Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   NIBR502773_RS19550 Genome accession   NZ_CP041189
Coordinates   4247444..4248310 (-) Length   288 a.a.
NCBI ID   WP_141156726.1    Uniprot ID   -
Organism   Pseudomonas sp. NIBRBAC000502773     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4242444..4253310
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NIBR502773_RS19510 (NIBR502773_19510) - 4242865..4244163 (-) 1299 WP_065924079.1 NAD(P)/FAD-dependent oxidoreductase -
  NIBR502773_RS19515 (NIBR502773_19515) - 4244224..4244397 (-) 174 WP_043293437.1 DUF3094 family protein -
  NIBR502773_RS19520 (NIBR502773_19520) - 4244452..4245081 (-) 630 WP_027604891.1 DUF1780 domain-containing protein -
  NIBR502773_RS19525 (NIBR502773_19525) - 4245186..4245653 (+) 468 WP_141156724.1 FAD/FMN-containing dehydrogenase -
  NIBR502773_RS19530 (NIBR502773_19530) - 4245650..4246339 (+) 690 WP_141156725.1 energy-coupling factor ABC transporter permease -
  NIBR502773_RS19535 (NIBR502773_19535) - 4246415..4246630 (+) 216 WP_003171680.1 hypothetical protein -
  NIBR502773_RS19540 (NIBR502773_19540) yacG 4246627..4246827 (-) 201 WP_027604888.1 DNA gyrase inhibitor YacG -
  NIBR502773_RS19545 (NIBR502773_19545) coaE 4246824..4247447 (-) 624 WP_115486604.1 dephospho-CoA kinase -
  NIBR502773_RS19550 (NIBR502773_19550) pilD 4247444..4248310 (-) 867 WP_141156726.1 A24 family peptidase Machinery gene
  NIBR502773_RS19555 (NIBR502773_19555) pilC 4248307..4249515 (-) 1209 WP_141156727.1 type II secretion system F family protein Machinery gene
  NIBR502773_RS19560 (NIBR502773_19560) - 4249718..4250128 (+) 411 WP_141157855.1 pilin -
  NIBR502773_RS19565 (NIBR502773_19565) - 4250164..4251564 (+) 1401 WP_141156728.1 O-antigen ligase -
  NIBR502773_RS19575 (NIBR502773_19575) - 4251836..4252141 (+) 306 WP_027604882.1 DUF6388 family protein -
  NIBR502773_RS31155 - 4252163..4252252 (+) 90 Protein_3827 outer membrane lipoprotein carrier protein LolA -
  NIBR502773_RS19580 (NIBR502773_19580) nadC 4252260..4253108 (-) 849 WP_027604881.1 carboxylating nicotinate-nucleotide diphosphorylase -

Sequence

Protein


Download         Length: 288 a.a.        Molecular weight: 31911.05 Da        Isoelectric Point: 7.4318

>NTDB_id=370314 NIBR502773_RS19550 WP_141156726.1 4247444..4248310(-) (pilD) [Pseudomonas sp. NIBRBAC000502773]
MSLLLNEHPLAFVTVALVLGLIVGSFLNVLVWRLPKMLEREWRAQAHEVLGLPAEPGGPTYNLMHPNSCCPHCDHPIRPW
ENIPLLSYLMLRGRCAHCQGTISPRYPFTELACGLISAWVAWHFGFGWQAAAVLVLSWGLLAMSLIDADHQLLPDVLVLP
LLWLGLIVNSFGLLTTLPDALWGTVIGYMSLWSVFWLFKLVTGKDGMGHGDFKLLALLGAWGGWQILPMTLLMSSLVGVF
VGLILMRLRKTLASTPMPFGPYLAIAGWIALLWGGQITDFYLQSVGFR

Nucleotide


Download         Length: 867 bp        

>NTDB_id=370314 NIBR502773_RS19550 WP_141156726.1 4247444..4248310(-) (pilD) [Pseudomonas sp. NIBRBAC000502773]
TTGAGCCTGCTGCTGAACGAGCACCCATTGGCCTTTGTCACAGTCGCGCTGGTACTGGGGCTGATCGTCGGCAGTTTCCT
CAACGTGCTGGTCTGGCGCCTGCCAAAAATGCTCGAACGGGAATGGCGTGCCCAGGCCCATGAAGTGCTCGGCTTGCCTG
CCGAACCTGGCGGGCCGACCTACAACCTGATGCACCCCAACTCATGCTGCCCACACTGTGACCATCCCATCCGGCCGTGG
GAAAATATCCCACTGCTCAGCTACCTGATGCTCAGGGGGCGCTGCGCCCATTGCCAGGGAACCATCAGCCCCCGCTACCC
TTTCACGGAACTCGCCTGCGGGTTGATCTCGGCCTGGGTCGCCTGGCATTTCGGCTTTGGCTGGCAGGCCGCAGCGGTGC
TGGTGTTGAGTTGGGGGTTGCTGGCAATGAGCCTGATCGACGCAGACCACCAGTTGCTCCCGGATGTTCTGGTGCTGCCA
TTGCTGTGGCTGGGCCTGATCGTCAACAGTTTTGGATTACTGACGACATTACCCGACGCACTATGGGGCACCGTGATCGG
CTACATGAGCCTGTGGAGCGTGTTCTGGCTGTTCAAGCTGGTCACCGGCAAAGACGGTATGGGCCACGGTGATTTCAAGT
TACTGGCCTTGCTCGGCGCCTGGGGCGGCTGGCAGATATTGCCGATGACACTGTTGATGTCGTCGCTGGTGGGGGTGTTT
GTCGGGTTGATCCTGATGCGCCTGCGCAAGACCCTGGCGTCCACGCCGATGCCGTTTGGTCCGTATCTGGCAATTGCCGG
CTGGATTGCATTGCTCTGGGGTGGTCAAATAACCGACTTCTATTTGCAGTCTGTCGGTTTCAGATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(134-243)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-124)


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 Vibrio cholerae strain A1552

52.982

98.958

0.524
  pilD Vibrio campbellii strain DS40M4

49.296

98.611

0.486
  pilD Acinetobacter baumannii D1279779

49.817

94.792

0.472
  pilD Acinetobacter nosocomialis M2

49.817

94.792

0.472
  pilD Neisseria gonorrhoeae MS11

50.37

93.75

0.472

Multiple sequence alignment