Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   SAMA_RS02000 Genome accession   NC_008700
Coordinates   443934..444848 (-) Length   304 a.a.
NCBI ID   WP_011758488.1    Uniprot ID   A1S2H2
Organism   Shewanella amazonensis SB2B     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 438934..449848
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SAMA_RS01980 (Sama_0363) mutT 441876..442271 (-) 396 WP_011758484.1 8-oxo-dGTP diphosphatase MutT -
  SAMA_RS01985 (Sama_0364) yacG 442313..442528 (-) 216 WP_011758485.1 DNA gyrase inhibitor YacG -
  SAMA_RS01990 (Sama_0365) zapD 442590..443324 (-) 735 WP_011758486.1 cell division protein ZapD -
  SAMA_RS01995 (Sama_0366) coaE 443317..443934 (-) 618 WP_011758487.1 dephospho-CoA kinase -
  SAMA_RS02000 (Sama_0367) pilD 443934..444848 (-) 915 WP_011758488.1 A24 family peptidase Machinery gene
  SAMA_RS02005 (Sama_0368) pilC 444884..446143 (-) 1260 WP_011758489.1 type II secretion system F family protein Machinery gene
  SAMA_RS02010 (Sama_0369) pilB 446213..447919 (-) 1707 WP_011758490.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SAMA_RS02015 (Sama_0370) - 447973..448446 (-) 474 WP_011758491.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -

Sequence

Protein


Download         Length: 304 a.a.        Molecular weight: 33880.27 Da        Isoelectric Point: 6.9391

>NTDB_id=27057 SAMA_RS02000 WP_011758488.1 443934..444848(-) (pilD) [Shewanella amazonensis SB2B]
MTEFISLMSQFPWLFILLAFLFAATIGSFLNVVIHRLPVMMKREWQQECNAYLEEYQPELVKKLGKANLDKPIDSYPERY
NLIVPGSSCPKCGTIIKPWHNLPVLGWIILGGKCASCKAPISSRYPIVEAFTGLTVAALAWHFGPTWQFVTAALLTFGLI
AMSGIDLDEMLLPDSLTLPLLWLGLLLNYHGLFTTLEDALIGAAAGYLSLWSVYWLFKLTTGKEGMGYGDFKLMGLFGAW
LGWQMLPLIILLSSLVGAVVGILMMVWKSHKRENPIPFGPYIAAAGWIALIWGQDIVSWYLGSL

Nucleotide


Download         Length: 915 bp        

>NTDB_id=27057 SAMA_RS02000 WP_011758488.1 443934..444848(-) (pilD) [Shewanella amazonensis SB2B]
ATGACTGAATTTATCTCCCTAATGAGCCAGTTTCCCTGGCTCTTTATTTTGCTCGCATTCCTGTTCGCAGCCACCATTGG
TAGCTTCCTCAATGTCGTAATTCATCGCTTGCCTGTGATGATGAAAAGAGAATGGCAGCAGGAATGTAATGCCTATCTTG
AAGAGTACCAACCTGAACTTGTAAAAAAGCTTGGCAAAGCGAATTTGGACAAGCCAATTGATAGCTATCCAGAACGTTAT
AACCTGATTGTGCCAGGCTCATCCTGCCCTAAGTGCGGTACTATCATTAAGCCCTGGCACAATCTGCCTGTACTGGGCTG
GATAATCCTTGGCGGTAAATGCGCTTCCTGCAAAGCCCCAATTTCCAGCCGTTATCCCATAGTGGAAGCCTTTACCGGCC
TGACTGTTGCAGCACTGGCGTGGCACTTTGGTCCCACGTGGCAATTTGTCACAGCAGCATTACTCACCTTTGGCTTAATT
GCCATGTCGGGAATCGACCTGGATGAAATGCTACTGCCAGACAGCCTCACTCTTCCTCTGCTGTGGCTGGGATTACTGCT
TAATTATCATGGCCTATTTACCACTCTGGAAGATGCACTCATTGGTGCTGCAGCCGGTTATCTGTCGCTTTGGTCTGTGT
ATTGGCTGTTTAAGCTCACCACAGGCAAAGAGGGCATGGGCTACGGTGATTTTAAACTCATGGGGCTCTTTGGTGCTTGG
CTCGGCTGGCAAATGCTGCCGTTAATTATTCTTCTCTCAAGCCTGGTCGGTGCTGTCGTTGGCATACTGATGATGGTTTG
GAAAAGCCATAAGCGTGAAAATCCCATCCCATTTGGTCCCTATATCGCGGCCGCTGGCTGGATAGCACTTATTTGGGGAC
AAGATATTGTCAGCTGGTATCTGGGTTCTCTTTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-143)

Type IV leader peptidase family (Peptidase_A24)

(154-262)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A1S2H2

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

49.834

99.013

0.493
  pilD Vibrio cholerae strain A1552

49.502

99.013

0.49
  pilD Acinetobacter baumannii D1279779

48.789

95.066

0.464
  pilD Acinetobacter nosocomialis M2

48.097

95.066

0.457
  pilD Neisseria gonorrhoeae MS11

41.86

99.013

0.414

Multiple sequence alignment