Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   RD110_RS06860 Genome accession   NZ_CP019236
Coordinates   1458556..1460292 (-) Length   578 a.a.
NCBI ID   WP_076197919.1    Uniprot ID   A0A1P8JT70
Organism   Rhodoferax koreense strain DCY-110     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1453556..1465292
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RD110_RS06830 (RD110_06830) zapD 1453640..1454395 (-) 756 WP_076197907.1 cell division protein ZapD -
  RD110_RS06835 (RD110_06835) coaE 1454421..1455020 (-) 600 WP_076197909.1 dephospho-CoA kinase -
  RD110_RS06840 (RD110_06840) - 1455034..1455903 (-) 870 WP_076197911.1 A24 family peptidase -
  RD110_RS06845 (RD110_06845) - 1456063..1456674 (+) 612 WP_076197913.1 2-hydroxychromene-2-carboxylate isomerase -
  RD110_RS06850 (RD110_06850) - 1456671..1457297 (+) 627 WP_076197915.1 glutathione binding-like protein -
  RD110_RS06855 (RD110_06855) pilC 1457314..1458531 (-) 1218 WP_076197917.1 type II secretion system F family protein Machinery gene
  RD110_RS06860 (RD110_06860) pilB 1458556..1460292 (-) 1737 WP_076197919.1 type IV-A pilus assembly ATPase PilB Machinery gene
  RD110_RS06865 (RD110_06865) - 1460375..1461379 (-) 1005 WP_076197921.1 RluA family pseudouridine synthase -
  RD110_RS06870 (RD110_06870) - 1461921..1465040 (+) 3120 WP_076197923.1 Rne/Rng family ribonuclease -

Sequence

Protein


Download         Length: 578 a.a.        Molecular weight: 62725.13 Da        Isoelectric Point: 5.6180

>NTDB_id=214317 RD110_RS06860 WP_076197919.1 1458556..1460292(-) (pilB) [Rhodoferax koreense strain DCY-110]
MAAVDSFKQDAPTVALPGLGRALILAGKLGQKAAEDIYRKAQTGRTSFIAELVGSGAVSAYDLAHTMSTAFAAPLLDIEA
IDLQRLPKDLLDAKICQAYRVVVLSKRNNRLIVATADPSDQEAAEKIKFSTQMGVDWIIAEYDKLSKLVDASAVSANEAM
EGLVGGGDFDFEDSVISAAADVAEVNTSEVEDAPVVKFLHKMLLDAFGMRASDLHFEPYEHNYRVRFRIDGELREIASPP
VAIKEKLASRIKVISRLDISEKRVPQDGKMKLKVGPDRVIDFRVSTLPTLFGEKIVIRILDPSSAKLGIDALGYEPEEKA
RLMHAIGRPYGMILVTGPTGSGKTVSLYTCLNLLNKPGVNIATAEDPSEINLPGVNQVNVNEKAGLTFAVALKSFLRQDP
DIIMVGEIRDLETADISIKAAQTGHLVLSTLHTNDAPTTLTRMRNMGIAPFNIASSVILITAQRLARRLCPQCKTPLDIP
NKTLLEAGYEEEELDGSWQTYGPVGCSACNNGYKGRVGIYQVMPISEEIQRIILRDGNAPEIAAQAKREGVRSLRQAGLY
KAKLGLTSLEEVLAVSNE

