Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LRK24_RS14960 Genome accession   NZ_CP088919
Coordinates   3243698..3245422 (+) Length   574 a.a.
NCBI ID   WP_007513926.1    Uniprot ID   A0A154QKD4
Organism   Rhodanobacter denitrificans strain DSM-24678     
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 3222496..3247378 3243698..3245422 within 0


Gene organization within MGE regions


Location: 3222496..3247378
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK24_RS14865 (LRK24_14865) - 3222956..3223312 (+) 357 WP_202946748.1 GtrA family protein -
  LRK24_RS14870 (LRK24_14870) - 3223452..3224822 (+) 1371 WP_007513896.1 glycosyltransferase family 39 protein -
  LRK24_RS14875 (LRK24_14875) - 3224958..3225401 (+) 444 WP_007513899.1 pilin -
  LRK24_RS14880 (LRK24_14880) pilE 3225744..3226175 (+) 432 WP_007513901.1 pilin Machinery gene
  LRK24_RS14885 (LRK24_14885) - 3226246..3228255 (+) 2010 WP_007513903.1 hypothetical protein -
  LRK24_RS14890 (LRK24_14890) - 3228255..3230225 (+) 1971 WP_043292834.1 hypothetical protein -
  LRK24_RS14895 (LRK24_14895) - 3230264..3231385 (+) 1122 WP_007513907.1 glycosyltransferase -
  LRK24_RS14900 (LRK24_14900) - 3231378..3232304 (+) 927 WP_043292835.1 NAD-dependent epimerase/dehydratase family protein -
  LRK24_RS14905 (LRK24_14905) - 3232274..3233320 (+) 1047 WP_007513911.1 glycosyltransferase -
  LRK24_RS14910 (LRK24_14910) - 3233412..3234563 (-) 1152 WP_007513913.1 glycoside hydrolase family 99-like domain-containing protein -
  LRK24_RS14915 (LRK24_14915) - 3234563..3235816 (-) 1254 WP_007513915.1 class I SAM-dependent methyltransferase -
  LRK24_RS14920 (LRK24_14920) - 3235813..3236772 (-) 960 WP_007513916.1 GDP-mannose 4,6-dehydratase -
  LRK24_RS14925 (LRK24_14925) - 3236772..3237797 (-) 1026 WP_007513917.1 glycosyltransferase family 2 protein -
  LRK24_RS14930 (LRK24_14930) - 3237797..3238648 (-) 852 WP_007513918.1 hypothetical protein -
  LRK24_RS14935 (LRK24_14935) - 3238664..3240172 (-) 1509 WP_007513919.1 oligosaccharide flippase family protein -
  LRK24_RS14940 (LRK24_14940) gmd 3240177..3241271 (-) 1095 WP_043292836.1 GDP-mannose 4,6-dehydratase -
  LRK24_RS14945 (LRK24_14945) - 3241315..3242172 (-) 858 WP_007513921.1 glycosyltransferase family 2 protein -
  LRK24_RS14950 (LRK24_14950) - 3242464..3242859 (-) 396 WP_007513922.1 type II toxin-antitoxin system VapC family toxin -
  LRK24_RS14955 (LRK24_14955) - 3242856..3243098 (-) 243 WP_007513924.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK24_RS14960 (LRK24_14960) pilB 3243698..3245422 (+) 1725 WP_007513926.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK24_RS14965 (LRK24_14965) pilC 3245567..3246838 (+) 1272 WP_007513928.1 type II secretion system F family protein Machinery gene
  LRK24_RS14970 (LRK24_14970) - 3246986..3247378 (+) 393 WP_007513930.1 DUF559 domain-containing protein -

