodes tmRNA which is required to rescue stalled ribosomes in a process known as trans- translation (PubMed:7511583).
- The staphylococcal inhibitory protein SPIN binds to human myeloperoxidase with picomolar affinity but only dampens halide oxidation
Leitgeb, The Journal of biological chemistry 2022 - “...10.1016/j.jmb.2007.05.022 17681537 Supporting information Supplemental data Acknowledgments The study was funded by the FWF Project P33997. Author contributions V. P. conceptualization; J. A. B. formal analysis; U. L. investigation; P. G. F. resources; V. P. writingoriginal draft; P. G. F., S. H., and C. O. writingreview...”
- Ferric dicitrate transport system (Fec) of Shigella flexneri 2a YSH6000 is encoded on a novel pathogenicity island carrying multiple antibiotic resistance genes
Luck, Infection and immunity 2001 - “...a b c % Similarityb Protein accession no. 49 45 66 P32053 (U36840) P52124 P33997 73 79 63 70 95 99 99 100 98 98 98 79 79 98 99 99 100 99, 73 93, 92.3 98 100 100...”
- Common and specific characteristics of the high-pathogenicity island of Yersinia enterocolitica
Rakin, Infection and immunity 1999 - “...R73 (G42465) and the prophage CP4-57 protein AlpA (P33997) and 36% similarity to a putative DNA-binding protein (the ORF88 product) of the bacteriophage P4...”
- Dynamics of the SetCD-regulated integration and excision of genomic islands mobilized by integrating conjugative elements of the SXT/R391 family
Daccord, Journal of bacteriology 2012 - “...MUSCLE with the transcriptional regulator AlpA from CP4-57 prophage (NP_417113) and the RDFs Xis encoded by ICEs of the SXT/R391 family (ACV96240), Hef of HPI...”
- In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements
Maciag, Nucleic acids research 2011 - “...derivative of OH157:H7 EDL 933 ( 19 ) alpA CP4-57 prophage gene, regulator of tmRNAs b2624 2.31 Metabolic functions fhuF Iron reductase b4367 1.83 Fur, OxyR ( 84 ) ydhR Putative monooxygenase b1667 1.91 artJ Arginine transporter b0860 2.13 Upregulated in a biofilm-growing rpoS mutant derivative...”
- YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
Herzberg, Journal of bacteriology 2006 - “...4 b0535 4 Phage related alpA intE cspB stfE b2624 b1140 b1557 b1157 Cell processes ampC pphB ibpB ORFs with unknown function yjiP yghG yfjR Description Protein...”
J417_04000 AlpA family transcriptional regulator from Dickeya zeae MS1
33% identity, 73% coverage
C1O30_RS04025, HJ580_03985 AlpA family transcriptional regulator from Dickeya zeae
33% identity, 73% coverage
- Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China
Zhang, Frontiers in plant science 2022 - “...prophage elements. The first specific regions in MS1-GI4 ( J417_03660 J417_04000 ), MS2-GI5 ( C1O30_RS03600 C1O30_RS04025 ), and MS2014-GI5 ( HJ580_03565 HJ580_03985 ) were exactly adjacent to MS1-P2 ( J417_04000 J417_04060 ), MS2-P1 ( C1O30_RS04025 C1O30_RS04090 ), and MS2014-P1 ( HJ580_03985 HJ580_04045 ), respectively. The second...”
- “...in MS1-GI4 ( J417_03660 J417_04000 ), MS2-GI5 ( C1O30_RS03600 C1O30_RS04025 ), and MS2014-GI5 ( HJ580_03565 HJ580_03985 ) were exactly adjacent to MS1-P2 ( J417_04000 J417_04060 ), MS2-P1 ( C1O30_RS04025 C1O30_RS04090 ), and MS2014-P1 ( HJ580_03985 HJ580_04045 ), respectively. The second specific regions in MS1-GI26 ( J417_13900...”
AchV4_0082 excisionase and transcriptional regulator from Achromobacter phage vB_AchrS_AchV4
36% identity, 64% coverage
PMI2608 prophage regulatory protein from Proteus mirabilis HI4320
45% identity, 66% coverage
ECs1575 putative DNA binding protein from Escherichia coli O157:H7 str. Sakai
46% identity, 58% coverage
RSc1897 HYPOTHETICAL PROTEIN from Ralstonia solanacearum GMI1000
38% identity, 62% coverage
A79_5463 conserved domain protein from Vibrio parahaemolyticus AQ3810
A79_2541 conserved domain protein from Vibrio parahaemolyticus AQ3810
39% identity, 63% coverage
SO_4821 helix-turn-helix transcriptional regulator from Shewanella oneidensis MR-1
35% identity, 63% coverage
Z1124 putative prophage regulatory protein from Escherichia coli O157:H7 EDL933
Z1563 putative prophage regulatory protein from Escherichia coli O157:H7 EDL933
38% identity, 51% coverage
- Excision of the Shigella resistance locus pathogenicity island in Shigella flexneri is stimulated by a member of a new subgroup of recombination directionality factors
Luck, Journal of bacteriology 2004 - “...(EHEC) strain O157:H7 EDL933 has revealed AlpA homologues, Z1124 and Z1563, on duplicate O islands 43 and 48, which have an integrase nearly identical...”
- “...with Dodd and Egan scores (5) for RoxSRL, AlpA, Vis, EHEC Z1124 or Z1563, and YP01904 of 6.35, 3.98, 5.25, 4.94, and 3.45, respectively, where a value of 2.5 is...”
- Excision of the Shigella resistance locus pathogenicity island in Shigella flexneri is stimulated by a member of a new subgroup of recombination directionality factors
Luck, Journal of bacteriology 2004 - “...strain O157:H7 EDL933 has revealed AlpA homologues, Z1124 and Z1563, on duplicate O islands 43 and 48, which have an integrase nearly identical with that...”
- “...Egan scores (5) for RoxSRL, AlpA, Vis, EHEC Z1124 or Z1563, and YP01904 of 6.35, 3.98, 5.25, 4.94, and 3.45, respectively, where a value of 2.5 is indicative of...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
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.
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