Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LDN84_RS04415 Genome accession   NZ_AP024238
Coordinates   939912..941645 (-) Length   577 a.a.
NCBI ID   WP_223909009.1    Uniprot ID   -
Organism   Rhodoferax lithotrophicus strain MIZ03     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 934912..946645
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LDN84_RS04385 (MIZ03_0928) - 935354..936121 (+) 768 WP_223908958.1 ParA family protein -
  LDN84_RS04390 (MIZ03_0929) - 936197..936421 (-) 225 WP_223908966.1 DNA gyrase inhibitor YacG -
  LDN84_RS04395 (MIZ03_0930) zapD 936418..937173 (-) 756 WP_223908969.1 cell division protein ZapD -
  LDN84_RS04400 (MIZ03_0931) coaE 937197..937814 (-) 618 WP_223908976.1 dephospho-CoA kinase -
  LDN84_RS04405 (MIZ03_0932) - 937817..938659 (-) 843 WP_223908986.1 A24 family peptidase -
  LDN84_RS04410 (MIZ03_0933) pilC 938662..939879 (-) 1218 WP_223909001.1 type II secretion system F family protein Machinery gene
  LDN84_RS04415 (MIZ03_0934) pilB 939912..941645 (-) 1734 WP_223909009.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LDN84_RS04420 (MIZ03_0935) greB 941777..942337 (+) 561 WP_223909015.1 transcription elongation factor GreB -
  LDN84_RS04425 (MIZ03_0936) - 942327..944582 (-) 2256 WP_223909018.1 bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase -
  LDN84_RS04430 (MIZ03_0937) rpoZ 944673..944876 (-) 204 WP_223909024.1 DNA-directed RNA polymerase subunit omega -
  LDN84_RS04435 (MIZ03_0938) gmk 944907..945524 (-) 618 WP_223909031.1 guanylate kinase -
  LDN84_RS04440 (MIZ03_0939) - 945558..946475 (-) 918 WP_223909034.1 YicC/YloC family endoribonuclease -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62613.10 Da        Isoelectric Point: 6.2052

>NTDB_id=84221 LDN84_RS04415 WP_223909009.1 939912..941645(-) (pilB) [Rhodoferax lithotrophicus strain MIZ03]
MAVIETTPPATSSNLPGLGRTLVMAGKLDQVVAQSLYAKSQTNRTSFIAELTGSGAVSAADLAHTMSLAFAAPLIDLAEV
DPNRLPKGLLDNKICQAYRVVVLGKRQNRLIVATADPSDQQSIEKIKFATQLNVDWVIAEYDKLLKLVSANTATATESID
SIVGDDFEFDELASEPASESATATSTSEVDDAPVVKFLHKMLIDAFTMRASDLHFEPYEHNYRVRFRIDGELREVASPPI
AIKDKLASRIKVISKMDISEKRVPQDGKMKLKIGPDRVIDFRVSTLPTMFGEKIVIRILDPSSAKLGIDALGYEPAEKER
LLSAINRPYGMILVTGPTGSGKTVSLYTCLNLLNNPGVNIATAEDPCEITLPGINQVSVNDKAGLTFAAALKSFLRQDPD
IIMVGEIRDIDTADIAIKAAQTGHLVLSTLHTNDAPTTLTRMRNMGIAPFNIASSVILITAQRLARRLCPNCKKPIDLPE
KALLDAGFQPEELDGSWKPYQPVGCSACNNGYKGRVGIYQVMPITEEIQRIILRDGSALEIAEQAKREGVRSLREAGLHK
VKLGLTSVAEVLAVSNQ

