Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SBAL678_RS43955 Genome accession   NC_016901
Coordinates   4740584..4742296 (+) Length   570 a.a.
NCBI ID   WP_006084368.1    Uniprot ID   -
Organism   Shewanella baltica OS678     
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 4732481..4781958 4740584..4742296 within 0


Gene organization within MGE regions


Location: 4732481..4781958
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SBAL678_RS43925 (Sbal678_4087) aceE 4732930..4735596 (-) 2667 WP_006083344.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  SBAL678_RS43930 (Sbal678_4088) pdhR 4735678..4736430 (-) 753 WP_006083345.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  SBAL678_RS43935 (Sbal678_4089) ampE 4736670..4737521 (-) 852 WP_006083346.1 beta-lactamase regulator AmpE -
  SBAL678_RS43940 (Sbal678_4090) ampD 4737591..4738154 (-) 564 WP_012197706.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SBAL678_RS43945 (Sbal678_4091) nadC 4738425..4739306 (+) 882 WP_006083348.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SBAL678_RS43950 (Sbal678_4092) - 4740023..4740478 (+) 456 WP_006084367.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  SBAL678_RS43955 (Sbal678_4093) pilB 4740584..4742296 (+) 1713 WP_006084368.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SBAL678_RS43960 (Sbal678_4094) pilC 4742445..4743716 (+) 1272 WP_006084369.1 type II secretion system F family protein Machinery gene
  SBAL678_RS43965 (Sbal678_4095) pilD 4743755..4744669 (+) 915 WP_006084370.1 A24 family peptidase Machinery gene
  SBAL678_RS43970 (Sbal678_4096) coaE 4744709..4745326 (+) 618 WP_006084371.1 dephospho-CoA kinase -
  SBAL678_RS43975 (Sbal678_4097) zapD 4745319..4746053 (+) 735 WP_006084372.1 cell division protein ZapD -
  SBAL678_RS43980 (Sbal678_4098) yacG 4746127..4746336 (+) 210 WP_006083355.1 DNA gyrase inhibitor YacG -
  SBAL678_RS43985 (Sbal678_4099) mutT 4746413..4746805 (+) 393 WP_006084373.1 8-oxo-dGTP diphosphatase MutT -
  SBAL678_RS43990 (Sbal678_4100) - 4747362..4747898 (+) 537 WP_006084374.1 thioredoxin family protein -
  SBAL678_RS43995 (Sbal678_4101) - 4747963..4748889 (-) 927 WP_006084375.1 exopolyphosphatase -
  SBAL678_RS44000 (Sbal678_4102) rhlB 4748890..4750206 (-) 1317 WP_006084377.1 ATP-dependent RNA helicase RhlB -
  SBAL678_RS44005 (Sbal678_4103) trxA 4750359..4750685 (+) 327 WP_006083360.1 thioredoxin TrxA -
  SBAL678_RS44010 (Sbal678_4104) rho 4750895..4752160 (+) 1266 WP_006083361.1 transcription termination factor Rho -
  SBAL678_RS44015 (Sbal678_4105) - 4752216..4753142 (-) 927 WP_006084378.1 LysR family transcriptional regulator -
  SBAL678_RS44020 (Sbal678_4106) - 4753277..4754299 (+) 1023 WP_006084380.1 zinc-binding alcohol dehydrogenase family protein -
