Detailed information    

insolico Bioinformatically predicted

Overview

Name   comM   Type   Machinery gene
Locus tag   VRB78_RS24185 Genome accession   NZ_CP142164
Coordinates   5347801..5349297 (+) Length   498 a.a.
NCBI ID   WP_338488825.1    Uniprot ID   -
Organism   Pseudomonas trivialis strain P_trivialis_B08_1     
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 5342378..5409829 5347801..5349297 within 0


Gene organization within MGE regions


Location: 5342378..5409829
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VRB78_RS24150 (VRB78_24150) xerC 5342378..5343277 (+) 900 WP_338488821.1 tyrosine recombinase XerC -
  VRB78_RS24155 (VRB78_24155) - 5343274..5343969 (+) 696 WP_338488823.1 HAD-IA family hydrolase -
  VRB78_RS24160 (VRB78_24160) sutA 5344113..5344451 (-) 339 WP_338478941.1 transcriptional regulator SutA -
  VRB78_RS24165 (VRB78_24165) - 5344553..5344978 (-) 426 WP_338478942.1 secondary thiamine-phosphate synthase enzyme YjbQ -
  VRB78_RS24170 (VRB78_24170) - 5345188..5346525 (-) 1338 WP_057006380.1 ammonium transporter -
  VRB78_RS24175 (VRB78_24175) glnK 5346560..5346898 (-) 339 WP_002555808.1 P-II family nitrogen regulator -
  VRB78_RS24180 (VRB78_24180) - 5347322..5347585 (+) 264 WP_338478943.1 accessory factor UbiK family protein -
  VRB78_RS24185 (VRB78_24185) comM 5347801..5349297 (+) 1497 WP_338488825.1 YifB family Mg chelatase-like AAA ATPase Machinery gene
  VRB78_RS24190 (VRB78_24190) - 5349338..5351314 (-) 1977 WP_338512091.1 methyl-accepting chemotaxis protein -
  VRB78_RS24195 (VRB78_24195) - 5351544..5352920 (+) 1377 WP_338488829.1 NorM family multidrug efflux MATE transporter -
  VRB78_RS24200 (VRB78_24200) - 5352970..5354634 (-) 1665 WP_338478947.1 bifunctional diguanylate cyclase/phosphodiesterase -
  VRB78_RS24205 (VRB78_24205) rep 5354891..5356900 (+) 2010 WP_057006374.1 DNA helicase Rep -
  VRB78_RS24210 (VRB78_24210) - 5356959..5357528 (+) 570 WP_003176890.1 xanthine phosphoribosyltransferase -
  VRB78_RS24215 (VRB78_24215) - 5357769..5359691 (-) 1923 WP_338488831.1 acetyl-CoA hydrolase/transferase C-terminal domain-containing protein -
  VRB78_RS24220 (VRB78_24220) - 5359825..5360250 (-) 426 WP_338491353.1 c-type cytochrome -
  VRB78_RS24225 (VRB78_24225) - 5360317..5360865 (-) 549 WP_338485494.1 cupin domain-containing protein -
  VRB78_RS24230 (VRB78_24230) alr 5360982..5362055 (-) 1074 WP_338488833.1 alanine racemase -
  VRB78_RS24235 (VRB78_24235) - 5362133..5362486 (-) 354 WP_338478952.1 RidA family protein -
  VRB78_RS24240 (VRB78_24240) dadA 5362458..5363759 (-) 1302 WP_338488835.1 D-amino acid dehydrogenase -
  VRB78_RS24245 (VRB78_24245) - 5363915..5364403 (+) 489 WP_003206849.1 Lrp/AsnC ligand binding domain-containing protein -
  VRB78_RS24250 (VRB78_24250) - 5364421..5364774 (-) 354 WP_305456616.1 YkgJ family cysteine cluster protein -
  VRB78_RS24255 (VRB78_24255) - 5364889..5366181 (+) 1293 WP_338488843.1 FAD-binding oxidoreductase -
  VRB78_RS24260 (VRB78_24260) - 5366182..5366406 (-) 225 WP_338488845.1 DUF1127 domain-containing protein -
  VRB78_RS24265 (VRB78_24265) - 5366572..5367996 (+) 1425 WP_338478956.1 PLP-dependent aminotransferase family protein -
  VRB78_RS24270 (VRB78_24270) - 5368059..5369627 (+) 1569 WP_338478957.1 phospholipase D family protein -
  VRB78_RS24275 (VRB78_24275) - 5369640..5370782 (-) 1143 WP_338478958.1 MFS transporter -
  VRB78_RS24280 (VRB78_24280) - 5370933..5372426 (-) 1494 WP_338478959.1 aldehyde dehydrogenase -
  VRB78_RS24285 (VRB78_24285) - 5372653..5373015 (+) 363 WP_209986437.1 cupin domain-containing protein -
  VRB78_RS24290 (VRB78_24290) rpmG 5373087..5373242 (-) 156 WP_003176906.1 50S ribosomal protein L33 -
