Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LCH15_RS04025 Genome accession   NZ_CP083938
Coordinates   889105..890847 (-) Length   580 a.a.
NCBI ID   WP_224649839.1    Uniprot ID   -
Organism   Comamonas thiooxydans strain CSUSB4     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 884105..895847
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LCH15_RS03995 (LCH15_03995) - 884620..885090 (+) 471 WP_052052682.1 NUDIX domain-containing protein -
  LCH15_RS04000 (LCH15_04000) - 885208..885417 (-) 210 WP_034357520.1 DNA gyrase inhibitor YacG -
  LCH15_RS04005 (LCH15_04005) zapD 885521..886276 (-) 756 WP_003062189.1 cell division protein ZapD -
  LCH15_RS04010 (LCH15_04010) coaE 886364..886990 (-) 627 WP_034357524.1 dephospho-CoA kinase -
  LCH15_RS04015 (LCH15_04015) - 886994..887863 (-) 870 WP_224649837.1 A24 family peptidase -
  LCH15_RS04020 (LCH15_04020) pilC 887863..889080 (-) 1218 WP_012837103.1 type II secretion system F family protein Machinery gene
  LCH15_RS04025 (LCH15_04025) pilB 889105..890847 (-) 1743 WP_224649839.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LCH15_RS04035 (LCH15_04035) - 891101..892030 (-) 930 WP_003062198.1 polyprenyl synthetase family protein -
  LCH15_RS04040 (LCH15_04040) rplU 892373..892684 (+) 312 WP_003058536.1 50S ribosomal protein L21 -
  LCH15_RS04045 (LCH15_04045) rpmA 892701..892958 (+) 258 WP_003058534.1 50S ribosomal protein L27 -
  LCH15_RS04050 (LCH15_04050) cgtA 893115..894230 (+) 1116 WP_034357529.1 Obg family GTPase CgtA -
  LCH15_RS04055 (LCH15_04055) proB 894341..895480 (+) 1140 WP_034381631.1 glutamate 5-kinase -

Sequence

Protein


Download         Length: 580 a.a.        Molecular weight: 63125.37 Da        Isoelectric Point: 5.2384

>NTDB_id=608622 LCH15_RS04025 WP_224649839.1 889105..890847(-) (pilB) [Comamonas thiooxydans strain CSUSB4]
MAAADTLQKNTPAPIAIPGLGRALISAGKVSQQAAENAAKKAATGKTPFITELSQSGEISALEIAETISMMFSTPLLDLN
AIDVQQLPRELLDPKISNAYRVLALSKRGNRLTIATADPTQQEAAEQIKFTTQLLVDWVVVEADKLQKLVEQTGKSVSES
LDTYSSSGDFDFDDVKIEDAPEEKDNAVGAEVEDAPVVKFLHKMLLDAFNMRASDLHFEPYEHNYRVRFRIDGELREIAS
PPIAIKDKLASRIKVISRLDISEKRVPQDGRMKLKVGPDRVIDFRVSTLPTLFGEKIVIRILDPSSAKMGIDALGYEPEE
KERLLKAINRPYGMILVTGPTGSGKTVSLYTCLNLLNQPGVNIATAEDPSEINMPGVNQVNVNEKAGLTFAAALKSFLRQ
DPDIIMVGEIRDLETADISIKAAQTGHLVLSTLHTNDAPTTLTRMRNMGIAPFNIASSVILITAQRLARRLCAHCKEPAD
IPHDALIDAGYDEAELDGSWVSYKPVGCPACNNGYKGRVGIYQVMPISEEIQRIILRDGSALEIAAQAKAEGVRSLRGSG
LHKVKLGLTSLEEVLAVTNE

