Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   JDW18_RS04120 Genome accession   NZ_CP066783
Coordinates   826615..828357 (-) Length   580 a.a.
NCBI ID   WP_218242478.1    Uniprot ID   -
Organism   Comamonas fluminis strain CJ34     
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 817521..857228 826615..828357 within 0


Gene organization within MGE regions


Location: 817521..857228
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JDW18_RS04080 argJ 819712..820941 (+) 1230 WP_218242470.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -
  JDW18_RS04085 - 821208..822143 (+) 936 WP_218242471.1 ATP-binding protein -
  JDW18_RS04090 - 822160..822627 (+) 468 WP_218242472.1 NUDIX domain-containing protein -
  JDW18_RS04095 - 822751..822960 (-) 210 WP_218242473.1 DNA gyrase inhibitor YacG -
  JDW18_RS04100 zapD 823029..823784 (-) 756 WP_218242474.1 cell division protein ZapD -
  JDW18_RS04105 coaE 823870..824493 (-) 624 WP_218242475.1 dephospho-CoA kinase -
  JDW18_RS04110 - 824503..825372 (-) 870 WP_218242476.1 A24 family peptidase -
  JDW18_RS04115 pilC 825372..826589 (-) 1218 WP_218242477.1 type II secretion system F family protein Machinery gene
  JDW18_RS04120 pilB 826615..828357 (-) 1743 WP_218242478.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JDW18_RS04125 - 828610..829701 (+) 1092 WP_013721479.1 site-specific integrase -
  JDW18_RS04130 - 829869..830852 (+) 984 WP_218242479.1 IS5 family transposase -
  JDW18_RS04135 - 831199..831690 (+) 492 WP_013721480.1 helix-turn-helix domain-containing protein -
  JDW18_RS04140 - 831687..832343 (+) 657 WP_013721481.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  JDW18_RS04145 - 832487..833185 (+) 699 WP_218242480.1 helix-turn-helix transcriptional regulator -
  JDW18_RS04150 - 833182..833715 (+) 534 WP_059401739.1 DUF6036 family nucleotidyltransferase -
  JDW18_RS04155 - 833799..838661 (+) 4863 WP_218242481.1 AAA domain-containing protein -
  JDW18_RS04160 - 838654..840213 (+) 1560 WP_059401741.1 hypothetical protein -
  JDW18_RS04165 - 840271..840810 (-) 540 WP_059401742.1 hypothetical protein -
  JDW18_RS04170 - 840807..841097 (-) 291 WP_059401743.1 hypothetical protein -
  JDW18_RS04175 - 841094..842083 (-) 990 WP_059401744.1 hypothetical protein -
  JDW18_RS22525 - 842183..842581 (+) 399 WP_246610271.1 hypothetical protein -
  JDW18_RS04185 - 842578..843288 (+) 711 WP_218242482.1 metallophosphoesterase -
  JDW18_RS04190 - 843427..843984 (+) 558 WP_218242483.1 HAD domain-containing protein -
  JDW18_RS04195 - 844010..845317 (-) 1308 WP_218242484.1 HipA domain-containing protein -
  JDW18_RS04200 - 845314..845586 (-) 273 WP_218242485.1 helix-turn-helix domain-containing protein -
  JDW18_RS04205 - 846458..846673 (+) 216 WP_054254674.1 helix-turn-helix domain-containing protein -
  JDW18_RS04210 - 846702..848786 (+) 2085 WP_218242486.1 protein adenylyltransferase SelO family protein -
  JDW18_RS04215 msrB 849354..849794 (+) 441 WP_034054008.1 peptide-methionine (R)-S-oxide reductase MsrB -
  JDW18_RS04220 - 849791..851011 (+) 1221 WP_008647313.1 bifunctional alpha/beta hydrolase/OsmC family protein -
  JDW18_RS04225 - 851044..851325 (+) 282 WP_034053981.1 DUF427 domain-containing protein -
  JDW18_RS04230 - 851322..852731 (+) 1410 WP_008647310.1 mercuric reductase -
  JDW18_RS04235 - 852749..853357 (+) 609 WP_008647302.1 sulfite oxidase-like oxidoreductase -
  JDW18_RS04240 - 853350..854111 (+) 762 WP_042797684.1 FAD-binding oxidoreductase -
  JDW18_RS04245 egtB 854133..855326 (+) 1194 WP_218242487.1 ergothioneine biosynthesis protein EgtB -
  JDW18_RS04250 egtD 855323..856300 (+) 978 WP_034053995.1 L-histidine N(alpha)-methyltransferase -
  JDW18_RS04255 - 856314..856760 (+) 447 WP_218242488.1 hypothetical protein -

Sequence

Protein


Download         Length: 580 a.a.        Molecular weight: 63078.33 Da        Isoelectric Point: 5.4504

>NTDB_id=522508 JDW18_RS04120 WP_218242478.1 826615..828357(-) (pilB) [Comamonas fluminis strain CJ34]
MAAADSLPKNPPAPIAIPGLGRALISAGKVSQQAAEAAAKKAAGSKTPFISELSQSGEISALEIAETISTMFSTPLLDLN
AVDTTQLPRELLDPKISSTYRVLALSKRGNRITVATADPTQQEVAEQIKFTTQMFVDWVVVEADKLHKLLEHTGKSVSES
LETYSSSGDFDFDDVKIEDAPDEKDNAIGAEVEDAPVVKFLHKMLLDAFNMRASDLHFEPYEHNYRVRFRIDGELREIAS
PPIAIKDKLASRIKVISRLDISEKRIPQDGRMKLKVGPDRVIDFRVSTLPTLFGEKIVIRILDPSSAKMGIDALGYEPEE
KERLLSAIKRPYGMILVTGPTGSGKTVSLYTCLNLLNQPGVNIATAEDPSEINMPGVNQVNVNEKAGLTFAAALKSFLRQ
DPDIIMVGEIRDLETADISIKAAQTGHLVLSTLHTNDAPTTLTRMRNMGIAPFNIASSVILITAQRLARRLCAQCKQPAD
IPHEALLDAGYSEEEVDGSWVSYKPVGCAACNNGYKGRVGIYQVMPISEEIQRIILRDGSAMDIAAQAKLEGVRSLRGSG
LHKVKLGLTSLEEVLAVTNE

