Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   DNO_RS05560 Genome accession   NC_009446
Coordinates   1172401..1174095 (-) Length   564 a.a.
NCBI ID   WP_012031430.1    Uniprot ID   A5EXL7
Organism   Dichelobacter nodosus VCS1703A     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 1173847..1217603 1172401..1174095 flank -248


Gene organization within MGE regions


Location: 1172401..1217603
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DNO_RS05560 (DNO_1126) pilB 1172401..1174095 (-) 1695 WP_012031430.1 type IV-A pilus assembly ATPase PilB Machinery gene
  DNO_RS05565 (DNO_1127) - 1174092..1174691 (-) 600 WP_187145767.1 aminodeoxychorismate/anthranilate synthase component II -
  DNO_RS05570 (DNO_1128) - 1174756..1175445 (+) 690 WP_012031432.1 recombination protein O N-terminal domain-containing protein -
  DNO_RS05575 (DNO_1129) rplM 1175668..1176099 (+) 432 WP_012031433.1 50S ribosomal protein L13 -
  DNO_RS05580 (DNO_1130) rpsI 1176109..1176498 (+) 390 WP_012031434.1 30S ribosomal protein S9 -
  DNO_RS05585 (DNO_1131) xerD 1176567..1177460 (-) 894 WP_012031435.1 site-specific tyrosine recombinase XerD -
  DNO_RS05590 (DNO_1132) - 1177536..1178867 (+) 1332 WP_012031436.1 Gldg family protein -
  DNO_RS05595 (DNO_1133) - 1178864..1179313 (+) 450 WP_012031437.1 hypothetical protein -
  DNO_RS05600 (DNO_1135) mutM 1179306..1180124 (+) 819 WP_012031438.1 bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase -
  DNO_RS05605 (DNO_1134) truD 1180081..1181100 (-) 1020 WP_012031439.1 tRNA pseudouridine(13) synthase TruD -
  DNO_RS05610 (DNO_1136) - 1181108..1183228 (-) 2121 WP_012031440.1 3-hydroxyacyl-CoA dehydrogenase family protein -
  DNO_RS05615 (DNO_1137) - 1183286..1185004 (-) 1719 WP_012031441.1 proline--tRNA ligase -
  DNO_RS05620 (DNO_1138) - 1185174..1185674 (-) 501 WP_012031442.1 hypothetical protein -
  DNO_RS05625 (DNO_1139) - 1185811..1186383 (-) 573 WP_012031443.1 hypothetical protein -
  DNO_RS05630 (DNO_1140) glmU 1186433..1187833 (-) 1401 WP_012031444.1 bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU -
  DNO_RS05635 (DNO_1141) - 1187959..1188393 (-) 435 WP_228369804.1 F0F1 ATP synthase subunit epsilon -
  DNO_RS05640 (DNO_1142) atpD 1188402..1189793 (-) 1392 WP_012031446.1 F0F1 ATP synthase subunit beta -
  DNO_RS05645 (DNO_1143) atpG 1189816..1190685 (-) 870 WP_012031447.1 F0F1 ATP synthase subunit gamma -
  DNO_RS05650 (DNO_1144) atpA 1190695..1192236 (-) 1542 WP_012031448.1 F0F1 ATP synthase subunit alpha -
  DNO_RS05655 (DNO_1145) - 1192238..1192792 (-) 555 WP_012031449.1 F0F1 ATP synthase subunit delta -
  DNO_RS05660 (DNO_1146) - 1192794..1193264 (-) 471 WP_012031450.1 F0F1 ATP synthase subunit B -
  DNO_RS05665 (DNO_1147) atpE 1193301..1193588 (-) 288 WP_012031451.1 F0F1 ATP synthase subunit C -
  DNO_RS05670 (DNO_1148) atpB 1193624..1194415 (-) 792 WP_012031452.1 F0F1 ATP synthase subunit A -
  DNO_RS07060 - 1194420..1194767 (-) 348 WP_123962261.1 hypothetical protein -
  DNO_RS05680 (DNO_1149) - 1194816..1195685 (-) 870 WP_012031453.1 ParB/RepB/Spo0J family partition protein -
  DNO_RS05685 (DNO_1150) rsmG 1195720..1196355 (-) 636 WP_012031454.1 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG -
  DNO_RS05690 (DNO_1151) - 1196348..1197829 (-) 1482 WP_012031455.1 leucyl aminopeptidase -
  DNO_RS05695 (DNO_1152) lptF 1197957..1199006 (+) 1050 WP_012031456.1 LPS export ABC transporter permease LptF -
  DNO_RS05700 (DNO_1153) lptG 1199003..1200052 (+) 1050 WP_012031457.1 LPS export ABC transporter permease LptG -
  DNO_RS05705 (DNO_1154) - 1200123..1200362 (-) 240 WP_012031458.1 accessory factor UbiK family protein -
  DNO_RS05710 (DNO_1155) - 1200411..1201934 (-) 1524 WP_164083955.1 DUF945 family protein -
  DNO_RS05715 (DNO_1157) - 1202175..1203980 (+) 1806 WP_012031461.1 potassium/proton antiporter -
  DNO_RS05720 (DNO_1158) - 1204040..1204384 (+) 345 WP_012031462.1 DMT family protein -
  DNO_RS05725 (DNO_1159) - 1204402..1206606 (+) 2205 WP_012031463.1 Tex family protein -
  DNO_RS05730 (DNO_1161) - 1206603..1207430 (+) 828 WP_012031464.1 Dam family site-specific DNA-(adenine-N6)-methyltransferase -
  DNO_RS05735 (DNO_1160) - 1207427..1208068 (-) 642 WP_012031465.1 BPL-N domain-containing protein -
  DNO_RS05740 (DNO_1162) - 1208219..1208782 (+) 564 WP_012031466.1 biotin transporter BioY -
  DNO_RS05745 (DNO_1163) trmA 1208820..1209905 (-) 1086 WP_012031467.1 tRNA (uridine(54)-C5)-methyltransferase TrmA -
  DNO_RS05750 (DNO_1164) - 1209909..1210739 (-) 831 WP_041729610.1 hypothetical protein -
  DNO_RS05755 (DNO_1165) - 1210835..1214431 (+) 3597 WP_012031469.1 UvrD-helicase domain-containing protein -
  DNO_RS05760 (DNO_1166) - 1214476..1214832 (-) 357 WP_012031470.1 hypothetical protein -
  DNO_RS05765 (DNO_1167) - 1215097..1216902 (-) 1806 WP_012031471.1 S8 family serine peptidase -