Nucleotide


Download         Length: 1743 bp        

>NTDB_id=608622 LCH15_RS04025 WP_224649839.1 889105..890847(-) (pilB) [Comamonas thiooxydans strain CSUSB4]
ATGGCTGCTGCCGACACTCTGCAAAAGAACACTCCTGCGCCCATTGCCATCCCAGGTTTAGGCAGGGCCCTGATTTCCGC
AGGAAAGGTTTCGCAGCAAGCCGCCGAGAACGCAGCCAAGAAAGCCGCCACAGGCAAGACCCCGTTCATCACCGAGCTCA
GCCAGTCTGGTGAAATCAGCGCGCTGGAAATTGCCGAAACCATTTCCATGATGTTCAGCACTCCGCTGCTGGACCTCAAC
GCCATCGACGTCCAGCAACTTCCGCGCGAGCTGCTGGACCCGAAAATCAGCAACGCCTATCGCGTGCTGGCACTCAGCAA
GCGCGGCAATCGGCTCACCATCGCCACGGCAGACCCTACTCAGCAGGAAGCTGCCGAACAGATCAAATTCACGACTCAGT
TGCTGGTGGACTGGGTGGTTGTCGAGGCCGACAAGCTGCAAAAGCTCGTCGAGCAGACCGGCAAGAGCGTCAGCGAATCT
CTGGACACCTATTCCAGTTCTGGAGACTTTGACTTTGACGACGTCAAGATCGAGGATGCCCCCGAGGAAAAAGACAATGC
CGTCGGCGCCGAGGTCGAAGATGCGCCGGTCGTCAAGTTTCTGCACAAGATGCTGCTGGACGCCTTCAATATGCGCGCGT
CCGACTTGCACTTCGAGCCCTACGAACACAATTACCGCGTGCGCTTTCGTATCGACGGCGAGCTGCGCGAGATTGCCTCT
CCACCGATTGCGATCAAGGACAAGCTGGCTTCGCGCATCAAGGTGATCTCGCGCCTGGACATCTCGGAGAAACGCGTTCC
GCAAGACGGCCGCATGAAGCTCAAGGTCGGCCCTGATCGCGTCATCGACTTTCGTGTCAGCACCTTGCCCACGCTGTTTG
GCGAAAAGATCGTGATCCGTATTCTGGACCCGAGCTCGGCCAAGATGGGCATCGATGCCCTCGGCTACGAACCCGAGGAA
AAAGAGCGCCTGCTCAAGGCCATCAACCGGCCCTACGGCATGATTCTGGTTACCGGCCCCACGGGCTCGGGCAAGACCGT
GTCGCTCTACACCTGCCTGAACCTGCTCAACCAGCCGGGCGTGAACATTGCCACCGCCGAAGACCCTTCCGAAATCAACA
TGCCCGGCGTCAACCAGGTGAATGTGAACGAGAAGGCCGGCCTGACTTTTGCTGCTGCGCTCAAGTCCTTTCTGCGCCAG
GATCCGGACATCATCATGGTCGGTGAAATCCGCGACCTGGAAACCGCCGACATCTCGATCAAGGCCGCCCAGACCGGGCA
CCTGGTGCTGTCCACGCTGCACACCAATGACGCTCCGACCACGCTGACGCGCATGCGCAATATGGGCATCGCCCCTTTCA
ATATTGCCTCCAGCGTGATCCTGATCACCGCCCAGCGTCTGGCACGACGCCTGTGCGCGCATTGCAAGGAACCCGCCGAC
ATACCGCACGACGCCCTGATCGATGCCGGCTACGACGAAGCCGAACTCGACGGCAGCTGGGTCAGCTACAAGCCTGTCGG
CTGCCCTGCCTGCAACAACGGCTACAAGGGACGTGTCGGTATTTATCAGGTGATGCCCATCAGCGAAGAAATTCAGCGCA
TCATCCTGCGTGACGGCAGCGCCCTGGAGATTGCCGCACAGGCCAAGGCCGAGGGAGTACGCTCTCTGCGCGGCTCGGGC
CTGCATAAAGTCAAGCTGGGTCTGACCTCACTCGAAGAAGTGCTGGCGGTCACCAACGAATAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(203-470)

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

(55-153)


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

54.355

98.966

0.538
  pilB Acinetobacter baumannii D1279779

55.026

97.759

0.538
  pilF Neisseria gonorrhoeae MS11

52.473

97.586

0.512
  pilB Legionella pneumophila strain ERS1305867

50.883

97.586

0.497
  pilB Vibrio cholerae strain A1552

47.08

94.483

0.445
  pilB Vibrio campbellii strain DS40M4

44.029

96.724

0.426
  pilB Vibrio parahaemolyticus RIMD 2210633

46.038

91.379

0.421
  pilF Thermus thermophilus HB27

37.925

100

0.384
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.421

98.276

0.378