  VRB78_RS24295 (VRB78_24295) rpmB 5373254..5373487 (-) 234 WP_003176907.1 50S ribosomal protein L28 -
  VRB78_RS24300 (VRB78_24300) - 5373946..5375538 (+) 1593 WP_338488847.1 ABC transporter substrate-binding protein -
  VRB78_RS24305 (VRB78_24305) radC 5375557..5376231 (-) 675 WP_338478961.1 DNA repair protein RadC -
  VRB78_RS24310 (VRB78_24310) coaBC 5376384..5377592 (+) 1209 WP_338488849.1 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase CoaBC -
  VRB78_RS24315 (VRB78_24315) dut 5377598..5378053 (+) 456 WP_209986446.1 dUTP diphosphatase -
  VRB78_RS24320 (VRB78_24320) - 5378121..5378321 (+) 201 WP_209986449.1 hypothetical protein -
  VRB78_RS24325 (VRB78_24325) - 5378300..5379715 (+) 1416 Protein_4779 phosphomannomutase/phosphoglucomutase -
  VRB78_RS24330 (VRB78_24330) argB 5379736..5380641 (+) 906 WP_209986455.1 acetylglutamate kinase -
  VRB78_RS24335 (VRB78_24335) pyrE 5380716..5381360 (-) 645 WP_338478963.1 orotate phosphoribosyltransferase -
  VRB78_RS24340 (VRB78_24340) - 5381443..5382222 (+) 780 WP_003195493.1 exodeoxyribonuclease III -
  VRB78_RS24345 (VRB78_24345) - 5382280..5382648 (-) 369 WP_003231635.1 DUF4870 domain-containing protein -
  VRB78_RS24350 (VRB78_24350) rph 5382672..5383394 (-) 723 WP_003176917.1 ribonuclease PH -
  VRB78_RS24355 (VRB78_24355) - 5383568..5384431 (+) 864 WP_338484713.1 YicC/YloC family endoribonuclease -
  VRB78_RS24360 (VRB78_24360) gmk 5384442..5385062 (+) 621 WP_338478965.1 guanylate kinase -
  VRB78_RS24365 (VRB78_24365) rpoZ 5385230..5385493 (+) 264 WP_003176920.1 DNA-directed RNA polymerase subunit omega -
  VRB78_RS24370 (VRB78_24370) spoT 5385554..5387659 (+) 2106 WP_338486302.1 bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase -
  VRB78_RS24375 (VRB78_24375) - 5387684..5388064 (+) 381 WP_003176922.1 RidA family protein -
  VRB78_RS24380 (VRB78_24380) - 5388124..5388864 (+) 741 WP_231422306.1 hypothetical protein -
  VRB78_RS24385 (VRB78_24385) - 5388932..5389783 (-) 852 WP_338488851.1 SDR family oxidoreductase -
  VRB78_RS24390 (VRB78_24390) exbB 5389974..5390945 (+) 972 WP_338488853.1 tonB-system energizer ExbB -
  VRB78_RS24395 (VRB78_24395) exbD 5390952..5391377 (+) 426 WP_003231649.1 TonB system transport protein ExbD -
  VRB78_RS24400 (VRB78_24400) - 5391374..5392120 (+) 747 WP_057006349.1 energy transducer TonB -
  VRB78_RS24405 (VRB78_24405) - 5392273..5393193 (+) 921 WP_338488855.1 LysR substrate-binding domain-containing protein -
  VRB78_RS24410 (VRB78_24410) recG 5393202..5395277 (+) 2076 WP_338488857.1 ATP-dependent DNA helicase RecG -
  VRB78_RS24415 (VRB78_24415) - 5395355..5396755 (+) 1401 WP_338478971.1 HDOD domain-containing protein -
  VRB78_RS24420 (VRB78_24420) - 5396886..5397260 (-) 375 WP_057006710.1 hypothetical protein -
  VRB78_RS24425 (VRB78_24425) tagQ 5397385..5398313 (-) 929 Protein_4799 type VI secretion system-associated lipoprotein TagQ -
  VRB78_RS24430 (VRB78_24430) - 5398397..5400109 (-) 1713 WP_338488859.1 SUMF1/EgtB/PvdO family nonheme iron enzyme -
  VRB78_RS24435 (VRB78_24435) - 5400102..5401286 (-) 1185 WP_338488861.1 ABC transporter permease -
  VRB78_RS24440 (VRB78_24440) - 5401286..5401990 (-) 705 WP_338488863.1 ABC transporter ATP-binding protein -
  VRB78_RS24445 (VRB78_24445) - 5401990..5404962 (-) 2973 WP_338488865.1 serine/threonine-protein kinase -
  VRB78_RS24450 (VRB78_24450) - 5404959..5405678 (-) 720 WP_338478976.1 protein phosphatase 2C domain-containing protein -
  VRB78_RS24455 (VRB78_24455) tagF 5405679..5406332 (-) 654 WP_057006340.1 type VI secretion system-associated protein TagF -
  VRB78_RS24460 (VRB78_24460) tssM 5406329..5409829 (-) 3501 WP_338488868.1 type VI secretion system membrane subunit TssM -

