Detailed information    

insolico Bioinformatically predicted

Overview

Name   comM   Type   Machinery gene
Locus tag   IYN96_RS04875 Genome accession   NZ_CP064871
Coordinates   1059441..1060499 (+) Length   352 a.a.
NCBI ID   WP_041183432.1    Uniprot ID   -
Organism   Xanthomonas oryzae pv. oryzicola strain YN01     
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 1039693..1082503 1059441..1060499 within 0


Gene organization within MGE regions


Location: 1039693..1082503
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  IYN96_RS04785 (IYN96_04780) - 1039908..1042289 (-) 2382 WP_048485368.1 DUF1631 domain-containing protein -
  IYN96_RS04790 (IYN96_04785) hemW 1042456..1043613 (-) 1158 WP_014504451.1 radical SAM family heme chaperone HemW -
  IYN96_RS04795 (IYN96_04790) rdgB 1043629..1044228 (-) 600 WP_024711477.1 RdgB/HAM1 family non-canonical purine NTP pyrophosphatase -
  IYN96_RS04800 (IYN96_04795) - 1044225..1044620 (-) 396 WP_047340130.1 VOC family protein -
  IYN96_RS04805 (IYN96_04800) rph 1044617..1045342 (-) 726 WP_047340129.1 ribonuclease PH -
  IYN96_RS04810 (IYN96_04805) - 1045452..1046312 (+) 861 WP_024711475.1 YicC/YloC family endoribonuclease -
  IYN96_RS04815 (IYN96_04810) gmk 1046428..1047039 (+) 612 WP_011038351.1 guanylate kinase -
  IYN96_RS04825 (IYN96_04820) rpoZ 1047308..1047607 (+) 300 WP_002812428.1 DNA-directed RNA polymerase subunit omega -
  IYN96_RS04830 (IYN96_04825) - 1047736..1049907 (+) 2172 WP_024711474.1 bifunctional (p)ppGpp synthetase/guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase -
  IYN96_RS04835 (IYN96_04830) - 1049987..1050367 (+) 381 WP_011257987.1 RidA family protein -
  IYN96_RS04840 (IYN96_04835) recG 1050388..1052541 (+) 2154 WP_047340128.1 ATP-dependent DNA helicase RecG -
  IYN96_RS04845 (IYN96_04840) - 1052674..1053612 (+) 939 WP_024711472.1 nucleoside hydrolase -
  IYN96_RS04850 (IYN96_04845) - 1053684..1053926 (+) 243 WP_005911911.1 type B 50S ribosomal protein L31 -
  IYN96_RS04855 (IYN96_04850) - 1054157..1055446 (+) 1290 WP_024711471.1 citrate synthase -
  IYN96_RS04865 (IYN96_04860) - 1055830..1056480 (-) 651 WP_011407794.1 hypothetical protein -
  IYN96_RS04870 (IYN96_04865) - 1056796..1059225 (-) 2430 WP_014504440.1 penicillin-binding protein 1A -
  IYN96_RS04875 (IYN96_04870) comM 1059441..1060499 (+) 1059 WP_041183432.1 pilus assembly protein PilM Machinery gene
  IYN96_RS04880 (IYN96_04875) - 1060499..1061281 (+) 783 WP_044750904.1 PilN domain-containing protein -
  IYN96_RS04885 (IYN96_04880) - 1061278..1061943 (+) 666 WP_014504437.1 type 4a pilus biogenesis protein PilO -
  IYN96_RS04890 (IYN96_04885) - 1061940..1062473 (+) 534 WP_024712440.1 pilus assembly protein PilP -
  IYN96_RS04895 (IYN96_04890) - 1062493..1064439 (+) 1947 WP_047340127.1 type IV pilus secretin PilQ family protein -
  IYN96_RS04905 (IYN96_04900) - 1065016..1066035 (+) 1020 WP_014504434.1 MoxR family ATPase -
  IYN96_RS04910 (IYN96_04905) - 1066056..1067018 (+) 963 WP_024712442.1 DUF58 domain-containing protein -
  IYN96_RS04915 (IYN96_04910) - 1067021..1067482 (+) 462 WP_011258002.1 DUF4381 domain-containing protein -
  IYN96_RS04920 (IYN96_04915) - 1067479..1068492 (+) 1014 WP_047340126.1 VWA domain-containing protein -
  IYN96_RS04925 (IYN96_04920) - 1068489..1070306 (+) 1818 WP_047340125.1 VWA domain-containing protein -
  IYN96_RS04930 (IYN96_04925) - 1070303..1072069 (+) 1767 WP_047340124.1 BatD family protein -
  IYN96_RS04940 (IYN96_04935) - 1072365..1072682 (+) 318 WP_024712445.1 DUF3658 domain-containing protein -
  IYN96_RS04945 (IYN96_04940) - 1072907..1073404 (+) 498 Protein_939 transposase -
  IYN96_RS04955 (IYN96_04950) - 1074608..1075039 (+) 432 Protein_941 cation:dicarboxylase symporter family transporter -
  IYN96_RS04960 (IYN96_04955) tkt 1075272..1077272 (+) 2001 WP_047340123.1 transketolase -
  IYN96_RS21475 - 1077379..1077498 (-) 120 Protein_943 alpha/beta hydrolase -
  IYN96_RS04965 (IYN96_04960) - 1077499..1078897 (+) 1399 Protein_944 TonB-dependent receptor -
  IYN96_RS04970 (IYN96_04965) - 1079234..1079335 (-) 102 Protein_945 M23 family peptidase -
  IYN96_RS04975 (IYN96_04970) - 1079338..1079727 (-) 390 Protein_946 L,D-transpeptidase -
  IYN96_RS04980 (IYN96_04975) - 1079939..1080479 (-) 541 Protein_947 peptidoglycan-binding domain-containing protein -
  IYN96_RS04985 (IYN96_04980) - 1080574..1081919 (-) 1346 Protein_948 IS5 family transposase -
  IYN96_RS04990 (IYN96_04985) - 1082045..1082284 (+) 240 WP_143703532.1 hypothetical protein -

