Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   CPA52_RS02040 Genome accession   NZ_CP023558
Coordinates   447393..448286 (-) Length   297 a.a.
NCBI ID   WP_039038009.1    Uniprot ID   -
Organism   Pseudoalteromonas marina strain ECSMB14103     
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)
ICE 422732..446610 447393..448286 flank 783


Gene organization within MGE regions


Location: 422732..448286
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  CPA52_RS01905 (CPA52_01905) dnaG 422732..424483 (-) 1752 WP_008128763.1 DNA primase -
  CPA52_RS01910 (CPA52_01910) - 424750..425196 (-) 447 WP_008128764.1 GatB/YqeY domain-containing protein -
  CPA52_RS01915 (CPA52_01915) rpsU 425216..425431 (-) 216 WP_002957797.1 30S ribosomal protein S21 -
  CPA52_RS01920 (CPA52_01920) rsmD 425577..426182 (-) 606 WP_039037997.1 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD -
  CPA52_RS01925 (CPA52_01925) ftsY 426389..428125 (+) 1737 WP_096801192.1 signal recognition particle-docking protein FtsY -
  CPA52_RS01930 (CPA52_01930) ftsE 428211..428888 (+) 678 WP_006794808.1 cell division ATP-binding protein FtsE -
  CPA52_RS01935 (CPA52_01935) ftsX 428885..429871 (+) 987 WP_039037998.1 permease-like cell division protein FtsX -
  CPA52_RS01940 (CPA52_01940) rpoH 430313..431176 (+) 864 WP_008128777.1 RNA polymerase sigma factor RpoH -
  CPA52_RS01945 (CPA52_01945) - 431302..431598 (+) 297 WP_158649124.1 hypothetical protein -
  CPA52_RS01950 (CPA52_01950) - 431576..431992 (+) 417 WP_039038000.1 hypothetical protein -
  CPA52_RS01955 (CPA52_01955) - 431998..432747 (-) 750 WP_052242901.1 divergent polysaccharide deacetylase family protein -
  CPA52_RS01960 (CPA52_01960) - 432828..434075 (-) 1248 WP_039038001.1 S41 family peptidase -
  CPA52_RS01965 (CPA52_01965) - 434110..435249 (-) 1140 WP_039038002.1 peptidoglycan DD-metalloendopeptidase family protein -
  CPA52_RS01970 (CPA52_01970) gpmM 435253..436797 (-) 1545 WP_006794824.1 2,3-bisphosphoglycerate-independent phosphoglycerate mutase -
  CPA52_RS01975 (CPA52_01975) - 437069..437500 (+) 432 WP_006794823.1 rhodanese-like domain-containing protein -
  CPA52_RS01980 (CPA52_01980) grxC 437533..437790 (+) 258 WP_006794822.1 glutaredoxin 3 -
  CPA52_RS01985 (CPA52_01985) secB 437825..438313 (+) 489 WP_006794821.1 protein-export chaperone SecB -
  CPA52_RS01990 (CPA52_01990) gpsA 438317..439324 (+) 1008 WP_039038003.1 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase -
  CPA52_RS01995 (CPA52_01995) trmL 439399..439863 (-) 465 WP_008128796.1 tRNA (uridine(34)/cytosine(34)/5- carboxymethylaminomethyluridine(34)-2'-O)- methyltransferase TrmL -
  CPA52_RS02000 (CPA52_02000) - 440020..440886 (+) 867 WP_082014446.1 cation diffusion facilitator family transporter -
  CPA52_RS02005 (CPA52_02005) - 440846..441793 (-) 948 WP_039038004.1 alpha/beta hydrolase -
  CPA52_RS02010 (CPA52_02010) - 441797..443212 (-) 1416 WP_039038005.1 ATP-binding protein -
  CPA52_RS02015 (CPA52_02015) - 443190..443879 (-) 690 WP_039038006.1 response regulator -
  CPA52_RS02020 (CPA52_02020) - 444063..444554 (+) 492 WP_039038007.1 Spy/CpxP family protein refolding chaperone -
  CPA52_RS02025 (CPA52_02025) yacG 444636..444866 (-) 231 WP_006794561.1 DNA gyrase inhibitor YacG -
  CPA52_RS02030 (CPA52_02030) pilB 444934..446610 (-) 1677 WP_008131082.1 type IV-A pilus assembly ATPase PilB Machinery gene
  CPA52_RS02035 (CPA52_02035) coaE 446743..447375 (-) 633 WP_039038008.1 dephospho-CoA kinase -
  CPA52_RS02040 (CPA52_02040) pilD 447393..448286 (-) 894 WP_039038009.1 A24 family peptidase Machinery gene

