Detailed information    

insolico Bioinformatically predicted

Overview

Name   comF   Type   Machinery gene
Locus tag   RJD40_RS00555 Genome accession   NZ_CP134280
Coordinates   126350..127057 (+) Length   235 a.a.
NCBI ID   WP_418113722.1    Uniprot ID   -
Organism   Vibrio scophthalmi strain 21FBVib0106     
Function   ssDNA transport into the cell (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 110147..150644 126350..127057 within 0


Gene organization within MGE regions


Location: 110147..150644
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RJD40_RS00495 (RJD40_00495) - 111931..113397 (-) 1467 WP_418113713.1 DNA/RNA helicase domain-containing protein -
  RJD40_RS00500 (RJD40_00500) - 113684..115066 (-) 1383 WP_418113714.1 DEAD/DEAH box helicase -
  RJD40_RS00505 (RJD40_00505) - 115060..115590 (-) 531 WP_418113715.1 hypothetical protein -
  RJD40_RS00510 (RJD40_00510) - 115693..116007 (+) 315 WP_418113716.1 helix-turn-helix domain-containing protein -
  RJD40_RS00515 (RJD40_00515) greB 116004..116483 (-) 480 WP_418113717.1 transcription elongation factor GreB -
  RJD40_RS00520 (RJD40_00520) gmtX 116503..117126 (-) 624 WP_418113718.1 gamma-mobile-trio protein GmtX -
  RJD40_RS00525 (RJD40_00525) - 117128..120235 (-) 3108 WP_418113719.1 VPA1269 family protein -
  RJD40_RS00530 (RJD40_00530) gmtY 120235..121530 (-) 1296 WP_418113720.1 gamma-mobile-trio recombinase GmtY -
  RJD40_RS00535 (RJD40_00535) greB 121864..122211 (+) 348 Protein_99 transcription elongation factor GreB -
  RJD40_RS00540 (RJD40_00540) - 122371..124701 (+) 2331 WP_418113721.1 Tex family protein -
  RJD40_RS00545 (RJD40_00545) - 124833..125303 (-) 471 WP_005596930.1 hypothetical protein -
  RJD40_RS00550 (RJD40_00550) bioH 125395..126237 (-) 843 WP_065429642.1 pimeloyl-ACP methyl ester esterase BioH -
  RJD40_RS00555 (RJD40_00555) comF 126350..127057 (+) 708 WP_418113722.1 ComF family protein Machinery gene
  RJD40_RS00560 (RJD40_00560) nfuA 127165..127752 (+) 588 WP_005596938.1 Fe-S biogenesis protein NfuA -
  RJD40_RS00565 (RJD40_00565) nudE 127996..128544 (+) 549 WP_418113723.1 ADP compounds hydrolase NudE -
  RJD40_RS00570 (RJD40_00570) cysQ 128570..129397 (+) 828 WP_406732401.1 3'(2'),5'-bisphosphate nucleotidase CysQ -
  RJD40_RS00575 (RJD40_00575) - 129962..132607 (+) 2646 WP_418113724.1 beta-N-acetylhexosaminidase -
  RJD40_RS00580 (RJD40_00580) recG 132833..134911 (-) 2079 WP_418113725.1 ATP-dependent DNA helicase RecG -
  RJD40_RS00585 (RJD40_00585) trmH 135228..135911 (-) 684 WP_418113726.1 tRNA (guanosine(18)-2'-O)-methyltransferase TrmH -
  RJD40_RS00590 (RJD40_00590) spoT 135978..138098 (-) 2121 WP_005596949.1 bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase -
  RJD40_RS00595 (RJD40_00595) rpoZ 138136..138408 (-) 273 WP_005596951.1 DNA-directed RNA polymerase subunit omega -
  RJD40_RS00600 (RJD40_00600) gmk 138521..139144 (-) 624 WP_005596953.1 guanylate kinase -
  RJD40_RS00605 (RJD40_00605) - 139682..141052 (+) 1371 WP_009386219.1 NCS2 family permease -
  RJD40_RS00610 (RJD40_00610) - 141179..141604 (+) 426 WP_069445836.1 phosphate-starvation-inducible protein PsiE -
  RJD40_RS00615 (RJD40_00615) pdxY 141884..142747 (+) 864 WP_009386217.1 pyridoxal kinase PdxY -
  RJD40_RS00620 (RJD40_00620) - 143006..144088 (-) 1083 WP_418113727.1 leucine-rich repeat domain-containing protein -
  RJD40_RS00625 (RJD40_00625) - 144908..145774 (-) 867 WP_005596962.1 YicC/YloC family endoribonuclease -
  RJD40_RS00630 (RJD40_00630) rph 145971..146687 (+) 717 WP_005596964.1 ribonuclease PH -
  RJD40_RS00635 (RJD40_00635) pyrE 146977..147618 (+) 642 WP_009386216.1 orotate phosphoribosyltransferase -
  RJD40_RS00640 (RJD40_00640) - 147855..148805 (-) 951 WP_418113728.1 Kdo(2)-lipid IV(A) acyltransferase -
  RJD40_RS00645 (RJD40_00645) slmA 148863..149453 (-) 591 WP_005596971.1 nucleoid occlusion factor SlmA -

