Detailed information    

insolico Bioinformatically predicted

Overview

Name   comM   Type   Machinery gene
Locus tag   K5Y35_RS08420 Genome accession   NZ_CP082236
Coordinates   1920229..1921722 (-) Length   497 a.a.
NCBI ID   WP_222834066.1    Uniprot ID   -
Organism   Pseudomonas sp. SC3(2021)     
Function   ssDNA binding (predicted from homology)   
DNA processing

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 1909482..1934348 1920229..1921722 within 0


Gene organization within MGE regions


Location: 1909482..1934348
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  K5Y35_RS08390 rep 1910032..1912041 (-) 2010 WP_123469818.1 DNA helicase Rep -
  K5Y35_RS08395 - 1912304..1913977 (+) 1674 WP_123469816.1 putative bifunctional diguanylate cyclase/phosphodiesterase -
  K5Y35_RS08400 - 1914161..1915558 (-) 1398 WP_222834064.1 NorM family multidrug efflux MATE transporter -
  K5Y35_RS08405 - 1915717..1916637 (+) 921 WP_123469812.1 LysR substrate-binding domain-containing protein -
  K5Y35_RS08410 - 1916822..1918798 (+) 1977 WP_128616383.1 methyl-accepting chemotaxis protein -
  K5Y35_RS08415 - 1919018..1920232 (+) 1215 WP_222834065.1 aldose 1-epimerase family protein -
  K5Y35_RS08420 comM 1920229..1921722 (-) 1494 WP_222834066.1 YifB family Mg chelatase-like AAA ATPase Machinery gene
  K5Y35_RS08425 - 1921869..1922066 (-) 198 WP_186744015.1 hypothetical protein -
  K5Y35_RS08430 - 1922270..1922539 (+) 270 WP_222834067.1 HigA family addiction module antitoxin -
  K5Y35_RS08435 - 1922534..1923061 (-) 528 WP_222834068.1 Bro-N domain-containing protein -
  K5Y35_RS08440 - 1923421..1923681 (-) 261 WP_222834069.1 accessory factor UbiK family protein -
  K5Y35_RS08445 glnK 1924095..1924433 (+) 339 WP_002555808.1 P-II family nitrogen regulator -
  K5Y35_RS08450 - 1924470..1925807 (+) 1338 WP_123469803.1 ammonium transporter -
  K5Y35_RS08455 - 1926023..1926448 (+) 426 WP_123469801.1 secondary thiamine-phosphate synthase enzyme YjbQ -
  K5Y35_RS08460 sutA 1926551..1926877 (+) 327 WP_222834070.1 transcriptional regulator SutA -
  K5Y35_RS08465 - 1927122..1927826 (-) 705 WP_123469798.1 HAD family hydrolase -
  K5Y35_RS08470 xerC 1927823..1928722 (-) 900 WP_222834071.1 tyrosine recombinase XerC -
  K5Y35_RS08475 - 1928725..1929450 (-) 726 WP_123469796.1 DUF484 family protein -
  K5Y35_RS08480 dapF 1929464..1930294 (-) 831 WP_007911094.1 diaminopimelate epimerase -
  K5Y35_RS08485 lysA 1930298..1931545 (-) 1248 WP_123469793.1 diaminopimelate decarboxylase -
  K5Y35_RS08490 lptM 1931555..1931728 (-) 174 WP_123469791.1 LPS translocon maturation chaperone LptM -
  K5Y35_RS08495 cyaY 1932054..1932386 (+) 333 WP_123454569.1 iron donor protein CyaY -
  K5Y35_RS08500 - 1932391..1932609 (+) 219 WP_123469790.1 DUF1289 domain-containing protein -
  K5Y35_RS08505 rnk 1932776..1933186 (+) 411 WP_123469788.1 nucleoside diphosphate kinase regulator -

Sequence

Protein


Download         Length: 497 a.a.        Molecular weight: 53049.29 Da        Isoelectric Point: 8.0172

>NTDB_id=600345 K5Y35_RS08420 WP_222834066.1 1920229..1921722(-) (comM) [Pseudomonas sp. SC3(2021)]
MSLSIVHSRAQIGVDAPAVTVEVHLANGLPSLTMVGLPEAAVKESKDRVRSAIINSGLHFPARRITLNLAPADLPKDGGR
FDLAIALGILSASVQVPCLTLDDVECLGELALSGAVRPVRGVLPAALAARKAGRALVVPRANAEEACLASGLKVFAVDHL
LEAVAHFNGHTPVEPYVSDGLMHASKPYPDLNEVQGQVAAKRALLIAAAGAHNLLFSGPPGTGKTLLASRLPGLLPPLSE
CEALEVAAIQSVASGVPLTHWPQRPFRQPHHSASGPALVGGSSKPQPGEITLAHHGVLFLDELPEFDRKVLEVLREPLES
GHIVIARAKDRVRFPARFQLVAAMNPCPCGYLGEPSGKCSCTPDMVQRYRNKLSGPLLDRIDLHLTVAREATALSPTMKP
GEDSASAAAVVAEARERQQKRQHCANAFLDLPGLKRHCKLSTADEKWLESACERLTLSLRSAHRLLKVARTLADLEEVDA
IKREHLAEALQYRPATP

