Detailed information    

experimental Experimentally validated

Overview

Name   comFA/cflA   Type   Machinery gene
Locus tag   SMSK321_RS10515 Genome accession   NZ_AEDT01000032
Coordinates   206342..207640 (-) Length   432 a.a.
NCBI ID   WP_000867726.1    Uniprot ID   -
Organism   Streptococcus mitis SK321     
Function   ssDNA transport into the cell   
DNA binding and uptake

Function

Upregulated in response to CSP as measured by RNA-seq.


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 159227..212973 206342..207640 within 0


Gene organization within MGE regions


Location: 159227..212973
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SMSK321_RS10330 (SMSK321_1577) - 159227..160393 (+) 1167 WP_000704661.1 tyrosine-type recombinase/integrase -
  SMSK321_RS10335 (SMSK321_1578) - 160585..162669 (+) 2085 WP_000803430.1 GH92 family glycosyl hydrolase -
  SMSK321_RS10340 (SMSK321_1579) - 162715..164397 (-) 1683 WP_000251208.1 alpha-L-fucosidase -
  SMSK321_RS12340 (SMSK321_1580) - 164399..168187 (-) 3789 WP_001250572.1 sugar-binding domain-containing protein -
  SMSK321_RS10350 (SMSK321_1581) - 168371..169255 (-) 885 WP_004235732.1 SPFH domain-containing protein -
  SMSK321_RS10355 (SMSK321_1582) - 169405..170556 (-) 1152 WP_000190393.1 iron-containing alcohol dehydrogenase -
  SMSK321_RS10360 (SMSK321_1583) adcA 171177..172682 (-) 1506 WP_000724064.1 zinc ABC transporter substrate-binding lipoprotein AdcA -
  SMSK321_RS10365 (SMSK321_1584) - 172692..173498 (-) 807 WP_000950036.1 metal ABC transporter permease -
  SMSK321_RS10370 (SMSK321_1585) - 173491..174195 (-) 705 WP_001269497.1 metal ABC transporter ATP-binding protein -
  SMSK321_RS10375 (SMSK321_1586) adcR 174195..174635 (-) 441 WP_001249308.1 zinc-dependent transcriptional regulator AdcR -
  SMSK321_RS10380 (SMSK321_1587) dltD 174790..176058 (-) 1269 WP_000919853.1 D-alanyl-lipoteichoic acid biosynthesis protein DltD -
  SMSK321_RS10385 (SMSK321_1588) dltC 176051..176290 (-) 240 WP_000351967.1 D-alanine--poly(phosphoribitol) ligase subunit DltC -
  SMSK321_RS0102840 dltB 176304..177548 (-) 1245 WP_000969744.1 D-alanyl-lipoteichoic acid biosynthesis protein DltB -
  SMSK321_RS10390 (SMSK321_1589) dltA 177545..179095 (-) 1551 WP_004235747.1 D-alanine--poly(phosphoribitol) ligase subunit DltA -
  SMSK321_RS10395 (SMSK321_1590) - 179116..179247 (-) 132 WP_000813667.1 teichoic acid D-Ala incorporation-associated protein DltX -
  SMSK321_RS10400 (SMSK321_1591) - 179559..180737 (-) 1179 WP_000071442.1 ryptide export MFS transporter -
  SMSK321_RS10405 (SMSK321_1592) - 180978..181682 (-) 705 WP_000980819.1 MIP/aquaporin family protein -
  SMSK321_RS10410 (SMSK321_1593) glpO 181752..183578 (-) 1827 WP_000395965.1 type 1 glycerol-3-phosphate oxidase -
  SMSK321_RS10415 (SMSK321_1594) glpK 183620..185128 (-) 1509 WP_000076785.1 glycerol kinase GlpK -
  SMSK321_RS10420 (SMSK321_1595) - 185288..186715 (-) 1428 WP_029692188.1 helix-turn-helix domain-containing protein -
  SMSK321_RS10425 (SMSK321_1596) hslO 186880..187752 (+) 873 WP_004235754.1 Hsp33 family molecular chaperone HslO -
  SMSK321_RS10430 (SMSK321_1597) dusB 187739..188719 (+) 981 WP_000183308.1 tRNA dihydrouridine synthase DusB -
  SMSK321_RS10435 (SMSK321_1598) - 188776..189462 (-) 687 WP_000764010.1 DUF1275 family protein -
  SMSK321_RS10440 (SMSK321_1599) - 189589..190272 (-) 684 WP_000730894.1 hypothetical protein -
  SMSK321_RS10445 (SMSK321_1600) - 190551..190781 (+) 231 WP_000933124.1 hypothetical protein -
  SMSK321_RS10450 (SMSK321_1601) - 190853..191626 (-) 774 WP_000132693.1 NUDIX domain-containing protein -
  SMSK321_RS10455 (SMSK321_1602) pnuC 191628..192407 (-) 780 WP_000736875.1 nicotinamide riboside transporter PnuC -
  SMSK321_RS10460 (SMSK321_1603) - 192417..193436 (-) 1020 WP_000730575.1 AAA family ATPase -
  SMSK321_RS10465 (SMSK321_1604) clpC 193584..196016 (-) 2433 WP_001109671.1 ATP-dependent Clp protease ATP-binding subunit Regulator
  SMSK321_RS10470 (SMSK321_1605) - 196018..196476 (-) 459 WP_001211265.1 CtsR family transcriptional regulator -
  SMSK321_RS0102850 - 196595..197323 (-) 729 WP_000136238.1 ABC transporter ATP-binding protein -
  SMSK321_RS10475 (SMSK321_1606) - 197323..198315 (-) 993 WP_004235755.1 ABC transporter substrate-binding protein -
  SMSK321_RS10480 - 198353..199120 (-) 768 Protein_200 ABC transporter permease -
  SMSK321_RS10485 (SMSK321_1608) - 199083..199373 (-) 291 WP_004235758.1 thiamine-binding protein -
  SMSK321_RS10490 (SMSK321_1609) cbpD 199625..200743 (-) 1119 WP_000703686.1 choline binding-anchored murein hydrolase CbpD Auxiliary factor
  SMSK321_RS10495 (SMSK321_1610) - 200833..201099 (-) 267 WP_001278169.1 Veg family protein -
  SMSK321_RS10500 (SMSK321_1611) dnaB 201101..202453 (-) 1353 WP_000852485.1 replicative DNA helicase -
  SMSK321_RS0102860 rplI 202497..202949 (-) 453 WP_000864214.1 50S ribosomal protein L9 -
  SMSK321_RS10505 (SMSK321_1612) - 202946..204919 (-) 1974 WP_000715142.1 DHH family phosphoesterase -
  SMSK321_RS10510 (SMSK321_1613) hpf 205055..205603 (-) 549 WP_000599100.1 ribosome hibernation-promoting factor, HPF/YfiA family -
  SMSK321_RS0102865 comFC/cflB 205683..206345 (-) 663 WP_000649958.1 ComF family protein Machinery gene
  SMSK321_RS10515 (SMSK321_1614) comFA/cflA 206342..207640 (-) 1299 WP_000867726.1 DEAD/DEAH box helicase Machinery gene
  SMSK321_RS10520 (SMSK321_1615) - 207697..208332 (+) 636 WP_000395766.1 YigZ family protein -
  SMSK321_RS12680 - 208426..208521 (+) 96 Protein_211 PH domain-containing protein -
  SMSK321_RS10525 (SMSK321_1616) cysK 208618..209544 (+) 927 WP_000029882.1 cysteine synthase A -
  SMSK321_RS10530 (SMSK321_1617) tsf 209666..210706 (-) 1041 WP_000808070.1 translation elongation factor Ts -
  SMSK321_RS10535 (SMSK321_1618) rpsB 210785..211564 (-) 780 WP_000268469.1 30S ribosomal protein S2 -
  SMSK321_RS10540 (SMSK321_1619) pcsB 211789..212973 (-) 1185 WP_000727021.1 peptidoglycan hydrolase PcsB -