Sequence

Protein


Download         Length: 498 a.a.        Molecular weight: 53628.82 Da        Isoelectric Point: 8.1011

>NTDB_id=922349 VRB78_RS24185 WP_338488825.1 5347801..5349297(+) (comM) [Pseudomonas trivialis strain P_trivialis_B08_1]
MSLAIVHSRAQVGVEAPAVTVEVHMANGLPSLTLVGLPETAVKESKDRVRSAILNSALQYPSRRITLNLAPADLPKDGGR
FDLAIALGILAASVQVPALMLDDVECLGELALSGEVRAVKGVLPAALAARKAGRTVIVPRANAEEACLASGLKVIAVDHL
LQVVAHLNGHVPIEPYKSDGLQYLNKPYPDLSEVQGQLSAKRALLIAAAGAHNLLLSGPPGTGKTLLASRLPGLLPPLSE
QEALEVAAIQSVVSLAPLSHWPHRPFRQPHHSASGPALVGGGSKPQPGEITLAHHGVLFLDELPEFDRKVLEVLREPLES
GHIVISRARDRVSFPARFQLVAAMNPCPCGYMGEPSGRCRCTPEQVQRYRNKLSGPLLDRIDLHLTVARETTALNPIQNE
GDTTANASARVAEARERQQQRQGCANAFLDLPGLREHCTLAKVDERWLETACERLTLSLRAAHRLLKVARTLADLEQQHA
ITRHHLQEALQYRPAALT