  SBAL678_RS44025 (Sbal678_4107) - 4754296..4754580 (+) 285 WP_006084381.1 putative quinol monooxygenase -
  SBAL678_RS44030 (Sbal678_4108) - 4754629..4755360 (-) 732 WP_006084382.1 fumarate reductase iron-sulfur subunit -
  SBAL678_RS44035 (Sbal678_4109) - 4755360..4757366 (-) 2007 WP_012197707.1 fumarate reductase flavoprotein subunit -
  SBAL678_RS44040 (Sbal678_4110) - 4757476..4758147 (-) 672 WP_006084385.1 fumarate reductase cytochrome b subunit -
  SBAL678_RS44045 (Sbal678_4111) - 4758320..4759042 (-) 723 WP_006084386.1 fumarate reductase cytochrome b subunit -
  SBAL678_RS44050 (Sbal678_4112) prmA 4759427..4760308 (+) 882 WP_012197708.1 50S ribosomal protein L11 methyltransferase -
  SBAL678_RS44055 (Sbal678_4113) dusB 4760483..4761451 (+) 969 WP_006083370.1 tRNA dihydrouridine synthase DusB -
  SBAL678_RS44060 (Sbal678_4114) fis 4761468..4761773 (+) 306 WP_006083371.1 DNA-binding transcriptional regulator Fis -
  SBAL678_RS44065 (Sbal678_4115) - 4762116..4765106 (+) 2991 WP_012197709.1 UvrD-helicase domain-containing protein -
  SBAL678_RS44070 (Sbal678_4116) ric 4765335..4766144 (+) 810 WP_012197710.1 iron-sulfur cluster repair di-iron protein -
  SBAL678_RS44075 (Sbal678_4117) - 4766277..4766780 (+) 504 WP_012197711.1 helix-turn-helix domain-containing protein -
  SBAL678_RS44080 (Sbal678_4118) - 4766810..4767388 (-) 579 WP_012090405.1 HupE/UreJ family protein -
  SBAL678_RS44085 (Sbal678_4119) - 4767512..4768243 (-) 732 WP_006083419.1 HAD-IA family hydrolase -
  SBAL678_RS44090 (Sbal678_4120) xerC 4768243..4769163 (-) 921 WP_012197712.1 tyrosine recombinase XerC -
  SBAL678_RS44095 (Sbal678_4121) - 4769221..4769850 (-) 630 WP_011848049.1 DUF484 family protein -
  SBAL678_RS44100 (Sbal678_4122) dapF 4769847..4770674 (-) 828 WP_006083422.1 diaminopimelate epimerase -
  SBAL678_RS44105 (Sbal678_4123) lysA 4770750..4771994 (-) 1245 WP_006084396.1 diaminopimelate decarboxylase -
  SBAL678_RS44110 (Sbal678_4124) - 4772058..4772249 (-) 192 WP_006083425.1 lipoprotein -
  SBAL678_RS44115 (Sbal678_4125) cyaY 4772329..4772658 (+) 330 WP_006083426.1 iron donor protein CyaY -
  SBAL678_RS44120 (Sbal678_4126) - 4772743..4775154 (-) 2412 WP_012197714.1 class I adenylate cyclase -
  SBAL678_RS44125 (Sbal678_4127) hemC 4775357..4776289 (+) 933 WP_012197715.1 hydroxymethylbilane synthase -
  SBAL678_RS44130 (Sbal678_4128) - 4776294..4777034 (+) 741 WP_012197716.1 uroporphyrinogen-III synthase -
  SBAL678_RS44135 (Sbal678_4129) - 4777095..4778276 (+) 1182 WP_012197717.1 uroporphyrinogen-III C-methyltransferase -
  SBAL678_RS44140 (Sbal678_4130) - 4778273..4779439 (+) 1167 WP_012197718.1 heme biosynthesis HemY N-terminal domain-containing protein -

