Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LRK55_RS03715 Genome accession   NZ_CP088925
Coordinates   785292..787016 (+) Length   574 a.a.
NCBI ID   WP_007513926.1    Uniprot ID   A0A154QKD4
Organism   Rhodanobacter denitrificans strain FW104-MT042     
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)
Genomic island 764350..788977 785292..787016 within 0


Gene organization within MGE regions


Location: 764350..788977
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK55_RS03625 (LRK55_03625) - 764350..766356 (+) 2007 WP_008438608.1 acyltransferase family protein -
  LRK55_RS03630 (LRK55_03630) - 766569..767012 (+) 444 WP_008438606.1 pilin -
  LRK55_RS03635 (LRK55_03635) pilE 767355..767795 (+) 441 WP_008438605.1 pilin Machinery gene
  LRK55_RS03640 (LRK55_03640) - 767860..769872 (+) 2013 WP_039954252.1 hypothetical protein -
  LRK55_RS03645 (LRK55_03645) - 769869..771863 (+) 1995 WP_008438601.1 hypothetical protein -
  LRK55_RS03650 (LRK55_03650) gmd 771942..773051 (+) 1110 WP_008438600.1 GDP-mannose 4,6-dehydratase -
  LRK55_RS03655 (LRK55_03655) - 773048..774010 (+) 963 WP_008438599.1 GDP-L-fucose synthase -
  LRK55_RS03660 (LRK55_03660) - 774007..774918 (+) 912 WP_008438598.1 hypothetical protein -
  LRK55_RS03665 (LRK55_03665) - 774918..776282 (+) 1365 WP_008438597.1 polysaccharide biosynthesis protein -
  LRK55_RS03670 (LRK55_03670) - 776306..777316 (-) 1011 WP_008438596.1 GDP-mannose 4,6-dehydratase -
  LRK55_RS03675 (LRK55_03675) - 777316..778578 (-) 1263 WP_008438595.1 class I SAM-dependent methyltransferase -
  LRK55_RS03680 (LRK55_03680) - 778575..779603 (-) 1029 WP_008438594.1 glycosyltransferase family 2 protein -
  LRK55_RS03685 (LRK55_03685) - 779851..780882 (+) 1032 WP_008438593.1 glycosyltransferase -
  LRK55_RS03690 (LRK55_03690) - 780902..781636 (-) 735 WP_008438592.1 class I SAM-dependent methyltransferase -
  LRK55_RS03695 (LRK55_03695) - 781633..782886 (-) 1254 WP_008438590.1 glycosyltransferase family 4 protein -
  LRK55_RS03700 (LRK55_03700) - 782879..783733 (-) 855 WP_008438588.1 glycosyltransferase family 2 protein -
  LRK55_RS03705 (LRK55_03705) - 784024..784419 (-) 396 WP_007513922.1 type II toxin-antitoxin system VapC family toxin -
  LRK55_RS03710 (LRK55_03710) - 784416..784658 (-) 243 WP_007513924.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK55_RS03715 (LRK55_03715) pilB 785292..787016 (+) 1725 WP_007513926.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK55_RS03720 (LRK55_03720) pilC 787159..788430 (+) 1272 WP_008438585.1 type II secretion system F family protein Machinery gene
  LRK55_RS03725 (LRK55_03725) - 788579..788977 (+) 399 WP_008438584.1 endonuclease domain-containing protein -

Sequence

Protein


Download         Length: 574 a.a.        Molecular weight: 62743.49 Da        Isoelectric Point: 6.3329

>NTDB_id=634028 LRK55_RS03715 WP_007513926.1 785292..787016(+) (pilB) [Rhodanobacter denitrificans strain FW104-MT042]
MSSQLQPSLAGLSGMARRLVSEGVMPEDVVRKAMADSSQQKATLGAWLLDRSLVDSAELTRIASAEFGMPMMDVAALNPA
TMPLDLISEALITKHQALPLFRRGKRLYVGIADPMQSHALDEIKFHSNCMVEPILVERGSLQRVIESLLNNMRNTMPDMG
GGDLDELDIEGGDDEGESSSGVDANANDDAPVVKFVNKILVDAIRRGASDIHFEPFETQYRVRLRMDGMLKAVANPPMKM
ANRISSRIKVMAQLDIAEKRVPQDGRIKLNLSKTRAVDFRVSTLPTLFGEKIVLRILDGSSARIGIEKLGYEPNQQKLYV
DAIHKPYGMVLVTGPTGSGKTVSLYTGLNMLNTAERNISTVEDPVEIRVEGINQVQQNVKRGMTFASALRSFLRQDPDVI
MVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAAQTISRLMNMGIAPYNITSSVTLIIAQRLARRLHDCKKPIELPPKVL
LDAGFTQADIDAGLTIYEAVGCDSCNEGYKGRVGIYQVMPMLEDIQKIILQGGNALQIAEVAKAAGINDLRASALLKVKQ
GLTSLTEIDRVTKE

