Detailed information    

insolico Bioinformatically predicted

Overview

Name   comM   Type   Machinery gene
Locus tag   EYC56_RS18540 Genome accession   NZ_CP036255
Coordinates   3941452..3942510 (-) Length   352 a.a.
NCBI ID   WP_053502376.1    Uniprot ID   -
Organism   Xanthomonas oryzae strain BB151-3     
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 3936780..3987540 3941452..3942510 within 0


Gene organization within MGE regions


Location: 3936780..3987540
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EYC56_RS18520 (EYC56_18520) - 3937506..3939458 (-) 1953 WP_053502378.1 type IV pilus secretin PilQ family protein -
  EYC56_RS18525 (EYC56_18525) - 3939478..3940011 (-) 534 WP_011257996.1 pilus assembly protein PilP -
  EYC56_RS18530 (EYC56_18530) - 3940008..3940673 (-) 666 WP_053502377.1 type 4a pilus biogenesis protein PilO -
  EYC56_RS18535 (EYC56_18535) - 3940670..3941452 (-) 783 WP_131074692.1 PilN domain-containing protein -
  EYC56_RS18540 (EYC56_18540) comM 3941452..3942510 (-) 1059 WP_053502376.1 pilus assembly protein PilM Machinery gene
  EYC56_RS18545 (EYC56_18545) - 3942725..3945154 (+) 2430 WP_165480792.1 penicillin-binding protein 1A -
  EYC56_RS18550 (EYC56_18550) - 3945484..3946134 (+) 651 WP_053502374.1 hypothetical protein -
  EYC56_RS18560 (EYC56_18560) - 3946518..3947807 (-) 1290 WP_024743468.1 citrate synthase -
  EYC56_RS18565 (EYC56_18565) - 3948038..3948280 (-) 243 WP_005911911.1 type B 50S ribosomal protein L31 -
  EYC56_RS18570 (EYC56_18570) - 3948352..3949290 (-) 939 WP_024743469.1 nucleoside hydrolase -
  EYC56_RS18575 (EYC56_18575) recG 3949416..3951569 (-) 2154 WP_053502373.1 ATP-dependent DNA helicase RecG -
  EYC56_RS18580 (EYC56_18580) - 3951590..3951970 (-) 381 WP_011257987.1 RidA family protein -
  EYC56_RS18585 (EYC56_18585) - 3952050..3954221 (-) 2172 WP_024711474.1 bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase -
  EYC56_RS18590 (EYC56_18590) rpoZ 3954350..3954649 (-) 300 WP_002812428.1 DNA-directed RNA polymerase subunit omega -
  EYC56_RS18600 (EYC56_18600) gmk 3954920..3955531 (-) 612 WP_053502372.1 guanylate kinase -
  EYC56_RS18605 (EYC56_18605) - 3955647..3956507 (-) 861 WP_024743474.1 YicC/YloC family endoribonuclease -
  EYC56_RS18610 (EYC56_18610) rph 3956617..3957342 (+) 726 WP_024711476.1 ribonuclease PH -
  EYC56_RS18615 (EYC56_18615) - 3957339..3957734 (+) 396 WP_131085245.1 VOC family protein -
  EYC56_RS18620 (EYC56_18620) rdgB 3957731..3958330 (+) 600 WP_053502370.1 RdgB/HAM1 family non-canonical purine NTP pyrophosphatase -
  EYC56_RS18625 (EYC56_18625) hemW 3958346..3959503 (+) 1158 WP_053502369.1 radical SAM family heme chaperone HemW -
  EYC56_RS18630 (EYC56_18630) - 3959670..3962090 (+) 2421 WP_131085247.1 DUF1631 domain-containing protein -
  EYC56_RS18635 (EYC56_18635) - 3962087..3962434 (+) 348 WP_011257976.1 PilZ domain-containing protein -
  EYC56_RS18640 (EYC56_18640) pepQ 3962633..3963958 (+) 1326 WP_131085249.1 Xaa-Pro dipeptidase -
  EYC56_RS18650 (EYC56_18650) - 3964260..3964660 (+) 401 Protein_3386 XVIPCD domain-containing protein -
  EYC56_RS18655 (EYC56_18655) - 3964845..3966185 (-) 1341 WP_053502365.1 aminopeptidase P N-terminal domain-containing protein -
  EYC56_RS18660 (EYC56_18660) - 3966196..3966738 (-) 543 WP_011407785.1 YecA family protein -
  EYC56_RS18665 (EYC56_18665) - 3966977..3967198 (+) 222 WP_024711481.1 TIGR02449 family protein -
  EYC56_RS18670 (EYC56_18670) - 3967195..3967494 (+) 300 WP_011257971.1 cell division protein ZapA -
  EYC56_RS18680 (EYC56_18680) - 3968103..3968693 (+) 591 WP_131074683.1 5-formyltetrahydrofolate cyclo-ligase -
  EYC56_RS18685 (EYC56_18685) - 3968690..3969160 (+) 471 WP_131077893.1 EVE domain-containing protein -
  EYC56_RS18690 (EYC56_18690) rpiA 3969245..3969892 (+) 648 WP_131085251.1 ribose-5-phosphate isomerase RpiA -
  EYC56_RS18695 (EYC56_18695) - 3970047..3970496 (+) 450 WP_053502361.1 DUF192 domain-containing protein -
  EYC56_RS18700 (EYC56_18700) - 3970646..3971527 (+) 882 WP_131085253.1 SirB1 family protein -
  EYC56_RS18705 (EYC56_18705) - 3971577..3971816 (-) 240 WP_024711486.1 rubredoxin -
  EYC56_RS18710 (EYC56_18710) thiE 3971840..3972463 (+) 624 WP_131085255.1 thiamine phosphate synthase -
  EYC56_RS24655 - 3972886..3975378 (-) 2493 Protein_3398 Oar protein -
  EYC56_RS24660 - 3976034..3976171 (+) 138 WP_165480793.1 hypothetical protein -
  EYC56_RS18725 (EYC56_18725) - 3976262..3976582 (+) 321 WP_131085259.1 helix-turn-helix transcriptional regulator -
  EYC56_RS18730 (EYC56_18730) - 3976617..3977492 (+) 876 WP_165480794.1 reverse transcriptase family protein -
  EYC56_RS18735 (EYC56_18735) - 3977528..3979024 (+) 1497 WP_131085263.1 hypothetical protein -
  EYC56_RS18740 (EYC56_18740) - 3979215..3980159 (+) 945 WP_131085265.1 hypothetical protein -
  EYC56_RS18745 (EYC56_18745) - 3980559..3981521 (-) 963 WP_131085267.1 IS1595 family transposase -
  EYC56_RS18750 (EYC56_18750) - 3981636..3982937 (-) 1302 WP_131085269.1 TniQ family protein -
  EYC56_RS18755 (EYC56_18755) - 3982940..3984001 (-) 1062 WP_131085271.1 AAA family ATPase -
  EYC56_RS18760 (EYC56_18760) - 3983998..3986406 (-) 2409 WP_131085273.1 DDE-type integrase/transposase/recombinase -
  EYC56_RS18765 (EYC56_18765) - 3986626..3986919 (-) 294 WP_131085275.1 hypothetical protein -