Nucleotide


Download         Length: 1494 bp        

>NTDB_id=600345 K5Y35_RS08420 WP_222834066.1 1920229..1921722(-) (comM) [Pseudomonas sp. SC3(2021)]
ATGTCCCTCTCCATCGTCCACAGCCGCGCCCAGATTGGCGTGGATGCTCCCGCTGTCACCGTCGAAGTCCATCTGGCCAA
CGGTCTGCCGTCGCTGACCATGGTTGGCCTGCCCGAGGCTGCGGTGAAGGAGAGCAAGGATCGGGTGCGCAGCGCGATCA
TCAATTCCGGGCTGCATTTTCCTGCGCGGCGGATCACCTTGAATCTGGCGCCGGCGGATTTGCCCAAGGATGGCGGGCGG
TTTGATCTGGCGATTGCCTTGGGGATTCTGTCCGCGAGTGTGCAGGTGCCGTGTCTGACGCTGGATGATGTGGAATGCCT
CGGTGAGCTGGCCTTGTCCGGCGCAGTGCGGCCGGTGCGCGGTGTGTTGCCGGCGGCACTCGCGGCGCGCAAGGCGGGTC
GTGCGCTGGTGGTGCCGCGAGCGAATGCCGAGGAGGCCTGCCTGGCTTCGGGGTTAAAGGTGTTTGCGGTGGATCATCTG
CTGGAGGCGGTGGCGCATTTCAACGGACATACACCGGTCGAGCCTTATGTGTCTGACGGGCTGATGCATGCCAGCAAGCC
TTATCCCGACTTGAATGAAGTGCAAGGGCAAGTGGCGGCGAAACGGGCATTGCTGATTGCCGCTGCGGGGGCGCATAACC
TGCTGTTCAGCGGGCCGCCGGGGACGGGCAAGACCTTGCTGGCGAGTCGCTTGCCGGGGCTGCTGCCGCCGCTGTCTGAA
TGCGAAGCACTGGAAGTGGCGGCGATTCAATCGGTCGCCAGCGGCGTGCCGCTGACCCATTGGCCACAGCGTCCTTTCCG
TCAACCGCACCACTCGGCATCCGGGCCGGCCCTGGTCGGTGGCAGTTCAAAACCGCAACCCGGCGAAATCACCCTCGCCC
ACCACGGCGTGCTGTTTCTCGACGAACTGCCGGAGTTTGATCGCAAGGTGCTGGAGGTGCTGCGCGAGCCGCTGGAGTCC
GGGCATATCGTGATCGCCCGAGCCAAGGATCGCGTGCGCTTTCCGGCGCGCTTCCAGTTGGTGGCGGCGATGAATCCGTG
TCCCTGTGGATATCTTGGCGAGCCGAGCGGCAAGTGTTCCTGTACGCCGGACATGGTGCAGCGCTATCGCAACAAACTGT
CGGGGCCATTGCTGGATCGAATTGATCTGCACCTGACAGTGGCGCGAGAGGCGACGGCGCTGAGTCCGACAATGAAACCG
GGAGAGGACAGTGCCAGTGCGGCAGCCGTGGTGGCCGAGGCCCGGGAGCGCCAGCAAAAGCGTCAGCATTGTGCCAATGC
GTTTCTCGATCTGCCGGGATTGAAGCGGCACTGCAAGTTATCCACAGCCGATGAGAAATGGCTGGAATCAGCCTGTGAAC
GACTGACGCTATCGCTGCGCTCAGCGCATCGCCTGCTCAAAGTCGCCCGGACACTGGCCGACCTTGAGGAAGTCGATGCA
ATCAAGCGTGAGCACTTGGCCGAGGCGCTGCAATACCGGCCGGCGACACCTTAA

Domains

Predicted by InterproScan.

Magnesium chelatase, subunit ChlI C-terminal (Mg_chelatase_C)

(401-493)

Subunit ChlI of Mg-chelatase (ChlI)

(21-142)

Magnesium chelatase, subunit ChlI (Mg_chelatase)

(190-390)


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 cholerae strain A1552

54.545

99.598

0.543
  comM Vibrio campbellii strain DS40M4

54.141

99.598

0.539
  comM Haemophilus influenzae Rd KW20

53.106

100

0.533
  comM Glaesserella parasuis strain SC1401

52.2

100

0.525
  comM Legionella pneumophila str. Paris

50.402

100

0.505
  comM Legionella pneumophila strain ERS1305867

50.402

100

0.505
  RA0C_RS07335 Riemerella anatipestifer ATCC 11845 = DSM 15868

45.908

100

0.463