Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   SHEW185_RS20385 Genome accession   NC_009665
Coordinates   4691744..4692670 (+) Length   308 a.a.
NCBI ID   WP_012090386.1    Uniprot ID   -
Organism   Shewanella baltica OS185     
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 4662537..4757723 4691744..4692670 within 0


Gene organization within MGE regions


Location: 4662537..4757723
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SHEW185_RS20305 (Shew185_3926) hxpB 4664355..4665014 (+) 660 WP_012090372.1 hexitol phosphatase HxpB -
  SHEW185_RS20310 (Shew185_3927) - 4665130..4665483 (+) 354 WP_012090373.1 DUF2845 domain-containing protein -
  SHEW185_RS20315 (Shew185_3928) - 4665563..4667605 (-) 2043 WP_012090374.1 M13 family metallopeptidase -
  SHEW185_RS20320 (Shew185_3929) - 4667825..4670041 (-) 2217 WP_014615289.1 patatin-like phospholipase family protein -
  SHEW185_RS20325 (Shew185_3930) - 4670339..4674832 (-) 4494 WP_012090376.1 EAL domain-containing protein -
  SHEW185_RS20330 (Shew185_3932) lpdA 4675289..4676716 (-) 1428 WP_012090377.1 dihydrolipoyl dehydrogenase -
  SHEW185_RS20335 (Shew185_3933) aceF 4676864..4678861 (-) 1998 WP_012090378.1 dihydrolipoyllysine-residue acetyltransferase -
  SHEW185_RS20340 (Shew185_3934) aceE 4678874..4681540 (-) 2667 WP_006083344.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  SHEW185_RS20345 (Shew185_3935) pdhR 4681622..4682374 (-) 753 WP_006083345.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  SHEW185_RS20350 (Shew185_3936) ampE 4682614..4683465 (-) 852 WP_012090379.1 beta-lactamase regulator AmpE -
  SHEW185_RS20355 (Shew185_3937) ampD 4683535..4684098 (-) 564 WP_012090380.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SHEW185_RS20360 (Shew185_3939) nadC 4684682..4685563 (+) 882 WP_012090381.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SHEW185_RS24205 (Shew185_3940) - 4686244..4686597 (+) 354 WP_012090382.1 type IV pilin protein -
  SHEW185_RS20370 (Shew185_3941) - 4686781..4688139 (-) 1359 WP_012090383.1 O-antigen ligase -
  SHEW185_RS20375 (Shew185_3942) pilB 4688570..4690282 (+) 1713 WP_012090384.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SHEW185_RS20380 (Shew185_3943) pilC 4690431..4691702 (+) 1272 WP_012090385.1 type II secretion system F family protein Machinery gene
  SHEW185_RS20385 (Shew185_3944) pilD 4691744..4692670 (+) 927 WP_012090386.1 A24 family peptidase Machinery gene
  SHEW185_RS20390 (Shew185_3945) coaE 4692710..4693327 (+) 618 WP_012090387.1 dephospho-CoA kinase -
  SHEW185_RS20395 (Shew185_3946) zapD 4693320..4694054 (+) 735 WP_012090388.1 cell division protein ZapD -
  SHEW185_RS20400 (Shew185_3947) yacG 4694128..4694337 (+) 210 WP_006083355.1 DNA gyrase inhibitor YacG -
  SHEW185_RS20405 (Shew185_3948) mutT 4694414..4694806 (+) 393 WP_012090389.1 8-oxo-dGTP diphosphatase MutT -
  SHEW185_RS20410 (Shew185_3949) - 4695037..4695573 (+) 537 WP_012090390.1 thioredoxin family protein -
  SHEW185_RS20415 (Shew185_3950) - 4695638..4696564 (-) 927 WP_012090391.1 exopolyphosphatase -
  SHEW185_RS20420 (Shew185_3951) rhlB 4696565..4697881 (-) 1317 WP_006084377.1 ATP-dependent RNA helicase RhlB -
  SHEW185_RS20425 (Shew185_3952) trxA 4698034..4698360 (+) 327 WP_006083360.1 thioredoxin TrxA -
  SHEW185_RS20430 (Shew185_3953) rho 4698570..4699835 (+) 1266 WP_011787892.1 transcription termination factor Rho -
  SHEW185_RS20435 (Shew185_3954) - 4699935..4703393 (-) 3459 WP_012090392.1 zinc-dependent metalloprotease -
