Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   CJA_RS13190 Genome accession   NC_010995
Coordinates   3213438..3214364 (+) Length   308 a.a.
NCBI ID   WP_012488326.1    Uniprot ID   B3PBG5
Organism   Cellvibrio japonicus Ueda107     
Function   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 3194456..3213384 3213438..3214364 flank 54


Gene organization within MGE regions


Location: 3194456..3214364
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  CJA_RS13125 (CJA_2719) - 3194507..3195325 (+) 819 WP_012488313.1 ABC transporter permease -
  CJA_RS13130 (CJA_2720) - 3195398..3196171 (+) 774 WP_012488314.1 ABC transporter ATP-binding protein -
  CJA_RS13135 (CJA_2721) - 3196202..3196939 (+) 738 WP_012488315.1 urea amidolyase associated protein UAAP1 -
  CJA_RS13140 (CJA_2722) - 3196957..3197598 (+) 642 WP_012488316.1 urea amidolyase associated protein UAAP2 -
  CJA_RS13145 (CJA_2723) uca 3197686..3201303 (+) 3618 WP_012488317.1 urea carboxylase -
  CJA_RS13150 (CJA_2724) - 3201370..3203835 (-) 2466 WP_012488318.1 DUF1631 domain-containing protein -
  CJA_RS13155 (CJA_2725) nadC 3204037..3204921 (+) 885 WP_012488319.1 carboxylating nicotinate-nucleotide diphosphorylase -
  CJA_RS13160 (CJA_2726) - 3204955..3207981 (-) 3027 WP_012488320.1 fused MFS/spermidine synthase -
  CJA_RS13165 (CJA_2727) tfpZ 3208083..3208826 (-) 744 WP_012488321.1 TfpX/TfpZ family type IV pilin accessory protein -
  CJA_RS19890 (CJA_2728) - 3208852..3209337 (-) 486 WP_012488322.1 pilin -
  CJA_RS20025 - 3209443..3209760 (-) 318 WP_238526867.1 pilin -
  CJA_RS20030 - 3209835..3209943 (-) 109 Protein_2594 pilin -
  CJA_RS13180 (CJA_2730) pilB 3210370..3212091 (+) 1722 WP_012488324.1 type IV-A pilus assembly ATPase PilB Machinery gene
  CJA_RS13185 (CJA_2731) pilC 3212098..3213384 (+) 1287 WP_012488325.1 type II secretion system F family protein Machinery gene
  CJA_RS13190 (CJA_2732) pilD 3213438..3214364 (+) 927 WP_012488326.1 prepilin peptidase Machinery gene

Sequence

Protein


Download         Length: 308 a.a.        Molecular weight: 33794.97 Da        Isoelectric Point: 5.2446

>NTDB_id=31130 CJA_RS13190 WP_012488326.1 3213438..3214364(+) (pilD) [Cellvibrio japonicus Ueda107]
MPLFDVLALYPSFTFISALILGLLVGSFLNVVIYRLPKMMEAEWREQCQQLIYEADHLVVTESEQANISLDSTSIAKKET
FNLCAPRSSCPHCGHNITALENIPIISYVFLGGKCSACKNTISLRYPSVELVTGVLSALAIAFFGATWAGLAALVLTWAL
IALTMIDLDTYLLPDDITLPLLWLGLIVNSFGLFTDLASAFWGAVAGYLTLWSVYQLFKLLTGKEGMGYGDFKLLAALGA
WMGWQMLPQIILLSSLVGAVIGITLIIVRGRDRNIPIPFGPYLAIAGWIAFLWGDRINATYLKIFVPS

Nucleotide


Download         Length: 927 bp        

>NTDB_id=31130 CJA_RS13190 WP_012488326.1 3213438..3214364(+) (pilD) [Cellvibrio japonicus Ueda107]
ATGCCACTGTTTGATGTACTTGCTTTATATCCATCATTTACCTTTATATCTGCCTTGATTTTAGGGTTATTGGTAGGCAG
TTTTTTAAATGTCGTTATCTATCGACTTCCCAAAATGATGGAGGCCGAATGGAGAGAGCAATGTCAACAATTGATATATG
AAGCAGACCACTTGGTTGTCACCGAATCAGAACAAGCAAATATTTCACTTGATTCTACTTCTATAGCCAAAAAAGAAACA
TTCAATCTGTGTGCGCCTCGCTCATCTTGTCCTCATTGCGGACACAATATCACTGCGTTGGAAAACATCCCGATCATCAG
TTATGTATTTTTAGGGGGTAAATGTTCCGCCTGCAAAAATACAATCTCCCTGCGCTATCCCTCGGTTGAGCTTGTAACTG
GCGTACTTTCTGCGCTAGCCATCGCGTTTTTCGGGGCAACCTGGGCAGGTTTGGCTGCATTGGTGCTTACCTGGGCACTG
ATCGCGTTGACCATGATTGATCTGGATACCTATCTGCTGCCTGATGACATTACCTTACCCTTGCTCTGGTTAGGGCTTAT
CGTAAACAGTTTTGGATTGTTTACTGATCTGGCCAGTGCTTTTTGGGGAGCGGTAGCGGGATACCTGACCCTCTGGTCTG
TTTATCAGTTGTTTAAGTTGTTAACCGGTAAGGAGGGTATGGGTTATGGCGATTTCAAGTTGCTGGCCGCATTGGGCGCA
TGGATGGGCTGGCAAATGCTGCCGCAAATCATCTTACTGTCTTCCCTGGTAGGTGCGGTGATTGGTATTACGTTGATCAT
TGTGAGAGGGCGCGACCGGAATATTCCTATCCCTTTTGGCCCTTATCTGGCGATTGCGGGCTGGATTGCTTTTCTCTGGG
GCGATAGGATTAACGCGACCTATCTCAAGATTTTTGTTCCTTCCTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(154-263)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-142)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB B3PBG5

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
  pilD Acinetobacter baumannii D1279779

53.819

93.506

0.503
  pilD Acinetobacter nosocomialis M2

53.472

93.506

0.5
  pilD Vibrio campbellii strain DS40M4

50.169

95.779

0.481
  pilD Vibrio cholerae strain A1552

48.355

98.701

0.477
  pilD Neisseria gonorrhoeae MS11

48.11

94.481

0.455

Multiple sequence alignment