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=84221 LDN84_RS04415 WP_223909009.1 939912..941645(-) (pilB) [Rhodoferax lithotrophicus strain MIZ03]
ATGGCAGTTATTGAAACCACCCCACCCGCAACATCAAGCAACCTTCCCGGATTGGGTCGCACTCTGGTCATGGCGGGCAA
GCTGGACCAAGTTGTGGCCCAGAGCCTGTACGCCAAATCTCAGACCAACCGCACCAGTTTTATTGCCGAGCTCACCGGTT
CAGGTGCTGTTTCGGCCGCCGATCTGGCTCACACCATGTCCTTGGCATTTGCGGCACCCCTGATTGATCTGGCGGAGGTT
GACCCCAATCGTTTACCCAAGGGTCTGCTTGACAACAAGATTTGCCAAGCCTACCGGGTGGTCGTTTTGGGTAAACGGCA
AAACCGGCTGATCGTGGCCACAGCCGACCCATCAGACCAGCAATCGATTGAAAAAATCAAGTTTGCCACCCAACTCAATG
TGGACTGGGTGATTGCTGAATACGACAAATTACTCAAGCTGGTGTCAGCCAATACGGCCACGGCCACCGAGTCTATCGAC
AGTATTGTGGGTGACGATTTTGAGTTTGACGAATTGGCCTCGGAACCCGCAAGTGAGAGCGCCACAGCAACAAGCACCTC
TGAGGTGGACGATGCCCCGGTGGTCAAATTTCTGCACAAAATGCTCATAGATGCATTCACCATGCGTGCCTCAGACTTGC
ATTTTGAACCCTACGAGCACAATTACCGGGTGCGTTTTCGCATTGACGGCGAGTTGCGTGAAGTGGCCTCGCCACCGATT
GCCATCAAGGACAAGCTGGCTTCACGCATCAAGGTGATCTCCAAAATGGACATCTCTGAAAAACGCGTGCCCCAAGATGG
CAAGATGAAACTCAAAATTGGCCCGGATCGGGTGATTGACTTTCGTGTCAGCACCCTGCCCACCATGTTTGGCGAAAAAA
TCGTGATCCGTATCCTGGATCCCAGCAGCGCCAAACTGGGTATTGATGCGCTGGGTTACGAGCCTGCCGAAAAAGAGCGC
TTGTTGTCAGCCATCAACCGCCCCTACGGCATGATTCTGGTGACGGGGCCGACCGGTTCAGGTAAAACTGTGTCGCTCTA
TACCTGCCTGAACCTGCTGAACAACCCAGGTGTCAACATTGCCACGGCAGAAGACCCCTGCGAAATCACCCTGCCCGGCA
TCAACCAGGTCAGCGTCAACGACAAAGCCGGACTGACCTTTGCTGCTGCCCTCAAGTCCTTCCTGCGGCAAGACCCGGAC
ATCATCATGGTGGGTGAAATTCGAGACATTGATACAGCAGATATCGCCATCAAAGCCGCACAAACAGGCCACTTGGTGCT
CTCAACTTTGCACACCAACGATGCGCCCACCACACTCACCCGGATGCGCAACATGGGCATTGCCCCCTTCAACATTGCAT
CCAGCGTGATTTTGATCACCGCACAACGCTTGGCCCGGCGCCTGTGCCCAAATTGCAAAAAGCCCATTGATCTGCCTGAA
AAAGCTCTGCTGGATGCCGGCTTTCAACCAGAAGAGCTCGACGGCAGCTGGAAACCGTACCAGCCCGTCGGCTGCAGTGC
CTGCAACAACGGCTACAAGGGCCGTGTCGGTATTTACCAGGTGATGCCCATCACTGAAGAAATCCAGCGCATCATCCTGC
GCGATGGCAGTGCCCTGGAGATTGCCGAACAAGCCAAACGGGAAGGCGTTCGCAGTCTGCGTGAAGCAGGTCTGCACAAA
GTCAAGCTGGGGCTGACTTCGGTCGCTGAAGTTCTGGCCGTCAGTAATCAATAG

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(200-467)

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

(53-149)


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

53.022

100

0.532
  pilB Acinetobacter baumannii D1279779

52.422

100

0.525
  pilF Neisseria gonorrhoeae MS11

51.865

97.574

0.506
  pilB Legionella pneumophila strain ERS1305867

50.356

97.4

0.49
  pilB Vibrio campbellii strain DS40M4

44.7

98.094

0.438
  pilB Vibrio parahaemolyticus RIMD 2210633

45.688

94.454

0.432
  pilB Vibrio cholerae strain A1552

47.776

89.601

0.428
  pilF Thermus thermophilus HB27

40.076

91.681

0.367

Multiple sequence alignment