Sequence

Protein


Download         Length: 570 a.a.        Molecular weight: 62818.24 Da        Isoelectric Point: 6.1229

>NTDB_id=43948 SBAL678_RS43955 WP_006084368.1 4740584..4742296(+) (pilB) [Shewanella baltica OS678]
MPTTGLHLGLSTLFIRKGLLNEEQMANAITKSRQNKHALVSTLVQSQLVSARAIAELCYEEYGTPLLDLNEFDLASIPED
FLNKKLIEKHRCLPLFKRGNRLYIGTSDPTNIAALEDFQFSAGLHAEAILVEEDKLAKALEKILEEDISGLDLGGMDEAA
LAAIEITDTDRRSEESTGESSDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPISLAGRLSA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTLWGEKIVMRILDSSSAQLGIEKLGYEPDQEKLYLEMLAKP
QGMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPECKQAEVIPEHELLRLGF
AQAQITQGFTTFKPIGCEHCSAGYKGRVGIYEVMKMSDEIARTIMEGGNSLQIASQAKAQGMRDLRQSGLLKVIHGVTSI
AEVNRVTSFG

Nucleotide


Download         Length: 1713 bp        

>NTDB_id=43948 SBAL678_RS43955 WP_006084368.1 4740584..4742296(+) (pilB) [Shewanella baltica OS678]
ATGCCTACTACAGGCTTGCATTTAGGTTTATCGACCCTTTTTATCCGCAAAGGTCTGCTAAATGAAGAGCAGATGGCTAA
CGCCATCACTAAATCCCGTCAAAACAAACACGCCCTTGTAAGCACTTTAGTTCAAAGTCAGCTGGTCTCTGCCCGTGCAA
TAGCCGAGCTTTGCTACGAAGAATACGGCACACCATTACTCGATCTTAATGAGTTTGATCTTGCATCAATTCCTGAAGAT
TTCCTCAATAAGAAACTCATTGAGAAACACCGTTGTTTACCCTTATTTAAACGCGGGAATCGCCTCTATATCGGCACATC
CGACCCGACCAACATTGCAGCCCTCGAAGACTTTCAATTTAGTGCAGGGCTGCATGCCGAAGCCATTCTGGTTGAAGAGG
ATAAACTTGCTAAGGCGCTGGAAAAAATTCTCGAAGAAGATATCAGCGGTCTCGATTTAGGCGGCATGGACGAAGCTGCG
CTGGCAGCGATAGAAATTACTGATACCGACAGACGTAGCGAAGAGTCTACTGGTGAGAGTAGTGACGATGCGCCTATTGT
TATCTATATCAATAAAATTTTAACCGATGCCATCCGCAAAGGTGCGTCAGATTTACACTTTGAACCCTATGAGAAACGCT
ACCGCATACGGTTTCGCATTGACGGTATTCTGCACGAAGTCTCTGAACCGCCGATTAGCCTCGCTGGTCGTTTATCGGCA
CGACTAAAGGTAATGTCGAAACTCGATATCGCCGAACGGCGCGTGCCGCAGGATGGTCGAATTAAGATGAAGCTTTCCCG
CACTAAATCTATCGACTTTCGGGTAAGTACCTTGCCGACGCTCTGGGGTGAAAAGATTGTAATGCGGATTTTGGACTCAT
CCTCCGCACAATTGGGCATTGAAAAGCTCGGTTACGAACCCGACCAAGAAAAGCTCTACCTTGAGATGCTAGCAAAGCCC
CAAGGGATGATTTTAGTGACCGGCCCTACGGGCTCAGGTAAAACCGTCTCCCTTTACACTGGGTTAAATATTCTCAATAC
AGAAGAGCGTAATATTTCTACCGCTGAAGATCCGGTTGAGATTAACCTTGAGGGTGTAAACCAAGTTCACATTAATTTAA
AGGCAGGGCTAACCTTCGCGTCCGCTTTACGTTCATTTCTACGCCAAGACCCCGATGTGGTGATGGTCGGGGAAATCCGC
GATCTTGAAACTGCAGAGATTGCCATTAAAGCGGCGCAAACGGGTCACTTAGTCTTATCAACCTTGCATACTAACTCGGC
AGCCGAAACCTTAACCCGTTTAATCAATATGGGTGTTCCAGGCTACAACATAGCTAGCTCTGTGAATCTGATTATTGCCC
AGCGCTTAGCGCGTCGTCTATGCCCCGAATGTAAACAAGCGGAAGTGATCCCCGAGCATGAATTACTTCGTCTAGGTTTT
GCCCAAGCACAAATTACTCAGGGCTTTACCACCTTTAAACCCATTGGCTGCGAACATTGCTCTGCAGGCTACAAGGGACG
GGTTGGCATTTATGAAGTGATGAAAATGTCTGACGAAATAGCCCGCACTATCATGGAAGGGGGGAACTCTTTACAAATCG
CCTCCCAAGCTAAAGCGCAAGGAATGCGGGATTTGCGTCAATCGGGATTATTGAAAGTGATCCACGGTGTTACTAGCATT
GCAGAAGTCAATCGCGTCACAAGTTTTGGCTAA

Domains

Predicted by InterproScan.

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

(43-144)

Type II/IV secretion system protein (T2SSE)

(192-459)


Secondary structure

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



3D structure

Source ID Structure

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 baylyi ADP1

59.18

98.421

0.582
  pilB Acinetobacter baumannii D1279779

58.899

95.614

0.563
  pilB Legionella pneumophila strain ERS1305867

55.872

98.596

0.551
  pilB Vibrio cholerae strain A1552

53.514

97.368

0.521
  pilB Vibrio parahaemolyticus RIMD 2210633

51.573

100

0.518
  pilB Vibrio campbellii strain DS40M4

51.327

99.123

0.509
  pilF Neisseria gonorrhoeae MS11

46.996

99.298

0.467
  pilF Thermus thermophilus HB27

39.046

99.298

0.388
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.71

97.895

0.379

Multiple sequence alignment