Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   C1H71_RS06450 Genome accession   NZ_CP025781
Coordinates   1466488..1467357 (+) Length   289 a.a.
NCBI ID   WP_130105824.1    Uniprot ID   A0A7G3G7Y6
Organism   Iodobacter fluviatilis strain PCH194     
Function   type IV pilus biogenesis and function (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)
ICE 1449815..1471479 1466488..1467357 within 0


Gene organization within MGE regions


Location: 1449815..1471479
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  C1H71_RS06365 (C1H71_06430) icd 1450432..1451655 (+) 1224 WP_130105810.1 NADP-dependent isocitrate dehydrogenase -
  C1H71_RS06370 (C1H71_06435) - 1451777..1451980 (-) 204 WP_046351602.1 cold-shock protein -
  C1H71_RS06375 (C1H71_06440) - 1452093..1452296 (-) 204 WP_046351601.1 cold-shock protein -
  C1H71_RS06380 (C1H71_06445) clpS 1452608..1452919 (+) 312 WP_130105811.1 ATP-dependent Clp protease adapter ClpS -
  C1H71_RS06385 (C1H71_06450) clpA 1452916..1455180 (+) 2265 WP_130105812.1 ATP-dependent Clp protease ATP-binding subunit ClpA -
  C1H71_RS06390 (C1H71_06455) - 1455265..1456089 (-) 825 WP_130105813.1 mechanosensitive ion channel family protein -
  C1H71_RS06395 (C1H71_06460) xerD 1456153..1457076 (-) 924 WP_130105814.1 site-specific tyrosine recombinase XerD -
  C1H71_RS21345 (C1H71_06465) - 1457054..1457542 (-) 489 WP_130105815.1 methylated-DNA--[protein]-cysteine S-methyltransferase -
  C1H71_RS06405 (C1H71_06470) rplS 1457622..1458005 (-) 384 WP_130105816.1 50S ribosomal protein L19 -
  C1H71_RS06410 (C1H71_06475) trmD 1458047..1458835 (-) 789 WP_374704454.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  C1H71_RS06415 (C1H71_06480) rimM 1458828..1459361 (-) 534 WP_262488407.1 ribosome maturation factor RimM -
  C1H71_RS06420 (C1H71_06485) rpsP 1459370..1459627 (-) 258 WP_130105818.1 30S ribosomal protein S16 -
  C1H71_RS06425 (C1H71_06490) ffh 1459857..1461209 (-) 1353 WP_130105819.1 signal recognition particle protein -
  C1H71_RS06430 (C1H71_06495) - 1461269..1462111 (+) 843 WP_130105820.1 inner membrane protein YpjD -
  C1H71_RS06435 (C1H71_06500) - 1462150..1463412 (+) 1263 WP_130105821.1 HlyC/CorC family transporter -
  C1H71_RS06440 (C1H71_06505) pilB 1463537..1465246 (+) 1710 WP_130105822.1 type IV-A pilus assembly ATPase PilB Machinery gene
  C1H71_RS06445 (C1H71_06510) pilC 1465265..1466488 (+) 1224 WP_130105823.1 type II secretion system F family protein Machinery gene
  C1H71_RS06450 (C1H71_06515) pilD 1466488..1467357 (+) 870 WP_130105824.1 A24 family peptidase Machinery gene
  C1H71_RS06455 (C1H71_06520) coaE 1467372..1467965 (+) 594 WP_130105825.1 dephospho-CoA kinase -
  C1H71_RS06460 (C1H71_06525) zapD 1468044..1468802 (+) 759 WP_130105826.1 cell division protein ZapD -
  C1H71_RS06465 (C1H71_06530) - 1468799..1468990 (+) 192 WP_130105827.1 DNA gyrase inhibitor YacG -
  C1H71_RS06470 (C1H71_06535) - 1469083..1469826 (+) 744 WP_130105828.1 GNAT family N-acetyltransferase -
  C1H71_RS06475 (C1H71_06540) - 1470011..1470685 (+) 675 WP_188053627.1 1-acyl-sn-glycerol-3-phosphate acyltransferase -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 31332.64 Da        Isoelectric Point: 7.8812

>NTDB_id=263740 C1H71_RS06450 WP_130105824.1 1466488..1467357(+) (pilD) [Iodobacter fluviatilis strain PCH194]
MIELFLDNPAIFGGFLFALGLLVGSFLNVVIHRIPKMMEQQFRQECQLIDAPIDAPMPQATCYNLIVPRSACPSCGHAIS
ALENIPVISYLMLKGRCRGCKIRISPRYPLVELLCATLTAVAGLHFGVTITAIAAILLTWFLIALVFIDADTYLLPDSIT
LPLLWLGLLFNLNNVFVPLDQAVIGAVAGYLVLWSVYWIFKLITGKEGMGYGDFKLLAALGAWFGWQALPSVILLSSISG
AVIGIALAILAKRGMGKPMPFGPYLGIAGWLTLIFGTTLQQMIFNGGAI

Nucleotide


Download         Length: 870 bp        

>NTDB_id=263740 C1H71_RS06450 WP_130105824.1 1466488..1467357(+) (pilD) [Iodobacter fluviatilis strain PCH194]
ATGATTGAGTTGTTTTTAGATAACCCCGCCATATTTGGCGGGTTTTTATTCGCACTAGGCTTATTGGTTGGTAGTTTTTT
AAATGTCGTAATCCATCGCATTCCCAAAATGATGGAGCAGCAATTCAGGCAAGAATGCCAGCTGATTGATGCCCCCATCG
ACGCGCCGATGCCACAAGCCACTTGCTATAACTTAATTGTTCCTCGCTCAGCCTGCCCCAGCTGTGGCCATGCAATAAGT
GCATTAGAAAATATTCCCGTGATTAGCTATCTAATGTTAAAGGGGCGCTGTCGAGGGTGCAAGATTCGCATTAGTCCACG
TTACCCCTTAGTCGAGCTACTTTGTGCAACGCTTACCGCTGTTGCTGGGCTGCACTTTGGAGTAACCATTACAGCCATCG
CAGCTATTTTACTCACATGGTTTTTGATCGCCTTAGTCTTTATTGATGCCGATACCTATTTACTGCCAGACAGCATCACG
CTGCCCTTGCTTTGGCTAGGACTTCTATTCAACTTAAATAATGTTTTTGTACCTTTAGATCAGGCTGTAATTGGGGCCGT
TGCCGGTTACCTTGTACTGTGGAGCGTGTACTGGATATTCAAACTCATTACCGGCAAGGAAGGAATGGGCTATGGTGACT
TCAAACTACTTGCAGCCCTTGGCGCATGGTTCGGATGGCAAGCACTGCCGAGCGTCATATTACTTTCGTCAATTAGCGGA
GCAGTAATCGGCATTGCACTCGCCATCCTTGCTAAACGCGGCATGGGAAAGCCTATGCCTTTTGGCCCTTATTTAGGTAT
TGCAGGCTGGCTCACATTAATTTTTGGCACCACGTTACAACAAATGATCTTTAATGGTGGAGCCATTTAG

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(19-126)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A7G3G7Y6

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 Vibrio campbellii strain DS40M4

51.399

98.962

0.509
  pilD Vibrio cholerae strain A1552

50.526

98.616

0.498
  pilD Acinetobacter baumannii D1279779

50.373

92.734

0.467
  pilD Acinetobacter nosocomialis M2

49.627

92.734

0.46
  pilD Neisseria gonorrhoeae MS11

50.196

88.235

0.443

Multiple sequence alignment