Sequence

Protein


Download         Length: 352 a.a.        Molecular weight: 37624.24 Da        Isoelectric Point: 4.3924

>NTDB_id=347713 EYC56_RS18540 WP_053502376.1 3941452..3942510(-) (comM) [Xanthomonas oryzae strain BB151-3]
MGLLPKSQSPLIGVDISSTAVKLLQLSRSGNRFRVEHYAVEPLPPNAVVEKNIVEVEAVGEAIRRAINRSGSKAKNAAAA
VAGSAVITKLIPMPADLDDSDMEAQVELEATNYIPYPIEEVNLDFEVLGPMPNSPDMVQVLLAASRSENVELRQSALELG
GLTAKVMDVEAFAVENAFALVASELPVAADAVVALVDIGATMTTLSVLRSGRSLYSREQVFGGKQLTDEVMRRYGLTYEE
AGLAKRQGGLPESYEVEVLEPFKEATVQQISRLLQFFYAGSEFNRVDCIVLAGGCAALARLPEMVEEQLGVTTVVANPLA
QMTLGPKVQAHALALDAPALMIATGLALRSFD

Nucleotide


Download         Length: 1059 bp        

>NTDB_id=347713 EYC56_RS18540 WP_053502376.1 3941452..3942510(-) (comM) [Xanthomonas oryzae strain BB151-3]
GTGGGGCTTTTACCCAAGAGTCAGTCGCCACTGATTGGTGTCGACATTAGTTCTACTGCCGTGAAGCTCTTGCAGCTATC
GCGCAGCGGGAACCGTTTTCGCGTGGAACATTACGCCGTGGAACCATTGCCGCCGAACGCGGTGGTGGAAAAGAACATCG
TCGAAGTGGAGGCGGTGGGCGAAGCCATTCGCCGCGCCATCAACCGGTCCGGCAGCAAGGCCAAGAACGCGGCCGCGGCC
GTGGCTGGGTCGGCGGTGATCACCAAGTTGATCCCGATGCCGGCCGATCTGGACGATAGCGACATGGAGGCCCAGGTCGA
ACTGGAAGCCACCAATTACATTCCGTACCCGATCGAGGAAGTGAATCTCGATTTCGAGGTGCTGGGCCCGATGCCCAACA
GCCCGGATATGGTCCAGGTGCTGCTGGCCGCATCGCGTTCGGAGAATGTGGAACTGCGCCAGTCTGCGCTGGAACTCGGT
GGTCTGACTGCCAAAGTGATGGACGTGGAGGCCTTCGCGGTCGAAAACGCCTTCGCCCTGGTCGCCAGCGAATTGCCGGT
GGCCGCTGACGCAGTCGTGGCGCTGGTGGATATCGGCGCCACCATGACCACGCTGAGCGTGCTGCGTTCCGGTCGCAGTC
TGTATAGCCGCGAACAGGTGTTCGGCGGCAAGCAGCTCACCGATGAAGTGATGCGCCGTTACGGACTCACCTACGAAGAA
GCTGGCCTGGCCAAGCGTCAGGGCGGTCTGCCGGAAAGCTACGAGGTCGAGGTGCTGGAGCCGTTCAAGGAAGCCACGGT
GCAGCAGATCAGCCGGTTGCTGCAGTTCTTCTATGCAGGCAGCGAGTTCAATCGCGTCGACTGCATCGTGCTGGCCGGCG
GTTGCGCCGCGCTGGCGCGCCTGCCGGAGATGGTGGAAGAGCAACTGGGGGTCACCACCGTGGTCGCCAACCCGCTTGCC
CAGATGACGCTGGGTCCGAAAGTCCAGGCCCATGCGCTGGCGCTGGATGCGCCTGCATTGATGATCGCCACCGGCCTGGC
CCTGAGGAGCTTCGACTGA

Domains

Predicted by InterproScan.

Type IV pilus assembly protein PilM; (PilM_2)

(13-351)


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
  comM Acinetobacter baylyi ADP1

51.282

99.716

0.511
  comM Acinetobacter nosocomialis M2

51.136

100

0.511
  pilM Acinetobacter baumannii D1279779

50.852

100

0.509
  pilM Legionella pneumophila strain ERS1305867

47.578

99.716

0.474

Multiple sequence alignment