Detailed information    

insolico Bioinformatically predicted

Overview

Name   comM   Type   Machinery gene
Locus tag   OGV19_RS24640 Genome accession   NZ_CP109603
Coordinates   5464447..5465934 (-) Length   495 a.a.
NCBI ID   WP_264311047.1    Uniprot ID   -
Organism   Pseudomonas putida strain SEH01     
Function   DNA uptake (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 5416024..5482999 5464447..5465934 within 0


Gene organization within MGE regions


Location: 5416024..5482999
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  OGV19_RS24425 rph 5416178..5416900 (+) 723 WP_264311017.1 ribonuclease PH -
  OGV19_RS24430 - 5416961..5417740 (-) 780 WP_003253401.1 exodeoxyribonuclease III -
  OGV19_RS24435 pyrE 5417821..5418462 (+) 642 WP_003253405.1 orotate phosphoribosyltransferase -
  OGV19_RS24440 argB 5418642..5419547 (-) 906 WP_027592158.1 acetylglutamate kinase -
  OGV19_RS24445 - 5419578..5420951 (-) 1374 Protein_4812 phosphomannomutase/phosphoglucomutase -
  OGV19_RS24450 dut 5421087..5421542 (-) 456 WP_264311018.1 dUTP diphosphatase -
  OGV19_RS24455 coaBC 5421548..5422759 (-) 1212 WP_027592161.1 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase CoaBC -
  OGV19_RS24460 radC 5422887..5423567 (+) 681 WP_264311019.1 RadC family protein -
  OGV19_RS24465 - 5423688..5425277 (-) 1590 WP_264311020.1 ABC transporter substrate-binding protein -
  OGV19_RS24470 rpmB 5425638..5425874 (+) 237 WP_003253504.1 50S ribosomal protein L28 -
  OGV19_RS24475 rpmG 5425886..5426041 (+) 156 WP_003253507.1 50S ribosomal protein L33 -
  OGV19_RS24480 - 5426115..5426474 (-) 360 WP_264311021.1 cupin domain-containing protein -
  OGV19_RS24485 - 5426671..5428164 (+) 1494 WP_264311022.1 aldehyde dehydrogenase -
  OGV19_RS24490 - 5428304..5429443 (+) 1140 WP_264311023.1 MFS transporter -
  OGV19_RS24495 - 5429525..5431081 (-) 1557 WP_264311024.1 phospholipase D family protein -
  OGV19_RS24500 - 5431142..5432572 (-) 1431 WP_264311025.1 PLP-dependent aminotransferase family protein -
  OGV19_RS24505 - 5432751..5432981 (+) 231 WP_264311026.1 DUF1127 domain-containing protein -
  OGV19_RS24510 - 5433014..5434306 (-) 1293 WP_264311027.1 NAD(P)/FAD-dependent oxidoreductase -
  OGV19_RS24515 - 5434440..5434793 (+) 354 WP_264311028.1 YkgJ family cysteine cluster protein -
  OGV19_RS24520 dadR 5434796..5435284 (-) 489 WP_003258963.1 transcriptional regulator DadR -
  OGV19_RS24525 dadA 5435440..5436744 (+) 1305 WP_264311029.1 D-amino acid dehydrogenase -
  OGV19_RS24530 alr 5436893..5437966 (+) 1074 WP_264311030.1 alanine racemase -
  OGV19_RS24535 - 5438091..5438639 (+) 549 WP_264311031.1 cupin domain-containing protein -
  OGV19_RS24540 - 5438794..5439198 (+) 405 WP_033692624.1 c-type cytochrome -
  OGV19_RS24545 - 5439426..5441282 (+) 1857 WP_264311032.1 acetyl-CoA hydrolase/transferase C-terminal domain-containing protein -
  OGV19_RS24550 - 5441405..5441977 (-) 573 WP_264311033.1 xanthine phosphoribosyltransferase -
  OGV19_RS24555 rep 5442043..5444052 (-) 2010 WP_099430788.1 DNA helicase Rep -
  OGV19_RS24560 - 5444340..5446004 (+) 1665 WP_264311034.1 putative bifunctional diguanylate cyclase/phosphodiesterase -
  OGV19_RS24565 - 5446037..5447425 (-) 1389 WP_264311035.1 NorM family multidrug efflux MATE transporter -
  OGV19_RS24570 - 5447581..5448534 (+) 954 WP_264311036.1 LysR substrate-binding domain-containing protein -
  OGV19_RS24575 - 5448538..5449932 (-) 1395 WP_264311037.1 VOC family protein -
  OGV19_RS24580 - 5450070..5450960 (-) 891 WP_264311038.1 LysR family transcriptional regulator -
  OGV19_RS24585 - 5451096..5452586 (+) 1491 WP_319026009.1 aldehyde dehydrogenase family protein -
  OGV19_RS24590 - 5452765..5454051 (+) 1287 WP_264311039.1 NAD(P)/FAD-dependent oxidoreductase -
  OGV19_RS24595 - 5454160..5455587 (-) 1428 WP_264311040.1 mechanosensitive ion channel family protein -
  OGV19_RS24600 ycaC 5455807..5456436 (+) 630 WP_264311041.1 isochorismate family cysteine hydrolase YcaC -
  OGV19_RS24605 - 5456554..5457120 (+) 567 WP_264311042.1 antibiotic biosynthesis monooxygenase -
  OGV19_RS24610 - 5457160..5457978 (+) 819 WP_264311043.1 alpha/beta fold hydrolase -
  OGV19_RS24615 - 5458266..5460107 (+) 1842 WP_264313998.1 amidohydrolase -
  OGV19_RS24620 - 5460196..5460321 (-) 126 Protein_4847 porin -
  OGV19_RS24625 - 5460570..5461481 (-) 912 WP_264311044.1 LysR substrate-binding domain-containing protein -
  OGV19_RS24630 ycaC 5461617..5462246 (+) 630 WP_264311045.1 isochorismate family cysteine hydrolase YcaC -
  OGV19_RS24635 - 5462477..5464264 (-) 1788 WP_264311046.1 monovalent cation:proton antiporter-2 (CPA2) family protein -
  OGV19_RS24640 comM 5464447..5465934 (-) 1488 WP_264311047.1 YifB family Mg chelatase-like AAA ATPase Machinery gene
  OGV19_RS24645 - 5466086..5466661 (-) 576 WP_264311048.1 PIN domain-containing protein -
  OGV19_RS24650 - 5466661..5467125 (-) 465 WP_264311049.1 helix-turn-helix domain-containing protein -
  OGV19_RS24655 - 5467499..5469511 (+) 2013 WP_264311050.1 DUF4034 domain-containing protein -
  OGV19_RS24660 - 5469537..5469965 (-) 429 WP_264311051.1 TOBE domain-containing protein -
  OGV19_RS24665 - 5469989..5470252 (-) 264 WP_264311052.1 accessory factor UbiK family protein -
  OGV19_RS24670 glnK 5470631..5470969 (+) 339 WP_002555808.1 P-II family nitrogen regulator -
  OGV19_RS24675 - 5471016..5472347 (+) 1332 WP_264311053.1 ammonium transporter -
  OGV19_RS24680 sutA 5472780..5473106 (+) 327 WP_264311054.1 transcriptional regulator SutA -
  OGV19_RS24685 - 5473212..5474431 (+) 1220 WP_264311055.1 IS3 family transposase -
  OGV19_RS24690 - 5474595..5475290 (-) 696 WP_264311056.1 HAD family hydrolase -
  OGV19_RS24695 xerC 5475287..5476186 (-) 900 WP_264311057.1 tyrosine recombinase XerC -
  OGV19_RS24700 - 5476186..5476896 (-) 711 WP_264311058.1 DUF484 family protein -
  OGV19_RS24705 dapF 5476910..5477740 (-) 831 WP_264311059.1 diaminopimelate epimerase -
  OGV19_RS24710 lysA 5477745..5478992 (-) 1248 WP_264311060.1 diaminopimelate decarboxylase -
  OGV19_RS24715 lptM 5479002..5479217 (-) 216 WP_264311061.1 LPS translocon maturation chaperone LptM -
  OGV19_RS24720 cyaY 5479409..5479741 (+) 333 WP_264311062.1 iron donor protein CyaY -
  OGV19_RS24725 - 5479743..5479955 (+) 213 WP_264311063.1 DUF1289 domain-containing protein -
  OGV19_RS24730 rnk 5480088..5480498 (+) 411 WP_264311064.1 nucleoside diphosphate kinase regulator -