Sequence

Protein


Download         Length: 235 a.a.        Molecular weight: 26893.33 Da        Isoelectric Point: 8.8447

>NTDB_id=879623 RJD40_RS00555 WP_418113722.1 126350..127057(+) (comF) [Vibrio scophthalmi strain 21FBVib0106]
MLIQWWQKNRQHVLAHYCQHCLLPIEGRDQPGPGSWLLCQACLEGLSIPSRCQCCGMTTLHPVAQCGHCLSQPPPWRQLY
CVGDYTPPLSDYVQQLKFARQLHYVEVLADLLALQVQPNIQMITYVPLHWHRQLWRGFNQSEFLARALAQRLGLPCRALF
KRTRATRSQRGMDRRQRQRNLRGAFTLTKGVTELQSVAIVDDVVTTGSTVQQLCKLLLDAGVKSVDIYCICRTPE

Nucleotide


Download         Length: 708 bp        

>NTDB_id=879623 RJD40_RS00555 WP_418113722.1 126350..127057(+) (comF) [Vibrio scophthalmi strain 21FBVib0106]
ATGTTAATCCAATGGTGGCAGAAAAACAGACAGCATGTGCTGGCTCATTATTGCCAACACTGTTTGCTGCCGATAGAGGG
GCGTGACCAGCCAGGCCCTGGGTCATGGTTATTGTGCCAAGCGTGCTTGGAAGGACTAAGCATACCGTCTCGTTGCCAGT
GTTGTGGTATGACAACGCTTCATCCGGTTGCTCAATGTGGTCATTGTTTGTCGCAACCGCCACCTTGGCGGCAACTCTAT
TGTGTTGGTGACTACACGCCGCCATTGTCCGATTATGTTCAGCAATTAAAGTTTGCTCGTCAGCTGCATTATGTTGAGGT
ATTGGCCGATCTGCTTGCTCTACAAGTCCAACCAAATATTCAGATGATCACTTATGTACCGTTACACTGGCATCGGCAAT
TGTGGCGTGGATTTAATCAAAGTGAATTTCTAGCGCGAGCGTTGGCGCAGCGACTCGGTCTTCCTTGCCGAGCATTGTTT
AAGCGTACTCGTGCTACTCGTTCGCAACGGGGTATGGATCGCCGGCAACGACAACGTAATTTACGTGGCGCATTTACGCT
GACGAAAGGCGTGACTGAACTTCAATCCGTCGCGATTGTTGATGATGTAGTGACGACAGGGAGTACTGTGCAGCAATTAT
GCAAATTACTACTTGATGCTGGAGTTAAAAGTGTTGATATTTACTGTATCTGCCGTACTCCTGAATGA

Domains

Predicted by InterproScan.

Phosphoribosyl transferase domain (Pribosyltran)

(144-234)


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
  comF Vibrio cholerae strain A1552

50.847

100

0.511
  comF Vibrio campbellii strain DS40M4

47.28

100

0.481