  SHEW185_RS20440 (Shew185_3955) - 4703416..4704285 (-) 870 WP_012090393.1 hypothetical protein -
  SHEW185_RS20445 - 4704350..4704769 (-) 420 WP_041411337.1 hypothetical protein -
  SHEW185_RS20450 (Shew185_3956) - 4705071..4706000 (-) 930 WP_012090394.1 LysR family transcriptional regulator -
  SHEW185_RS20455 (Shew185_3957) - 4706135..4707157 (+) 1023 WP_012090395.1 zinc-binding alcohol dehydrogenase family protein -
  SHEW185_RS20460 (Shew185_3958) - 4707154..4707438 (+) 285 WP_012090396.1 putative quinol monooxygenase -
  SHEW185_RS20465 (Shew185_3959) - 4707488..4708219 (-) 732 WP_012090397.1 fumarate reductase iron-sulfur subunit -
  SHEW185_RS20470 (Shew185_3960) - 4708219..4710225 (-) 2007 WP_012090398.1 fumarate reductase flavoprotein subunit -
  SHEW185_RS20475 (Shew185_3961) - 4710335..4711006 (-) 672 WP_012090399.1 fumarate reductase cytochrome b subunit -
  SHEW185_RS20480 (Shew185_3962) - 4711179..4711901 (-) 723 WP_012090400.1 fumarate reductase cytochrome b subunit -
  SHEW185_RS20485 (Shew185_3963) prmA 4712286..4713167 (+) 882 WP_012090401.1 50S ribosomal protein L11 methyltransferase -
  SHEW185_RS20490 (Shew185_3964) dusB 4713342..4714310 (+) 969 WP_006083370.1 tRNA dihydrouridine synthase DusB -
  SHEW185_RS20495 (Shew185_3965) fis 4714327..4714632 (+) 306 WP_006083371.1 DNA-binding transcriptional regulator Fis -
  SHEW185_RS20500 (Shew185_3966) - 4714974..4717964 (+) 2991 WP_012090402.1 UvrD-helicase domain-containing protein -
  SHEW185_RS20505 (Shew185_3967) ric 4718193..4719002 (+) 810 WP_012090403.1 iron-sulfur cluster repair di-iron protein -
  SHEW185_RS20510 (Shew185_3968) - 4719134..4719637 (+) 504 WP_012090404.1 helix-turn-helix domain-containing protein -
  SHEW185_RS20515 (Shew185_3969) - 4719667..4720245 (-) 579 WP_012090405.1 HupE/UreJ family protein -
  SHEW185_RS20520 (Shew185_3970) - 4720369..4721100 (-) 732 WP_006083419.1 HAD-IA family hydrolase -
  SHEW185_RS20525 (Shew185_3971) xerC 4721100..4722020 (-) 921 WP_012090406.1 tyrosine recombinase XerC -
  SHEW185_RS20530 (Shew185_3972) - 4722077..4722706 (-) 630 WP_011848049.1 DUF484 family protein -
  SHEW185_RS20535 (Shew185_3973) dapF 4722703..4723530 (-) 828 WP_006083422.1 diaminopimelate epimerase -
  SHEW185_RS20540 (Shew185_3974) lysA 4723607..4724851 (-) 1245 WP_012090407.1 diaminopimelate decarboxylase -
  SHEW185_RS20545 (Shew185_3975) - 4724915..4725106 (-) 192 WP_006083425.1 LPS translocon maturation chaperone LptM -
  SHEW185_RS20550 (Shew185_3976) cyaY 4725186..4725515 (+) 330 WP_006083426.1 iron donor protein CyaY -
  SHEW185_RS20555 (Shew185_3977) - 4725600..4728011 (-) 2412 WP_012090408.1 class I adenylate cyclase -
  SHEW185_RS20560 (Shew185_3978) hemC 4728214..4729146 (+) 933 WP_011848051.1 hydroxymethylbilane synthase -
  SHEW185_RS20565 (Shew185_3979) - 4729151..4729891 (+) 741 WP_012090409.1 uroporphyrinogen-III synthase -
  SHEW185_RS20570 (Shew185_3980) - 4729952..4731133 (+) 1182 WP_012090410.1 uroporphyrinogen-III C-methyltransferase -
  SHEW185_RS20575 (Shew185_3981) - 4731130..4732296 (+) 1167 WP_012090411.1 heme biosynthesis HemY N-terminal domain-containing protein -
  SHEW185_RS20580 (Shew185_3982) - 4732730..4752745 (+) 20016 WP_041411340.1 S-layer family protein -
  SHEW185_RS20585 (Shew185_3983) - 4752837..4755014 (+) 2178 WP_006084409.1 type I secretion system permease/ATPase -
  SHEW185_RS20590 (Shew185_3984) - 4755011..4756393 (+) 1383 WP_006083434.1 HlyD family type I secretion periplasmic adaptor subunit -