Sequence

Protein


Download         Length: 564 a.a.        Molecular weight: 62559.73 Da        Isoelectric Point: 5.1638

>NTDB_id=28056 DNO_RS05560 WP_012031430.1 1172401..1174095(-) (pilB) [Dichelobacter nodosus VCS1703A]
MSEYDELIAYMVKNKVATPEQLKEVQISVQKKRGNFLQQLLSDGLLDASKLSKINREVYNLPIVALRELNIRRELTAQFK
EAVVRKHTAMPVYANGGRLFIATIDPNNRSMLEEFKYQGKFTSVEPIIANLDAIEALIEEHYAGLGGMDDLFDDETEEKD
LDAISNALGGLDANEEEAPVVRFVTGMLLDAIRTGASDLHFEPYETTYRVRFRRDGVLQEVAAPPPSIATRITARLKVMA
DLDIAEKRVPQDGRIKLYVSDTKAIDFRVNSLPTLWGEKIVLRILDSSAAKLNIEILGFEPDQKQQYLDAISKPQGLVLV
TGPTGSGKTVSLYTGLNILNKPTVNISTAEDPVEINLPGINQVNVNPKTGLDFSAALKAFLRQDPDIIMVGEIRDITTAE
IAVKAAQTGHLVLSTLHTNDVPQTIARLVNIGIEPYNIAASVNLIMAQRLARRLCNNCKIRDRKHHTEELLALGFHEEDL
DDLKIYAPKGCERCSYQGYRGRAGIYQVVPISEAIAELILKNASAAEIAEQCLKEGYLDLRQAALNKVKQGLTSIEEVLR
VTSE