Sequence

Protein


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

>NTDB_id=633930 LRK24_RS14960 WP_007513926.1 3243698..3245422(+) (pilB) [Rhodanobacter denitrificans strain DSM-24678]
MSSQLQPSLAGLSGMARRLVSEGVMPEDVVRKAMADSSQQKATLGAWLLDRSLVDSAELTRIASAEFGMPMMDVAALNPA
TMPLDLISEALITKHQALPLFRRGKRLYVGIADPMQSHALDEIKFHSNCMVEPILVERGSLQRVIESLLNNMRNTMPDMG
GGDLDELDIEGGDDEGESSSGVDANANDDAPVVKFVNKILVDAIRRGASDIHFEPFETQYRVRLRMDGMLKAVANPPMKM
ANRISSRIKVMAQLDIAEKRVPQDGRIKLNLSKTRAVDFRVSTLPTLFGEKIVLRILDGSSARIGIEKLGYEPNQQKLYV
DAIHKPYGMVLVTGPTGSGKTVSLYTGLNMLNTAERNISTVEDPVEIRVEGINQVQQNVKRGMTFASALRSFLRQDPDVI
MVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAAQTISRLMNMGIAPYNITSSVTLIIAQRLARRLHDCKKPIELPPKVL
LDAGFTQADIDAGLTIYEAVGCDSCNEGYKGRVGIYQVMPMLEDIQKIILQGGNALQIAEVAKAAGINDLRASALLKVKQ
GLTSLTEIDRVTKE

Nucleotide


Download         Length: 1725 bp        

>NTDB_id=633930 LRK24_RS14960 WP_007513926.1 3243698..3245422(+) (pilB) [Rhodanobacter denitrificans strain DSM-24678]
ATGTCATCTCAATTACAGCCGTCGCTCGCGGGCTTGTCCGGCATGGCCCGCCGGTTGGTCTCCGAAGGCGTGATGCCGGA
GGACGTGGTACGCAAGGCCATGGCCGACAGCAGCCAGCAGAAGGCCACGCTGGGCGCCTGGCTGCTGGACCGCAGCCTGG
TCGACAGCGCCGAGCTGACCCGGATCGCCTCGGCCGAATTCGGCATGCCGATGATGGACGTGGCCGCGCTGAACCCGGCC
ACGATGCCGCTGGACCTGATCAGCGAGGCGCTGATCACCAAGCACCAGGCGCTGCCGCTGTTCCGCCGCGGCAAGCGGCT
GTACGTGGGCATCGCCGACCCGATGCAGTCGCATGCGCTGGACGAGATCAAGTTCCACTCCAACTGCATGGTGGAGCCGA
TCCTGGTGGAGCGCGGCTCGCTGCAGCGGGTGATCGAGAGCCTGCTCAACAACATGCGCAACACCATGCCCGACATGGGC
GGCGGCGACCTCGACGAGCTGGACATCGAGGGCGGCGACGACGAGGGCGAGTCGAGCAGCGGCGTCGACGCGAATGCGAA
CGACGACGCGCCAGTGGTGAAGTTCGTCAACAAGATCCTGGTCGACGCGATCCGCCGCGGCGCCTCGGACATCCATTTCG
AGCCGTTCGAAACCCAATACCGCGTGCGCCTGCGCATGGACGGCATGCTGAAGGCGGTGGCCAACCCGCCGATGAAGATG
GCCAACCGCATCTCCTCGCGCATCAAGGTAATGGCCCAGCTGGACATCGCCGAGAAGCGCGTGCCGCAGGACGGCCGCAT
CAAGCTCAACCTGTCCAAGACCCGCGCGGTCGACTTCCGCGTGAGCACGCTGCCGACGCTGTTCGGCGAGAAGATCGTGC
TGCGCATCCTGGACGGCTCCTCGGCCAGGATCGGCATCGAGAAGCTGGGCTACGAGCCGAACCAGCAGAAGCTCTACGTC
GATGCGATCCACAAGCCGTACGGCATGGTGCTGGTCACCGGCCCCACCGGCTCGGGCAAGACGGTGTCGCTGTACACCGG
CCTGAACATGCTCAACACCGCCGAGCGCAACATCTCGACGGTGGAAGACCCGGTGGAAATCCGTGTCGAGGGCATCAACC
AGGTGCAGCAGAACGTGAAGCGCGGCATGACCTTCGCCAGCGCGCTGCGCTCGTTCCTGCGCCAGGACCCGGACGTGATC
ATGGTCGGCGAGATCCGCGACCTGGAGACCGCCGAGATCGCGATCAAGGCGGCGCAGACCGGTCACATGGTGCTGTCCAC
GCTGCACACCAACGACGCGGCGCAGACCATCTCGCGCCTGATGAACATGGGCATCGCGCCGTACAACATCACCTCGTCGG
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