Nucleotide


Download         Length: 1743 bp        

>NTDB_id=522508 JDW18_RS04120 WP_218242478.1 826615..828357(-) (pilB) [Comamonas fluminis strain CJ34]
ATGGCTGCTGCCGATTCGCTGCCCAAAAACCCTCCAGCTCCTATCGCTATTCCCGGCCTGGGACGTGCGCTGATCTCGGC
TGGCAAGGTCTCTCAGCAGGCAGCGGAGGCTGCTGCCAAAAAAGCAGCAGGCAGCAAAACCCCTTTCATCTCGGAACTGA
GCCAGTCCGGCGAAATCAGCGCATTGGAGATTGCCGAGACAATCTCCACCATGTTCAGCACACCGCTGCTGGACCTCAAT
GCGGTTGACACCACGCAGCTCCCCCGCGAGCTGCTGGACCCCAAGATCAGCAGCACCTACCGTGTTCTGGCCCTGAGCAA
ACGGGGCAATCGCATCACTGTTGCCACTGCCGACCCCACCCAGCAGGAAGTCGCCGAACAAATCAAGTTCACGACGCAGA
TGTTTGTGGACTGGGTGGTTGTTGAGGCCGACAAGCTTCACAAGCTACTTGAGCACACCGGCAAAAGTGTCAGCGAGTCT
CTGGAGACTTACTCCAGCTCGGGCGACTTCGACTTTGACGATGTCAAGATTGAAGATGCACCTGACGAAAAAGACAACGC
CATTGGTGCCGAGGTTGAAGACGCTCCCGTCGTCAAGTTTCTGCACAAGATGCTGCTTGATGCATTCAATATGCGTGCTT
CGGACTTGCACTTCGAGCCGTACGAACACAATTACCGAGTCCGCTTTCGTATCGACGGCGAATTGCGTGAAATTGCCTCG
CCACCCATTGCCATCAAGGACAAGCTGGCTTCGCGCATCAAGGTGATCTCGCGCCTGGATATTTCGGAAAAACGCATTCC
CCAAGACGGACGCATGAAGCTCAAGGTGGGACCAGATCGCGTCATCGACTTCCGTGTCAGCACCTTGCCCACGCTGTTTG
GCGAAAAGATCGTGATCCGTATTCTGGATCCCAGCTCCGCCAAGATGGGCATTGATGCGCTGGGCTACGAGCCCGAGGAA
AAAGAGCGCCTCCTCTCCGCCATCAAGCGCCCCTACGGCATGATTCTGGTCACCGGCCCCACAGGGTCGGGCAAGACCGT
GTCGCTCTATACCTGTCTGAATCTGCTCAATCAGCCAGGCGTGAACATTGCCACCGCAGAAGACCCCTCCGAAATCAACA
TGCCTGGCGTTAACCAGGTCAATGTGAACGAGAAGGCAGGTCTGACTTTTGCCGCGGCACTCAAATCCTTTCTGCGCCAG
GATCCGGACATCATCATGGTTGGTGAAATTCGCGACCTGGAAACGGCCGACATCTCCATCAAGGCCGCGCAGACTGGTCA
CTTGGTGCTATCAACACTGCACACCAACGATGCACCCACCACGCTGACCCGGATGCGCAATATGGGCATCGCCCCCTTCA
ATATTGCCTCCAGCGTGATTTTGATTACCGCCCAGCGCCTGGCACGCCGCCTGTGTGCGCAGTGCAAGCAGCCTGCCGAC
ATTCCGCATGAGGCCTTGCTGGATGCCGGATACAGCGAAGAGGAAGTCGATGGCAGCTGGGTCAGCTACAAGCCCGTGGG
CTGCGCTGCCTGCAACAATGGCTATAAAGGGCGAGTCGGCATCTACCAGGTCATGCCTATCAGCGAGGAAATTCAGCGCA
TCATCTTGCGCGATGGCAGCGCAATGGATATTGCTGCACAGGCCAAGCTGGAAGGCGTGCGCTCCTTGCGTGGGTCTGGC
CTGCACAAAGTAAAGCTGGGCCTGACCTCGCTTGAAGAAGTGCTGGCCGTGACCAACGAGTAA

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

54.007

98.966

0.534
  pilB Acinetobacter baumannii D1279779

54.433

97.241

0.529
  pilF Neisseria gonorrhoeae MS11

53.004

97.586

0.517
  pilB Legionella pneumophila strain ERS1305867

49.558

97.414

0.483
  pilB Vibrio cholerae strain A1552

46.293

95.345

0.441
  pilB Vibrio parahaemolyticus RIMD 2210633

44.928

95.172

0.428
  pilB Vibrio campbellii strain DS40M4

44.727

94.828

0.424
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.895

98.276

0.372
  pilF Thermus thermophilus HB27

37.653

98.448

0.371