Sequence

Protein


Download         Length: 495 a.a.        Molecular weight: 52840.60 Da        Isoelectric Point: 7.9067

>NTDB_id=748400 OGV19_RS24640 WP_264311047.1 5464447..5465934(-) (comM) [Pseudomonas putida strain SEH01]
MSLALVHSRAQVGVQAPAVSVETHLANGLPHLTLVGLPETTVKESKDRVRSAIVNSSLDYPARRITQNLAPADLPKDGGR
YDLAIALGILAASGQVPVATLCDIECLGELALSGQLRPVQGVLPAALAAREAGRALVVPRENAEEASLAGGLVVYAVGHL
LELVAHLNGQVPLPPYAANGLVLNSRPYPDLSEVQGQVAAKRALLLAAAGAHNLLFTGPPGTGKTLLASRLPGLLPPLDE
REALEVAAIQSVSGHAPLNSWPQRPFRHPHHSASGPALVGGSSRPQPGEITLAHHGVLFLDELPEFERRVLEVLREPLES
GEIVIARARDKVRFPARFQLVAAMNPCPCGYLGDPTGRCRCSTEQIQRYRNKLSGPLLDRIDLHLTVARETTTLNNQPSG
ETSAAVAERVAEARELQQRRQGCANAFLDLNGLRRHCLLQAADQAWLETACERLSLSLRAAHRLLKVARTLADLEGVASI
ARAHLAEALQYRPGS