Sequence

Protein


Download         Length: 352 a.a.        Molecular weight: 37636.30 Da        Isoelectric Point: 4.3882

>NTDB_id=505484 IYN96_RS04875 WP_041183432.1 1059441..1060499(+) (comM) [Xanthomonas oryzae pv. oryzicola strain YN01]
MGLLPKSQSPLIGVDISSTAVKLLQLSRSGNRFRVEHYAVEPLPPNAVVEKNIVEVDAVGEAIRRAINRSGSKAKNAAAA
VAGSAVITKLIPMPADLDDSDMEAQVELEATNYIPYPIEEVNLDFEVLGPMPNIPDMVQVLLAASRSENVELRQSALELG
GLTAKVMDVEAFAVENAFALVASELPVAADAVVALVDIGATMTTLSVLRSGRSLYSREQVFGGKQLTDEVMRRYGLTYEE
AGLAKRQGGLPESYEVEVLEPFKEATVQQISRLLQFFYAGSEFNRVDCIVLAGGCAALARLPEMVEEQLGVTTVVANPLA
QMTLGPKVQAHALALDAPALMIATGLALRSFD

Nucleotide


Download         Length: 1059 bp        

>NTDB_id=505484 IYN96_RS04875 WP_041183432.1 1059441..1060499(+) (comM) [Xanthomonas oryzae pv. oryzicola strain YN01]
GTGGGGCTTTTACCCAAGAGTCAGTCGCCACTGATTGGTGTCGACATTAGTTCTACTGCCGTGAAGCTCTTGCAGCTATC
GCGCAGCGGGAACCGTTTTCGCGTGGAACATTACGCCGTGGAACCGTTGCCGCCGAACGCGGTGGTGGAAAAGAACATCG
TCGAAGTGGATGCGGTGGGCGAAGCCATTCGCCGCGCCATCAACCGGTCCGGCAGCAAGGCCAAGAACGCGGCCGCGGCC
GTGGCTGGGTCGGCGGTGATCACCAAGTTGATCCCGATGCCGGCCGATCTGGACGATAGCGACATGGAGGCCCAGGTCGA
ACTGGAAGCCACCAATTACATTCCGTACCCGATCGAGGAAGTGAATCTCGATTTCGAGGTGCTGGGCCCGATGCCCAACA
TCCCGGATATGGTCCAGGTGCTGCTGGCCGCATCGCGTTCGGAGAATGTGGAACTGCGCCAGTCGGCGCTGGAACTCGGT
GGTCTGACTGCCAAAGTGATGGACGTGGAGGCCTTCGCGGTCGAAAACGCCTTCGCCCTGGTCGCCAGCGAATTGCCGGT
GGCCGCTGACGCAGTCGTGGCGCTGGTGGATATCGGCGCCACCATGACCACGCTGAGCGTGCTGCGTTCCGGTCGCAGTC
TGTATAGCCGCGAACAGGTGTTCGGCGGCAAGCAGCTCACCGATGAAGTGATGCGCCGTTATGGACTCACCTACGAAGAA
GCTGGCCTGGCCAAGCGTCAGGGCGGTCTGCCGGAAAGCTACGAGGTCGAGGTGCTGGAGCCGTTCAAGGAAGCCACGGT
GCAGCAGATCAGCCGGTTGCTGCAGTTCTTCTATGCAGGCAGCGAGTTCAATCGCGTCGACTGCATCGTGCTGGCCGGCG
GTTGCGCCGCGCTGGCGCGCCTGCCGGAGATGGTGGAAGAGCAACTGGGGGTCACCACAGTGGTCGCCAACCCGCTTGCC
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

50.997

99.716

0.509
  comM Acinetobacter nosocomialis M2

50.852

100

0.509
  pilM Acinetobacter baumannii D1279779

50.568

100

0.506
  pilM Legionella pneumophila strain ERS1305867

47.578

99.716

0.474