Nucleotide


Download         Length: 1497 bp        

>NTDB_id=922349 VRB78_RS24185 WP_338488825.1 5347801..5349297(+) (comM) [Pseudomonas trivialis strain P_trivialis_B08_1]
ATGTCCCTCGCCATCGTCCACAGCCGCGCCCAGGTTGGCGTCGAAGCGCCCGCCGTCACTGTCGAGGTGCATATGGCCAA
TGGTTTGCCGTCCCTGACGCTGGTGGGGTTGCCCGAAACCGCCGTCAAGGAAAGCAAGGACCGCGTACGCAGCGCCATTC
TCAATTCGGCCCTGCAATACCCGTCGCGCCGCATCACCCTCAACCTCGCGCCCGCCGACCTGCCCAAGGATGGCGGGCGT
TTTGATTTGGCGATTGCGCTGGGCATTCTGGCGGCCAGTGTGCAGGTGCCAGCGTTGATGCTCGATGACGTGGAGTGCCT
CGGGGAATTGGCATTGTCCGGCGAGGTGCGCGCCGTCAAAGGTGTGTTGCCGGCGGCGCTGGCCGCGCGCAAGGCCGGGC
GCACCGTGATAGTGCCGCGGGCGAATGCCGAGGAGGCGTGCCTGGCGTCGGGTTTGAAGGTCATAGCGGTGGATCACCTG
CTGCAGGTGGTCGCGCACCTGAATGGGCATGTGCCGATTGAGCCTTACAAGTCAGACGGCTTGCAGTACTTGAACAAGCC
GTATCCGGACCTGAGCGAAGTGCAGGGCCAGCTCTCGGCCAAGCGCGCCCTGCTGATCGCAGCGGCGGGCGCGCATAACC
TGCTGCTCAGCGGCCCTCCCGGCACCGGCAAGACCCTGCTCGCCAGCCGCCTGCCAGGCCTGCTGCCCCCGCTGAGTGAG
CAGGAGGCGCTGGAAGTCGCGGCGATTCAATCGGTCGTCAGCTTGGCGCCCTTGAGCCACTGGCCGCATCGGCCGTTTCG
CCAACCCCATCACTCTGCATCCGGCCCGGCCCTGGTGGGCGGCGGGTCAAAACCGCAACCGGGTGAAATCACGCTGGCGC
ACCATGGCGTGCTGTTCCTCGATGAATTGCCGGAGTTTGACCGCAAGGTGCTGGAGGTGCTGCGCGAACCCCTGGAGTCA
GGGCACATCGTGATCTCCCGCGCCCGTGACCGCGTGAGTTTCCCCGCGCGCTTTCAACTGGTGGCCGCGATGAACCCGTG
CCCTTGCGGGTATATGGGCGAGCCTAGTGGTCGCTGTCGCTGTACGCCGGAACAGGTTCAGCGCTATCGCAACAAGCTCT
CCGGACCCTTGCTGGACCGAATTGACCTGCACCTGACCGTGGCACGGGAGACCACCGCGCTCAATCCCATTCAAAACGAG
GGTGACACAACAGCCAACGCCTCGGCGCGCGTTGCCGAGGCGCGCGAGCGTCAACAGCAACGCCAGGGGTGTGCAAATGC
CTTTCTGGACCTGCCGGGATTGCGCGAGCACTGCACGCTGGCAAAGGTCGACGAGCGCTGGCTGGAGACGGCCTGCGAAC
GGCTGACGTTGTCCCTGCGTGCGGCACACCGGCTGCTCAAGGTGGCGCGCACGCTGGCGGACCTGGAACAACAACACGCC
ATCACGCGTCACCATCTGCAAGAGGCGCTGCAATACCGCCCGGCGGCACTTACTTGA

Domains

Predicted by InterproScan.

Subunit ChlI of Mg-chelatase (ChlI)

(21-142)

Magnesium chelatase, subunit ChlI (Mg_chelatase)

(190-391)

Magnesium chelatase, subunit ChlI C-terminal (Mg_chelatase_C)

(402-493)


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

55.758

99.398

0.554
  comM Glaesserella parasuis strain SC1401

55.09

100

0.554
  comM Vibrio cholerae strain A1552

55.242

99.598

0.55
  comM Haemophilus influenzae Rd KW20

54.2

100

0.544
  comM Legionella pneumophila str. Paris

51.205

100

0.512
  comM Legionella pneumophila strain ERS1305867

51.205

100

0.512
  RA0C_RS07335 Riemerella anatipestifer ATCC 11845 = DSM 15868

46.72

100

0.472