Nucleotide


Download         Length: 1725 bp        

>NTDB_id=634028 LRK55_RS03715 WP_007513926.1 785292..787016(+) (pilB) [Rhodanobacter denitrificans strain FW104-MT042]
ATGTCATCTCAATTACAGCCGTCGCTCGCGGGCTTGTCCGGCATGGCCCGCCGGTTGGTATCTGAAGGGGTAATGCCCGA
GGACGTGGTACGCAAGGCCATGGCCGACAGCAGCCAGCAGAAGGCCACGCTGGGCGCCTGGCTGCTGGACCGCAGCTTGG
TCGACAGCGCCGAACTGACCCGGATCGCCTCGGCCGAATTCGGCATGCCGATGATGGACGTGGCCGCGCTGAACCCGGCC
ACGATGCCGCTGGACCTGATCAGCGAGGCGCTGATCACCAAGCACCAGGCGCTGCCGCTGTTCCGCCGCGGCAAGCGGCT
GTACGTGGGCATCGCCGACCCGATGCAGTCGCATGCGCTGGACGAGATCAAGTTCCACTCCAACTGCATGGTGGAGCCGA
TCCTGGTGGAGCGCGGCTCGCTGCAGCGGGTGATCGAGAGCCTGCTCAACAACATGCGCAACACCATGCCCGACATGGGC
GGCGGCGACCTCGACGAGCTGGACATCGAGGGCGGCGACGACGAGGGCGAGTCGAGCAGCGGCGTCGACGCGAATGCGAA
CGACGACGCGCCGGTGGTGAAGTTCGTCAACAAGATCCTGGTCGACGCGATCCGCCGCGGCGCCTCGGACATCCATTTCG
AGCCGTTCGAAACCCAATACCGCGTGCGCCTGCGCATGGACGGCATGCTGAAGGCGGTGGCCAACCCGCCGATGAAGATG
GCCAACCGCATCTCCTCGCGCATCAAGGTGATGGCCCAGCTGGACATCGCCGAGAAGCGCGTGCCGCAGGACGGCCGCAT
CAAGCTCAACCTGTCCAAGACCCGCGCGGTCGACTTCCGCGTGAGCACGCTGCCCACGCTGTTCGGCGAGAAGATCGTGC
TGCGCATCCTGGACGGCTCCTCGGCCAGGATCGGCATCGAGAAGCTGGGCTACGAGCCGAACCAGCAGAAGCTCTACGTC
GATGCGATCCACAAGCCGTACGGCATGGTGCTGGTCACCGGCCCCACCGGCTCGGGCAAGACGGTGTCGCTGTACACCGG
CCTGAACATGCTCAACACCGCCGAGCGCAACATCTCGACGGTGGAAGACCCGGTGGAAATCCGCGTCGAGGGCATCAACC
AGGTGCAGCAGAACGTGAAGCGCGGCATGACCTTTGCCAGCGCGCTGCGCTCGTTCCTGCGCCAGGACCCGGACGTGATC
ATGGTCGGCGAGATCCGCGACCTGGAGACCGCCGAGATCGCGATCAAGGCGGCGCAGACCGGTCACATGGTGCTGTCCAC
CCTGCACACCAACGACGCGGCGCAGACCATCTCGCGCCTGATGAACATGGGCATCGCGCCGTACAACATCACCTCGTCGG
TGACCCTGATCATCGCCCAGCGCCTGGCGCGGCGCCTGCACGACTGCAAGAAGCCGATCGAGCTGCCGCCCAAGGTGCTG
CTGGACGCCGGCTTCACCCAGGCCGACATCGACGCGGGGCTGACCATCTACGAGGCCGTCGGCTGCGACAGCTGCAACGA
GGGTTACAAGGGTCGCGTGGGTATCTATCAGGTAATGCCGATGCTGGAGGATATCCAGAAGATCATCCTGCAAGGTGGCA
ATGCACTGCAGATCGCCGAGGTGGCCAAGGCCGCCGGCATCAACGACCTGCGCGCGTCGGCCCTGCTGAAGGTGAAGCAG
GGGCTGACCAGCCTGACCGAGATCGACCGCGTCACCAAGGAATGA

Domains

Predicted by InterproScan.

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

(49-152)

Type II/IV secretion system protein (T2SSE)

(198-465)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A154QKD4

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

55.044

98.432

0.542
  pilB Acinetobacter baumannii D1279779

53.603

99.129

0.531
  pilB Legionella pneumophila strain ERS1305867

49.824

98.955

0.493
  pilB Vibrio cholerae strain A1552

50.659

92.509

0.469
  pilB Vibrio parahaemolyticus RIMD 2210633

49.529

92.509

0.458
  pilB Vibrio campbellii strain DS40M4

49.529

92.509

0.458
  pilF Neisseria gonorrhoeae MS11

47.048

97.387

0.458
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.268

100

0.385
  pilF Thermus thermophilus HB27

38.198

96.69

0.369