Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   FD644_RS17920 Genome accession   NZ_CP040182
Coordinates   3893128..3893970 (-) Length   280 a.a.
NCBI ID   WP_071681046.1    Uniprot ID   -
Organism   Serratia fonticola strain MS5     
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)
Prophage 3866465..3904946 3893128..3893970 within 0


Gene organization within MGE regions


Location: 3866465..3904946
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  FD644_RS17750 (FD644_17750) yejK 3866465..3867469 (-) 1005 WP_024486230.1 nucleoid-associated protein YejK -
  FD644_RS17755 (FD644_17755) - 3867631..3867858 (+) 228 WP_071681022.1 YejL family protein -
  FD644_RS17760 (FD644_17760) yejM 3867868..3869652 (+) 1785 WP_071681023.1 LPS biosynthesis-modulating metalloenzyme YejM -
  FD644_RS17770 (FD644_17770) - 3870004..3871254 (+) 1251 WP_071681024.1 integrase domain-containing protein -
  FD644_RS17775 (FD644_17775) - 3871354..3872046 (+) 693 WP_254698849.1 hypothetical protein -
  FD644_RS17780 (FD644_17780) - 3872273..3872485 (+) 213 WP_071681025.1 AlpA family transcriptional regulator -
  FD644_RS17785 (FD644_17785) - 3872619..3873389 (+) 771 WP_071681026.1 antA/AntB antirepressor family protein -
  FD644_RS26605 - 3873516..3873830 (-) 315 WP_081366984.1 YlcI/YnfO family protein -
  FD644_RS26610 - 3874027..3874221 (+) 195 WP_175415627.1 host cell division inhibitor Icd-like protein -
  FD644_RS17800 (FD644_17800) - 3874437..3874736 (+) 300 WP_071681028.1 DUF4222 domain-containing protein -
  FD644_RS17805 (FD644_17805) - 3874736..3877504 (+) 2769 WP_071681136.1 TOPRIM and DUF927 domain-containing protein -
  FD644_RS17810 (FD644_17810) - 3877683..3877871 (+) 189 WP_137751170.1 hypothetical protein -
  FD644_RS17815 (FD644_17815) - 3877864..3878463 (+) 600 WP_137751171.1 hypothetical protein -
  FD644_RS17820 (FD644_17820) - 3878466..3878885 (+) 420 WP_071681030.1 tail fiber assembly protein -
  FD644_RS17825 (FD644_17825) - 3878981..3879376 (-) 396 WP_071681031.1 hypothetical protein -
  FD644_RS17830 (FD644_17830) - 3879366..3879623 (-) 258 WP_071681032.1 hypothetical protein -
  FD644_RS17835 (FD644_17835) - 3879633..3880520 (-) 888 WP_071681033.1 hypothetical protein -
  FD644_RS17840 (FD644_17840) - 3880792..3881316 (+) 525 WP_071681034.1 helix-turn-helix domain-containing protein -
  FD644_RS17845 (FD644_17845) - 3882261..3882476 (+) 216 WP_071681035.1 hypothetical protein -
  FD644_RS27010 - 3882625..3883014 (+) 390 WP_071681036.1 hypothetical protein -
  FD644_RS26915 - 3883395..3883529 (-) 135 WP_256221054.1 hypothetical protein -
  FD644_RS17855 (FD644_17855) - 3883970..3884275 (+) 306 WP_254698850.1 hypothetical protein -
  FD644_RS17860 (FD644_17860) - 3884565..3884783 (+) 219 WP_254698851.1 hypothetical protein -
  FD644_RS17865 (FD644_17865) - 3884797..3885057 (-) 261 WP_071681039.1 excisionase -
  FD644_RS17870 (FD644_17870) - 3885054..3885548 (-) 495 WP_071681040.1 toxin YdaT family protein -
  FD644_RS17875 (FD644_17875) - 3885679..3885942 (+) 264 WP_217497032.1 DUF4224 domain-containing protein -
  FD644_RS17880 (FD644_17880) - 3886044..3886307 (+) 264 WP_071681041.1 excisionase -
  FD644_RS17885 (FD644_17885) - 3886745..3887215 (-) 471 WP_071681042.1 hypothetical protein -
  FD644_RS17890 (FD644_17890) - 3887527..3887769 (+) 243 WP_021178442.1 DinI family protein -
  FD644_RS17900 (FD644_17900) - 3888041..3888964 (-) 924 WP_071681043.1 LysR family transcriptional regulator -
  FD644_RS17905 (FD644_17905) - 3889130..3890545 (+) 1416 WP_071681044.1 M20 family metallopeptidase -
  FD644_RS17910 (FD644_17910) - 3890542..3891819 (+) 1278 WP_071681045.1 MFS transporter -
  FD644_RS17915 (FD644_17915) - 3891901..3892995 (-) 1095 WP_081366987.1 succinylglutamate desuccinylase/aspartoacylase family protein -
  FD644_RS17920 (FD644_17920) pilD 3893128..3893970 (-) 843 WP_071681046.1 A24 family peptidase Machinery gene
  FD644_RS17925 (FD644_17925) - 3894020..3894763 (-) 744 WP_071681047.1 type II secretion system protein N -
  FD644_RS17930 (FD644_17930) gspM 3894753..3895241 (-) 489 WP_071681048.1 type II secretion system protein GspM -
  FD644_RS17935 (FD644_17935) gspL 3895234..3896433 (-) 1200 WP_071681049.1 type II secretion system protein GspL -
  FD644_RS17940 (FD644_17940) gspK 3896433..3897419 (-) 987 WP_071681050.1 type II secretion system minor pseudopilin GspK -
  FD644_RS17945 (FD644_17945) gspJ 3897416..3898015 (-) 600 WP_071681051.1 type II secretion system minor pseudopilin GspJ -
  FD644_RS17950 (FD644_17950) gspI 3898012..3898377 (-) 366 WP_137751172.1 type II secretion system minor pseudopilin GspI -
  FD644_RS17955 (FD644_17955) gspH 3898374..3898925 (-) 552 WP_071681053.1 type II secretion system minor pseudopilin GspH -
  FD644_RS17960 (FD644_17960) gspG 3898925..3899353 (-) 429 WP_059201257.1 type II secretion system major pseudopilin GspG -
  FD644_RS17965 (FD644_17965) gspF 3899382..3900605 (-) 1224 WP_071681054.1 type II secretion system inner membrane protein GspF -
  FD644_RS17970 (FD644_17970) gspE 3900607..3902112 (-) 1506 WP_071681055.1 type II secretion system ATPase GspE -
  FD644_RS17975 (FD644_17975) gspD 3902109..3904073 (-) 1965 WP_037375612.1 type II secretion system secretin GspD -
  FD644_RS17980 (FD644_17980) gspC 3904092..3904946 (-) 855 WP_071681056.1 type II secretion system protein GspC -

