Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   LRK52_RS04550 Genome accession   NZ_CP088980
Coordinates   1019821..1021545 (-) Length   574 a.a.
NCBI ID   WP_235645798.1    Uniprot ID   -
Organism   Rhodanobacter denitrificans strain FW104-R5     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1014821..1026545
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  LRK52_RS04520 (LRK52_04520) - 1015330..1015818 (+) 489 WP_015447031.1 dihydrofolate reductase -
  LRK52_RS04525 (LRK52_04525) - 1015818..1016234 (+) 417 WP_027490755.1 NUDIX domain-containing protein -
  LRK52_RS04530 (LRK52_04530) coaE 1016371..1016991 (-) 621 WP_027490754.1 dephospho-CoA kinase -
  LRK52_RS04535 (LRK52_04535) pilD 1016988..1017845 (-) 858 WP_027490753.1 A24 family peptidase Machinery gene
  LRK52_RS04540 (LRK52_04540) - 1017860..1018258 (-) 399 WP_008438584.1 endonuclease domain-containing protein -
  LRK52_RS04545 (LRK52_04545) pilC 1018407..1019678 (-) 1272 WP_027490752.1 type II secretion system F family protein Machinery gene
  LRK52_RS04550 (LRK52_04550) pilB 1019821..1021545 (-) 1725 WP_235645798.1 type IV-A pilus assembly ATPase PilB Machinery gene
  LRK52_RS04555 (LRK52_04555) - 1022179..1022421 (+) 243 WP_007513924.1 AbrB/MazE/SpoVT family DNA-binding domain-containing protein -
  LRK52_RS04560 (LRK52_04560) - 1022418..1022813 (+) 396 WP_007513922.1 type II toxin-antitoxin system VapC family toxin -
  LRK52_RS04565 (LRK52_04565) - 1023105..1023959 (+) 855 WP_027490750.1 glycosyltransferase family 2 protein -
  LRK52_RS04570 (LRK52_04570) - 1023952..1025205 (+) 1254 WP_027490749.1 glycosyltransferase family 4 protein -
  LRK52_RS04575 (LRK52_04575) - 1025202..1025498 (+) 297 WP_027490748.1 hypothetical protein -
  LRK52_RS04580 (LRK52_04580) - 1025495..1026445 (+) 951 WP_027490747.1 glycosyltransferase family 2 protein -

Sequence

Protein


Download         Length: 574 a.a.        Molecular weight: 62687.39 Da        Isoelectric Point: 6.3337

>NTDB_id=634381 LRK52_RS04550 WP_235645798.1 1019821..1021545(-) (pilB) [Rhodanobacter denitrificans strain FW104-R5]
MSSQLQPSLAGLSGMARRLVSEGVMPEDVVRKAMADSSQQKATLGAWLLDRSLVDSAELTRIASAEFGMPMMDVAALNPA
TMPLDLISEALITKHQALPLFRRGKRLYVGIADPMQSHALDEIKFHSNCMVEPILVERGSLQRVIETLLNNMRNTMPEMG
GGELDELDIEGGDDEGESSSGVDANANDDAPVVKFVNKILVDAIRRGASDIHFEPFETQYRVRLRMDGMLKAVANPPMKM
ANRISSRIKVMAQLDIAEKRVPQDGRIKLNLSKTRAVDFRVSTLPTLFGEKIVLRILDGSSARIGIEKLGYEPNQQKLYV
DAIHKPYGMVLVTGPTGSGKTVSLYTGLNMLNTAERNISTVEDPVEIRVEGINQVQQNVKRGMTFASALRSFLRQDPDVI
MVGESRDLETAEIAIKAAQTGHMVLSTLHTNDAAQTISRLMNMGIAPYNITSSVTLIIAQRLARRLHDCKKPIELPPKVL
LDAGFTQADIDAGLTIYEAGGCDGCNEGYKGRVGIYQVMPMLEDIQKIILQGGNALQIAEVAKAAGINDLRASALLKVKQ
GLTSLTEIDRVTKE