Nucleotide


Download         Length: 1488 bp        

>NTDB_id=748400 OGV19_RS24640 WP_264311047.1 5464447..5465934(-) (comM) [Pseudomonas putida strain SEH01]
ATGTCACTTGCCCTCGTCCACAGCCGCGCCCAGGTTGGCGTGCAGGCACCGGCGGTCAGCGTCGAAACACATCTGGCCAA
CGGGCTCCCCCACCTGACCCTGGTCGGCCTGCCCGAAACCACGGTCAAGGAAAGCAAAGACCGGGTACGCAGCGCCATCG
TCAATTCCAGCCTGGATTACCCCGCCAGGCGCATCACGCAGAACCTGGCACCTGCCGACCTGCCCAAGGATGGCGGGCGC
TATGACCTGGCCATTGCCCTGGGCATTCTCGCCGCCAGTGGGCAGGTCCCGGTGGCTACCCTTTGTGACATCGAGTGCCT
GGGCGAACTGGCGCTGTCCGGCCAACTGCGCCCCGTGCAGGGTGTGCTGCCGGCGGCTCTGGCGGCAAGAGAAGCGGGCC
GCGCCCTGGTAGTACCACGGGAAAACGCCGAGGAAGCAAGCCTTGCAGGCGGGCTTGTGGTGTATGCCGTCGGGCACCTG
CTGGAACTGGTCGCCCACCTGAACGGCCAAGTGCCTCTGCCGCCCTATGCCGCCAATGGCCTGGTCTTGAACAGCCGGCC
CTACCCCGACCTCAGCGAGGTACAGGGCCAGGTGGCGGCCAAGCGCGCCTTGCTGCTGGCCGCAGCCGGGGCCCATAACC
TGCTGTTTACCGGCCCACCCGGTACCGGCAAGACACTGCTTGCCAGCCGCCTGCCAGGGCTTCTGCCGCCGCTGGATGAG
CGCGAAGCACTGGAGGTGGCGGCCATTCAGTCGGTCAGCGGCCATGCGCCGCTAAACAGCTGGCCGCAACGCCCCTTCCG
CCACCCGCACCACTCCGCCTCTGGCCCTGCACTGGTAGGCGGCAGCAGTCGGCCACAGCCCGGCGAGATCACCTTGGCGC
ACCATGGTGTGCTGTTTCTCGATGAATTGCCCGAATTTGAGCGGCGCGTGCTGGAGGTATTGCGCGAACCGCTCGAATCC
GGCGAGATCGTGATCGCAAGAGCCCGGGACAAGGTGCGTTTCCCCGCGCGTTTTCAGCTGGTGGCGGCAATGAACCCCTG
CCCTTGCGGCTACCTGGGCGACCCCACCGGCCGCTGCCGCTGCAGCACCGAGCAGATCCAGCGTTATCGCAATAAGCTGT
CGGGGCCGCTGCTGGACCGCATCGACCTGCACCTGACCGTAGCGCGTGAAACCACCACCCTGAACAACCAACCCAGCGGC
GAGACCAGCGCCGCAGTCGCCGAGCGGGTGGCCGAAGCGCGTGAACTGCAGCAACGCCGGCAAGGGTGCGCAAATGCCTT
TCTCGACCTCAACGGCTTGCGCCGCCATTGCCTGCTACAGGCAGCGGACCAGGCGTGGTTGGAAACTGCCTGCGAGCGCC
TGAGCCTGTCGCTACGCGCTGCCCATCGGTTGCTGAAAGTGGCGCGCACGCTGGCGGATCTGGAGGGTGTGGCATCGATT
GCCAGGGCTCACCTGGCCGAGGCGCTGCAGTATCGGCCTGGGAGTTGA

Domains

Predicted by InterproScan.

Magnesium chelatase, subunit ChlI (Mg_chelatase)

(190-391)

Subunit ChlI of Mg-chelatase (ChlI)

(21-142)

Magnesium chelatase, subunit ChlI C-terminal (Mg_chelatase_C)

(400-492)


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 Vibrio campbellii strain DS40M4

56.513

100

0.57
  comM Haemophilus influenzae Rd KW20

56

100

0.566
  comM Vibrio cholerae strain A1552

56.364

100

0.564
  comM Glaesserella parasuis strain SC1401

55.09

100

0.558
  comM Legionella pneumophila str. Paris

49.9

100

0.503
  comM Legionella pneumophila strain ERS1305867

49.9

100

0.503
  RA0C_RS07335 Riemerella anatipestifer ATCC 11845 = DSM 15868

47.316

100

0.481