Sequence

Protein


Download         Length: 297 a.a.        Molecular weight: 32791.03 Da        Isoelectric Point: 7.5495

>NTDB_id=248368 CPA52_RS02040 WP_039038009.1 447393..448286(-) (pilD) [Pseudoalteromonas marina strain ECSMB14103]
MQSIIEVMQSQLWFYLTTVGLVSLCVGSFLNVVIYRLPLMMQREWQSECRLLLEDELNTNQAKPKNTSEHFNLVKPNSTC
PKCKTAIKPWQNIPIISWLILKGKCASCSNPISIRYPAIEAITALLSLVVAYTFGATEQALLYIVITWALVALTFIDIDH
MLLPDQLTLPLVWLALIAAVAGITITPSDAIMGAAFGYLSLWSVFWLFKLLTGKEGMGYGDFKLLALFGALLGWQSLLTI
ILLSSVVGAIIGIALLTIQGKDKATPIPFGPYLAIAGWITLLWGNQLQSAYFNLIGY

Nucleotide


Download         Length: 894 bp        

>NTDB_id=248368 CPA52_RS02040 WP_039038009.1 447393..448286(-) (pilD) [Pseudoalteromonas marina strain ECSMB14103]
ATGCAAAGTATTATTGAAGTAATGCAAAGCCAACTGTGGTTTTATTTAACCACCGTTGGCTTAGTTAGTTTATGTGTGGG
TAGTTTTTTAAACGTAGTTATCTACCGTTTGCCGCTTATGATGCAGCGAGAGTGGCAAAGCGAGTGTAGGCTATTACTTG
AAGACGAGCTCAATACCAATCAAGCTAAACCAAAAAACACCAGCGAGCATTTTAATCTTGTAAAACCCAACTCTACCTGC
CCTAAATGTAAAACGGCCATTAAGCCTTGGCAAAATATTCCTATCATTAGCTGGTTAATACTTAAAGGTAAATGCGCAAG
TTGTAGTAACCCTATCTCTATTCGATACCCTGCTATTGAGGCCATTACCGCTCTATTAAGTTTAGTGGTTGCTTATACCT
TTGGCGCAACAGAACAAGCATTATTATACATAGTGATCACGTGGGCACTTGTGGCACTTACCTTTATTGATATAGACCAC
ATGTTACTGCCTGACCAGCTCACTTTACCGCTTGTTTGGCTGGCACTGATTGCCGCTGTTGCCGGAATTACAATTACGCC
AAGTGATGCAATTATGGGTGCCGCTTTTGGTTATTTAAGCTTATGGAGTGTTTTTTGGTTATTTAAATTGCTAACAGGCA
AAGAAGGCATGGGCTATGGCGACTTTAAACTGTTAGCGTTATTTGGTGCTCTGCTAGGCTGGCAATCGTTACTCACTATA
ATACTGCTTTCAAGTGTTGTTGGCGCCATTATTGGTATCGCCTTGTTAACTATTCAGGGTAAAGATAAAGCAACCCCTAT
TCCATTTGGGCCCTACCTAGCAATTGCTGGTTGGATCACGTTACTGTGGGGTAACCAATTGCAAAGCGCGTATTTTAACT
TAATTGGTTACTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(145-253)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(22-134)


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
  pilD Acinetobacter baumannii D1279779

53.242

98.653

0.525
  pilD Acinetobacter nosocomialis M2

53.242

98.653

0.525
  pilD Vibrio cholerae strain A1552

53.082

98.316

0.522
  pilD Vibrio campbellii strain DS40M4

52.74

98.316

0.519
  pilD Neisseria gonorrhoeae MS11

46.241

89.562

0.414

Multiple sequence alignment