Sequence

Protein


Download         Length: 280 a.a.        Molecular weight: 30837.16 Da        Isoelectric Point: 8.1670

>NTDB_id=362495 FD644_RS17920 WP_071681046.1 3893128..3893970(-) (pilD) [Serratia fonticola strain MS5]
MSLLLDFTVAFPLIWLCVAGILGAIVGSFLNVVIYRLPVMLEKQWQREALVQLGLPLPESIPRFDLLLPRSCCPHCQHPI
AARDNIPLLSFLLLKGKARCCGERIPRRYPLVEVATAMMFVLTALIFPLGFPLLGAWILLSFLLTLAVIDHHTQLLPDVL
TLPLLWMGLLFNIQGHFVSLEQATIGAVAGYVCLWSVFWLFKLATGKEALGYGDFKLLAALGAWLGWQALPQVILVAAAS
GLLVTLIQRGLAKQDLNQALAFGPWLAVSGAVNMFIPWSF

Nucleotide


Download         Length: 843 bp        

>NTDB_id=362495 FD644_RS17920 WP_071681046.1 3893128..3893970(-) (pilD) [Serratia fonticola strain MS5]
TTGAGTTTATTACTGGATTTCACGGTTGCATTTCCCCTCATCTGGCTGTGTGTCGCGGGGATATTGGGGGCCATAGTGGG
TAGCTTTCTCAACGTGGTGATTTATCGGTTACCGGTGATGCTGGAAAAGCAATGGCAGCGTGAGGCGCTCGTACAACTGG
GGCTGCCCCTACCTGAATCCATACCGCGTTTTGATCTGCTATTACCGCGTTCCTGTTGCCCGCATTGCCAGCATCCTATT
GCGGCCAGGGACAATATCCCCCTGCTGAGTTTTCTGTTGTTAAAGGGTAAGGCTCGTTGCTGTGGTGAGCGGATCCCAAG
GCGCTACCCGCTGGTTGAAGTGGCAACGGCTATGATGTTTGTTCTGACGGCGCTTATATTCCCGCTAGGTTTCCCCTTGC
TGGGCGCTTGGATCTTGCTCTCCTTTTTGCTGACGCTGGCAGTTATTGACCATCACACACAACTGTTGCCAGATGTGCTG
ACGTTGCCACTGCTGTGGATGGGACTTTTATTCAATATTCAGGGGCATTTTGTCTCGTTGGAACAGGCGACGATTGGCGC
AGTGGCAGGTTATGTCTGCCTATGGAGCGTGTTCTGGCTATTCAAGCTGGCAACCGGTAAAGAGGCTCTCGGCTATGGTG
ATTTTAAATTACTTGCGGCGTTAGGGGCCTGGTTAGGTTGGCAAGCGTTGCCACAGGTGATTTTGGTGGCGGCGGCCAGT
GGGCTGCTGGTTACGCTGATACAGCGCGGGTTGGCGAAACAAGATCTTAATCAAGCGTTAGCCTTTGGCCCCTGGCTCGC
CGTGTCGGGCGCGGTCAATATGTTTATACCCTGGAGCTTTTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(138-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-126)


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 campbellii strain DS40M4

48.913

98.571

0.482
  pilD Vibrio cholerae strain A1552

49.621

94.286

0.468
  pilD Neisseria gonorrhoeae MS11

50.988

90.357

0.461
  pilD Acinetobacter baumannii D1279779

43.548

88.571

0.386
  pilD Acinetobacter nosocomialis M2

43.145

88.571

0.382

Multiple sequence alignment