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=214317 RD110_RS06860 WP_076197919.1 1458556..1460292(-) (pilB) [Rhodoferax koreense strain DCY-110]
ATGGCCGCAGTCGATTCGTTTAAACAGGACGCCCCCACGGTCGCGCTGCCAGGGCTCGGCCGCGCACTGATACTGGCCGG
CAAGCTCGGTCAAAAAGCGGCGGAAGACATCTACCGCAAGGCGCAGACCGGCCGCACCAGCTTCATTGCCGAACTGGTCG
GCTCGGGTGCCGTGTCGGCCTACGATCTGGCGCACACCATGTCCACCGCGTTCGCGGCACCGCTGCTGGACATCGAGGCC
ATCGACCTGCAGCGCCTGCCCAAGGACCTGCTCGACGCCAAGATCTGCCAGGCCTACCGCGTGGTGGTGCTGAGCAAGCG
CAACAACCGGCTGATCGTCGCCACGGCCGACCCGTCCGACCAGGAGGCTGCCGAGAAGATCAAGTTCTCCACCCAGATGG
GCGTGGACTGGATCATTGCCGAATACGACAAGCTCTCCAAGCTGGTCGATGCCAGCGCGGTATCGGCCAACGAGGCCATG
GAAGGCCTGGTCGGCGGCGGCGATTTCGATTTCGAGGACAGCGTGATCTCTGCGGCCGCCGACGTGGCCGAGGTGAACAC
CTCCGAGGTCGAAGACGCGCCGGTGGTGAAGTTCCTGCACAAGATGCTGCTCGACGCGTTCGGCATGCGCGCCTCCGACC
TGCACTTCGAGCCCTACGAACACAACTACCGCGTGCGCTTCCGCATCGACGGCGAACTGCGCGAGATCGCCTCGCCGCCG
GTGGCCATCAAGGAAAAGCTGGCCTCGCGCATCAAGGTCATCTCGCGGCTGGACATCTCCGAGAAACGCGTGCCGCAGGA
CGGCAAGATGAAGCTCAAGGTCGGCCCCGACCGCGTGATCGACTTCCGCGTGAGCACCCTGCCCACGCTGTTCGGCGAGA
AGATCGTGATCCGGATCCTGGACCCGAGCAGCGCCAAGCTCGGCATCGACGCGCTCGGCTACGAACCCGAGGAAAAGGCG
CGGCTGATGCATGCCATCGGCCGGCCCTACGGCATGATCCTGGTGACCGGGCCCACCGGCTCGGGCAAGACCGTGTCGCT
CTACACCTGCCTGAACCTCTTGAACAAGCCGGGCGTGAACATCGCCACCGCCGAAGACCCGTCGGAAATCAACCTGCCCG
GCGTGAACCAGGTGAACGTGAACGAGAAGGCCGGACTGACCTTCGCCGTGGCGCTCAAGTCCTTCCTGCGACAGGATCCA
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAAACCGCTGACATCTCGATCAAGGCCGCGCAGACCGGCCACCTGGT
GCTGTCCACGCTGCACACCAACGACGCGCCGACCACCCTCACCCGCATGCGCAACATGGGCATCGCGCCGTTCAACATCG
CCTCCAGCGTGATCCTGATCACCGCGCAGCGGCTGGCGCGGCGCCTCTGTCCGCAGTGCAAGACGCCGCTGGACATCCCG
AACAAGACGCTGCTCGAAGCCGGCTACGAGGAAGAAGAACTCGACGGCAGCTGGCAGACCTACGGCCCGGTCGGCTGCTC
GGCCTGCAACAACGGCTACAAGGGCCGTGTCGGCATCTACCAGGTGATGCCGATCTCCGAGGAAATCCAGCGCATCATCC
TGCGGGACGGCAATGCGCCGGAGATCGCCGCCCAGGCCAAGCGCGAAGGCGTGCGCTCGCTGCGCCAGGCCGGCCTGTAC
AAGGCCAAGCTGGGACTGACCTCGCTGGAAGAAGTGCTCGCGGTGAGCAACGAGTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(52-150)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A1P8JT70

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

53.779

98.443

0.529
  pilB Acinetobacter baumannii D1279779

53.263

98.097

0.522
  pilF Neisseria gonorrhoeae MS11

51.418

97.578

0.502
  pilB Legionella pneumophila strain ERS1305867

50.353

97.924

0.493
  pilB Vibrio campbellii strain DS40M4

43.662

98.27

0.429
  pilB Vibrio parahaemolyticus RIMD 2210633

44.182

95.156

0.42
  pilB Vibrio cholerae strain A1552

45.489

90.138

0.41
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

40.414

92.042

0.372
  pilF Thermus thermophilus HB27

37.833

97.405

0.369

Multiple sequence alignment