Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LRK53_RS05940 Genome accession   NZ_CP088923
Coordinates   1372532..1374256 (-) Length   574 a.a.
NCBI ID   WP_027493028.1    Uniprot ID   -
Organism   Rhodanobacter thiooxydans strain FW510-R12     
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 1374734..1397082 1372532..1374256 flank 478


Gene organization within MGE regions


Location: 1372532..1397082
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK53_RS05940 (LRK53_05940) pilB 1372532..1374256 (-) 1725 WP_027493028.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK53_RS05945 (LRK53_05945) - 1374734..1374976 (+) 243 WP_027493027.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK53_RS05950 (LRK53_05950) - 1374973..1375368 (+) 396 WP_027493026.1 type II toxin-antitoxin system VapC family toxin -
  LRK53_RS05955 (LRK53_05955) - 1375524..1375850 (-) 327 WP_051257590.1 DUF86 domain-containing protein -
  LRK53_RS05960 (LRK53_05960) - 1375889..1376179 (-) 291 WP_027493024.1 nucleotidyltransferase family protein -
  LRK53_RS05965 (LRK53_05965) - 1376511..1377365 (+) 855 WP_027493023.1 glycosyltransferase family 2 protein -
  LRK53_RS05970 (LRK53_05970) - 1377358..1378518 (+) 1161 WP_027493022.1 glycosyltransferase family 4 protein -
  LRK53_RS05975 (LRK53_05975) - 1378511..1379281 (+) 771 WP_081666625.1 class I SAM-dependent methyltransferase -
  LRK53_RS05980 (LRK53_05980) - 1379278..1380345 (+) 1068 WP_081666624.1 glycosyltransferase family 4 protein -
  LRK53_RS05985 (LRK53_05985) - 1380357..1381358 (+) 1002 WP_037089869.1 class I SAM-dependent methyltransferase -
  LRK53_RS05990 (LRK53_05990) - 1381358..1382209 (+) 852 WP_185754653.1 glycosyltransferase -
  LRK53_RS05995 (LRK53_05995) - 1382206..1383456 (-) 1251 WP_051257587.1 oligosaccharide flippase family protein -
  LRK53_RS06000 (LRK53_06000) - 1383453..1385438 (-) 1986 WP_051257586.1 hypothetical protein -
  LRK53_RS06005 (LRK53_06005) - 1385438..1387453 (-) 2016 WP_235642652.1 tetratricopeptide repeat protein -
  LRK53_RS06010 (LRK53_06010) pilE 1387525..1387980 (-) 456 WP_027493018.1 pilin Machinery gene
  LRK53_RS06015 (LRK53_06015) pilA 1388325..1388768 (-) 444 WP_027493017.1 pilin Machinery gene
  LRK53_RS06020 (LRK53_06020) - 1388922..1389239 (-) 318 WP_185754656.1 DUF86 domain-containing protein -
  LRK53_RS06025 (LRK53_06025) - 1389308..1389544 (-) 237 WP_235642561.1 nucleotidyltransferase domain-containing protein -
  LRK53_RS06030 (LRK53_06030) - 1389569..1390297 (-) 729 WP_051257585.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  LRK53_RS06035 (LRK53_06035) - 1390290..1390760 (-) 471 WP_235642562.1 helix-turn-helix domain-containing protein -
  LRK53_RS06040 (LRK53_06040) - 1390866..1391105 (-) 240 WP_051257583.1 HigA family addiction module antitoxin -
  LRK53_RS06045 (LRK53_06045) - 1391176..1391316 (-) 141 Protein_1204 type II toxin-antitoxin system RelE/ParE family toxin -
  LRK53_RS06050 (LRK53_06050) - 1391480..1391866 (-) 387 WP_037089861.1 nucleotidyltransferase domain-containing protein -
  LRK53_RS06055 (LRK53_06055) - 1392134..1392748 (+) 615 WP_027493013.1 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
  LRK53_RS06060 (LRK53_06060) - 1392773..1393636 (+) 864 WP_037089858.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  LRK53_RS06065 (LRK53_06065) - 1393835..1395964 (+) 2130 WP_027493012.1 S9 family peptidase -
  LRK53_RS06070 (LRK53_06070) - 1396666..1397082 (+) 417 WP_235642563.1 nucleotidyltransferase family protein -

Sequence

Protein


Download         Length: 574 a.a.        Molecular weight: 63022.83 Da        Isoelectric Point: 5.9164

>NTDB_id=634016 LRK53_RS05940 WP_027493028.1 1372532..1374256(-) (pilB) [Rhodanobacter thiooxydans strain FW510-R12]
MSSQLQPSLVGLSGMARRLVSEGVMPEDVVRKAMLDSNQQKASLSAWLLDHNLVDSTELTRVASAEFGMPMMDVAVLNPA
TMPLDLISEALITKHQALPLFRRGKRLFVGIADPMQSHALDEIKFHSNCMVEPILVERDSLQRVIESLLNNMRNTMPDMG
GGELDELDIEGGEDEGESSSGIDANANDDAPVVKFVNKILIDAIRRGASDIHFEPFETQYRVRLRMDGILKAVSSPPMKM
ANRISSRIKVMAQLDIAEKRVPQDGRIKLNLSKTRAIDFRVSTLPTLFGEKIVLRILDGSSARMGIEKLGYEPDQQKLYV
DAIHKPYGMVLVTGPTGSGKTVSLYTGLNMLNTAERNISTVEDPVEIRVEGINQVQQNVKRGMTFASALRSFLRQDPDVI
MVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAAQTVSRLMNMGIAPYNITSSVSLIIAQRLARRLHDCKKPVELPPKVL
LDAGFTQADIDAGLTIYEAVGCDSCNEGYKGRVGIYQVMPMLEEIQKIILQGGNALQIAEVARAAGINDLRASALLKVKQ
GLTSLIEIDRVTKE