Nucleotide


Download         Length: 1695 bp        

>NTDB_id=28056 DNO_RS05560 WP_012031430.1 1172401..1174095(-) (pilB) [Dichelobacter nodosus VCS1703A]
ATGAGTGAGTATGATGAACTGATTGCCTATATGGTAAAAAATAAGGTGGCAACGCCTGAGCAGCTGAAGGAAGTACAAAT
CAGCGTGCAGAAAAAACGGGGCAATTTTTTGCAACAGTTATTAAGCGATGGTTTGCTTGATGCCAGTAAATTGTCAAAAA
TTAATCGGGAAGTTTATAACTTGCCGATCGTTGCTTTGCGTGAATTAAATATTCGTCGGGAATTAACAGCGCAGTTTAAA
GAAGCGGTGGTGCGCAAACATACCGCAATGCCGGTTTATGCCAACGGCGGACGTTTATTTATCGCTACCATCGATCCCAA
TAACCGCAGCATGCTGGAAGAGTTTAAATATCAAGGTAAATTTACTTCCGTTGAGCCGATTATCGCTAATCTTGACGCCA
TCGAAGCCTTGATTGAAGAGCACTATGCAGGGCTCGGCGGCATGGACGATTTGTTTGATGATGAAACGGAAGAAAAAGAT
TTAGATGCAATCAGTAATGCGTTAGGTGGGCTGGACGCAAACGAAGAAGAAGCGCCGGTGGTGCGTTTTGTAACGGGAAT
GCTGTTAGATGCTATTCGAACTGGTGCTTCCGACTTGCACTTTGAACCTTATGAAACCACTTATCGCGTACGTTTTCGCC
GTGACGGTGTATTGCAAGAAGTAGCAGCGCCGCCACCAAGCATCGCAACGCGTATTACCGCGCGTTTAAAAGTTATGGCG
GATTTGGATATTGCCGAAAAACGGGTACCGCAGGACGGACGGATTAAGCTTTACGTATCCGATACAAAAGCCATCGACTT
CCGGGTGAACTCGTTACCAACTTTGTGGGGTGAGAAAATTGTTCTGCGGATTTTGGACAGTTCCGCTGCCAAATTGAATA
TTGAAATTCTTGGTTTTGAGCCTGATCAAAAACAACAATATTTAGATGCCATTTCTAAACCGCAGGGTTTGGTTTTGGTA
ACGGGACCGACGGGATCCGGTAAAACCGTTTCTTTATACACCGGATTAAATATCCTCAATAAACCAACGGTTAATATTTC
TACCGCTGAAGACCCTGTGGAAATTAACTTACCAGGAATTAATCAGGTTAACGTAAACCCGAAAACCGGTTTGGACTTCT
CTGCCGCCTTGAAAGCGTTCTTACGGCAAGACCCTGACATCATCATGGTTGGGGAAATTCGGGATATCACTACTGCTGAA
ATCGCGGTTAAAGCAGCACAAACAGGGCACTTGGTGTTATCAACTTTGCACACCAACGACGTGCCGCAAACCATTGCGCG
TTTAGTTAATATCGGAATTGAACCTTACAACATTGCCGCTTCCGTAAACTTGATTATGGCGCAGCGGTTGGCAAGGCGTT
TGTGCAATAACTGCAAAATTAGGGATCGTAAACACCACACTGAAGAATTGCTTGCTTTAGGTTTCCATGAAGAAGATTTG
GACGATTTGAAAATTTATGCTCCTAAAGGGTGTGAACGCTGCAGTTATCAAGGTTATCGCGGTCGGGCGGGGATTTACCA
AGTGGTTCCCATTTCGGAGGCGATTGCGGAATTGATTTTGAAAAATGCTTCCGCTGCCGAAATTGCAGAGCAATGTTTAA
AAGAAGGCTATCTTGATTTGCGCCAAGCAGCGTTGAATAAAGTCAAGCAAGGGCTGACCAGTATCGAAGAAGTGTTACGT
GTAACGAGCGAATAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(187-453)

Type II secretion system (T2SS), protein E, N-terminal domain (MshEN)

(40-144)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A5EXL7

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  pilB Acinetobacter baumannii D1279779

55.601

87.057

0.484
  pilB Acinetobacter baylyi ADP1

54.728

88.121

0.482
  pilF Neisseria gonorrhoeae MS11

48.736

98.227

0.479
  pilB Legionella pneumophila strain ERS1305867

48.987

96.277

0.472
  pilB Vibrio cholerae strain A1552

45.122

100

0.459
  pilB Vibrio campbellii strain DS40M4

45.741

95.745

0.438
  pilB Vibrio parahaemolyticus RIMD 2210633

46.869

93.44

0.438
  pilB/pilB1 Synechocystis sp. PCC 6803

40.909

93.617

0.383
  pilF Thermus thermophilus HB27

37.968

99.468

0.378

Multiple sequence alignment