Sequence

Protein


Download         Length: 308 a.a.        Molecular weight: 34333.87 Da        Isoelectric Point: 7.6848

>NTDB_id=28611 SHEW185_RS20385 WP_012090386.1 4691744..4692670(+) (pilD) [Shewanella baltica OS185]
MSEFISILGQSLNQSPWLFIALSFIFAATIGSFLNVVIHRFPVMMKREWQQECNQYLQEYHEDIVKKIGIEQLNKPIDAF
PEKYNLVVPGSACPKCKTAIKPWHNLPLLGWLMLKGKCAACNAPISARYPIIEFITGLLIATLAWHFGPSWQFVFASILT
FVLVALTGIDLDEMLLPDQMTLPLLWLGLIINLNHTFASPTDAIIGAAAGYLSLWSIFWLFKILTGKEGMGYGDFKLLAV
FGAWLGWQMLPLVILLSSLVGAVVGITMIVSKRLKQGNPIPFGPYIAAAGWIALLFGQQIVDWYLSTL

Nucleotide


Download         Length: 927 bp        

>NTDB_id=28611 SHEW185_RS20385 WP_012090386.1 4691744..4692670(+) (pilD) [Shewanella baltica OS185]
ATGTCAGAATTCATCTCCATTTTGGGCCAGTCTCTAAACCAGAGTCCTTGGCTCTTTATTGCTTTAAGCTTTATTTTTGC
CGCTACCATTGGTAGTTTTTTAAACGTGGTGATCCACAGATTTCCTGTGATGATGAAACGAGAATGGCAACAAGAATGCA
ATCAGTATTTGCAGGAATACCACGAAGACATAGTCAAAAAAATCGGTATAGAACAACTCAATAAACCTATAGATGCCTTC
CCTGAAAAGTACAATCTTGTTGTGCCTGGTTCAGCCTGCCCTAAATGTAAAACGGCGATTAAACCTTGGCATAATTTACC
CCTATTAGGCTGGTTAATGCTCAAGGGGAAATGCGCCGCCTGTAACGCCCCTATTTCTGCTCGTTACCCTATTATTGAAT
TCATCACAGGGCTACTTATCGCGACTTTAGCTTGGCATTTTGGTCCAAGCTGGCAGTTTGTTTTTGCTAGCATACTCACC
TTTGTGCTTGTAGCACTGACAGGTATCGATCTTGATGAGATGTTGCTCCCCGACCAAATGACGCTACCGTTGCTTTGGCT
CGGCTTGATAATCAATCTAAATCATACCTTTGCGAGCCCAACCGATGCCATTATCGGCGCGGCGGCAGGCTATTTGAGTC
TATGGTCCATTTTCTGGTTGTTTAAAATCCTCACAGGTAAAGAAGGCATGGGTTATGGCGACTTTAAATTACTCGCCGTG
TTCGGTGCTTGGCTTGGCTGGCAAATGCTGCCGCTGGTGATTTTACTTTCGTCCCTCGTTGGCGCAGTCGTTGGCATCAC
TATGATTGTCAGTAAACGCCTCAAACAAGGTAATCCAATCCCATTTGGCCCATATATTGCCGCAGCTGGCTGGATAGCTT
TGCTATTTGGGCAACAGATTGTCGATTGGTACCTATCGACACTGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(158-266)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(25-147)


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

51.864

95.779

0.497
  pilD Acinetobacter nosocomialis M2

48.197

99.026

0.477
  pilD Vibrio campbellii strain DS40M4

49.66

95.455

0.474
  pilD Acinetobacter baumannii D1279779

47.386

99.351

0.471
  pilD Neisseria gonorrhoeae MS11

44.33

94.481

0.419

Multiple sequence alignment