Nucleotide


Download         Length: 1725 bp        

>NTDB_id=634016 LRK53_RS05940 WP_027493028.1 1372532..1374256(-) (pilB) [Rhodanobacter thiooxydans strain FW510-R12]
ATGTCATCTCAATTGCAGCCGTCACTTGTGGGCCTGTCCGGCATGGCCCGCCGGTTGGTCTCCGAGGGCGTGATGCCCGA
GGACGTGGTCCGCAAGGCCATGCTCGACAGCAACCAGCAGAAGGCCTCGCTGAGTGCCTGGCTGCTGGACCACAACCTGG
TCGACAGCACCGAACTGACCCGGGTCGCCTCGGCCGAATTCGGCATGCCGATGATGGACGTGGCCGTACTGAACCCTGCC
ACGATGCCGCTGGACCTGATTAGCGAGGCGCTGATCACCAAGCACCAGGCGTTGCCGCTGTTCCGTCGCGGCAAGCGCTT
GTTCGTGGGCATCGCCGACCCGATGCAGTCGCATGCGCTGGACGAGATCAAGTTCCACTCCAACTGCATGGTGGAACCGA
TCCTGGTGGAGCGCGACTCGCTGCAGCGGGTGATCGAGAGCCTGCTCAACAATATGCGCAACACCATGCCCGACATGGGT
GGCGGCGAGCTGGACGAGCTGGATATCGAGGGCGGCGAGGACGAGGGTGAGTCGAGCAGCGGCATCGACGCGAACGCGAA
CGACGACGCGCCGGTGGTGAAGTTCGTCAACAAGATCCTGATCGACGCCATCCGCCGCGGCGCCTCGGACATCCATTTTG
AGCCGTTCGAGACGCAGTACCGGGTGCGCCTGCGCATGGACGGCATCCTCAAGGCGGTGTCCAGCCCGCCGATGAAGATG
GCCAACCGCATCTCCTCGCGCATCAAGGTGATGGCGCAGTTGGACATCGCCGAGAAGCGCGTGCCGCAGGACGGCCGCAT
CAAGCTCAACCTGTCCAAGACCCGCGCCATCGACTTCCGCGTGAGCACGCTGCCCACATTGTTCGGCGAGAAGATCGTGC
TGCGCATCCTGGACGGCTCCTCGGCCCGCATGGGCATCGAGAAGCTGGGCTACGAGCCGGACCAGCAGAAGCTCTACGTC
GACGCGATCCACAAGCCGTACGGCATGGTGCTGGTCACCGGCCCCACCGGCTCGGGCAAGACGGTGTCGCTGTACACCGG
CCTGAACATGCTCAACACCGCCGAGCGCAATATCTCGACGGTGGAGGACCCGGTGGAAATCCGCGTCGAGGGCATCAACC
AGGTGCAGCAGAACGTGAAGCGCGGCATGACCTTCGCCAGCGCGCTGCGCTCGTTCCTGCGCCAGGACCCGGACGTGATC
ATGGTCGGCGAGATCCGCGACCTGGAAACCGCCGAGATCGCGATCAAGGCGGCGCAGACCGGCCACATGGTGCTCTCCAC
CCTGCACACCAACGACGCTGCGCAGACCGTTTCGCGCCTGATGAACATGGGCATTGCGCCGTACAACATCACCTCGTCGG
TGAGCCTGATCATCGCCCAGCGCCTGGCGCGACGCCTGCACGACTGCAAGAAGCCGGTCGAGCTGCCGCCCAAGGTGCTG
CTGGACGCCGGCTTCACCCAGGCCGACATCGACGCCGGATTGACCATCTACGAGGCCGTCGGCTGCGACAGCTGCAACGA
GGGCTACAAGGGCCGCGTGGGCATCTACCAGGTGATGCCGATGCTGGAGGAGATCCAGAAGATCATCCTGCAGGGCGGCA
ACGCGCTGCAGATCGCCGAGGTGGCCAGGGCCGCCGGCATCAACGACTTGCGCGCATCGGCCCTGCTCAAGGTGAAGCAG
GGCCTGACCAGCCTGATCGAGATCGACCGCGTCACCAAGGAATGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(198-465)

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

(48-152)


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

55.221

98.432

0.544
  pilB Acinetobacter baumannii D1279779

54.306

99.129

0.538
  pilB Legionella pneumophila strain ERS1305867

50

98.955

0.495
  pilB Vibrio cholerae strain A1552

51.119

93.38

0.477
  pilB Vibrio campbellii strain DS40M4

50.56

93.38

0.472
  pilF Neisseria gonorrhoeae MS11

48.122

97.387

0.469
  pilB Vibrio parahaemolyticus RIMD 2210633

50

93.38

0.467
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.879

100

0.392
  pilF Thermus thermophilus HB27

38.364

95.819

0.368