Nucleotide


Download         Length: 1725 bp        

>NTDB_id=634381 LRK52_RS04550 WP_235645798.1 1019821..1021545(-) (pilB) [Rhodanobacter denitrificans strain FW104-R5]
ATGTCATCTCAATTACAGCCGTCGCTTGCGGGCTTGTCCGGCATGGCCCGCCGGTTGGTCTCCGAAGGCGTGATGCCGGA
GGACGTGGTACGCAAGGCCATGGCCGACAGCAGCCAGCAGAAGGCCACGCTGGGCGCCTGGCTGCTGGACCGCAGCCTGG
TCGACAGCGCCGAACTGACCCGGATCGCCTCGGCCGAATTCGGCATGCCGATGATGGACGTGGCCGCGCTGAACCCGGCC
ACGATGCCGCTGGACCTGATCAGCGAGGCGCTGATCACCAAGCACCAGGCGCTGCCGCTGTTCCGCCGCGGCAAGCGGCT
GTACGTGGGCATCGCCGACCCGATGCAGTCGCATGCGCTGGACGAGATCAAGTTCCACTCCAACTGCATGGTGGAGCCGA
TCCTGGTGGAGCGTGGCTCGCTGCAGCGAGTGATCGAAACCCTGCTCAACAACATGCGCAACACCATGCCCGAGATGGGC
GGGGGCGAGCTGGACGAGCTGGACATCGAGGGCGGCGACGACGAGGGCGAGTCGAGCAGCGGCGTCGATGCGAACGCGAA
CGACGACGCGCCGGTGGTGAAGTTCGTCAACAAGATCCTGGTCGACGCGATCCGCCGCGGCGCCTCGGACATCCATTTCG
AGCCGTTCGAGACGCAGTACCGCGTGCGCCTGCGCATGGACGGCATGCTGAAGGCGGTGGCCAACCCGCCGATGAAGATG
GCCAACCGCATCTCCTCGCGCATCAAGGTGATGGCCCAGCTGGACATCGCCGAGAAGCGCGTGCCGCAGGACGGCCGCAT
CAAGCTCAACCTGTCCAAGACCCGCGCGGTCGACTTTCGCGTGAGCACGCTGCCGACGCTGTTCGGCGAGAAGATCGTGC
TGCGCATCCTGGACGGCTCCTCGGCCAGGATCGGCATCGAGAAGCTGGGCTACGAGCCGAACCAGCAGAAGCTCTACGTC
GATGCGATCCATAAGCCGTACGGCATGGTGCTGGTCACCGGCCCCACCGGCTCGGGCAAGACGGTGTCGCTGTACACCGG
CCTGAACATGCTCAACACCGCCGAGCGCAACATCTCGACGGTGGAAGACCCGGTGGAAATCCGCGTCGAGGGCATCAACC
AGGTGCAGCAGAACGTGAAGCGCGGCATGACCTTTGCCAGCGCGCTGCGCTCGTTCCTGCGCCAGGACCCGGACGTGATC
ATGGTCGGCGAGAGCCGCGACCTGGAGACCGCCGAGATCGCGATCAAGGCGGCGCAGACCGGTCACATGGTGCTGTCCAC
CCTGCACACCAACGACGCGGCGCAGACCATCTCGCGCCTGATGAACATGGGCATCGCGCCGTACAACATCACCTCGTCGG
TGACCCTGATCATCGCCCAGCGCCTGGCGCGGCGCCTGCACGACTGCAAGAAGCCGATCGAGCTGCCGCCCAAGGTGCTG
CTGGACGCCGGCTTCACCCAGGCCGACATCGACGCGGGGCTGACCATCTATGAAGCCGGCGGCTGCGACGGCTGCAACGA
GGGCTACAAGGGCCGTGTCGGCATCTACCAGGTGATGCCGATGCTGGAGGATATCCAGAAGATCATTCTGCAAGGCGGCA
ACGCGCTGCAGATCGCCGAGGTGGCCAAGGCCGCCGGCATCAACGACCTGCGCGCGTCGGCCCTGCTGAAGGTGAAGCAG
GGGCTGACCAGCCTGACCGAGATCGACCGCGTCACCAAGGAATGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(198-465)

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

(49-152)


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

54.867

98.432

0.54
  pilB Acinetobacter baumannii D1279779

53.251

99.129

0.528
  pilB Legionella pneumophila strain ERS1305867

49.387

99.477

0.491
  pilB Vibrio cholerae strain A1552

50.847

92.509

0.47
  pilB Vibrio parahaemolyticus RIMD 2210633

49.718

92.509

0.46
  pilB Vibrio campbellii strain DS40M4

49.718

92.509

0.46
  pilF Neisseria gonorrhoeae MS11

46.691

97.387

0.455
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.099

100

0.383
  pilF Thermus thermophilus HB27

38.198

96.69

0.369