Sequence

Protein


Download         Length: 432 a.a.        Molecular weight: 49657.69 Da        Isoelectric Point: 8.3631

>NTDB_id=535 SMSK321_RS10515 WP_000867726.1 206342..207640(-) (comFA/cflA) [Streptococcus mitis SK321]
MKVNPNYLGRLFTENELTKEERQLAEKLPAMRKEKGKLFCQRCDSAILDEWYLPIGAYYCRECLLMKRVRSDQVLYYFPQ
EDFAKQDILKWRGQLTPFQEKVSEGLIQAVDKQEPILVHAVTGAGKTEMIYQVVAKVINAGGAVCLASPRIDVCLELYKR
LQDDFACEISLLYGESEPYFRTPLVVSTTHQLLKFYQAFDLLIVDEVDAFPYVDNPMLYHAVKNSVKENGLRIFLTATST
DELDRKVRIGELKRLSLPRRFHGNPLIIPKPVWLSDFNRYLEKKCLSPKLKSYIEKQRKTGYPLLIFASEIKKGEQLKEI
LQKEFPHEKIGFVSSVTEDRLEQVQAFRDGELTILISTTILERGVTFPCVDVFVVEANHRLFTKSSLIQIGGRVGRSMDR
PTGDLLFFHDGLNTSIKKAIKEIQQMNKEAGL

Nucleotide


Download         Length: 1299 bp        

>NTDB_id=535 SMSK321_RS10515 WP_000867726.1 206342..207640(-) (comFA/cflA) [Streptococcus mitis SK321]
ATGAAAGTAAATCCAAATTATCTCGGTCGGTTGTTTACGGAGAATGAATTAACTAAAGAGGAACGTCAGTTGGCGGAGAA
ACTTCCAGCAATGAGAAAGGAGAAAGGGAAACTTTTCTGTCAACGTTGTGATAGTGCTATTTTAGATGAATGGTATTTGC
CCATCGGTGCTTACTATTGTAGGGAGTGTTTGCTGATGAAGCGAGTCAGGAGTGATCAAGTTTTATACTATTTTCCGCAG
GAGGATTTTGCGAAGCAAGATATTCTTAAATGGCGTGGTCAATTAACTCCTTTTCAAGAGAAGGTATCAGAGGGACTAAT
TCAAGCTGTAGACAAGCAGGAACCAATCTTGGTTCACGCTGTAACAGGAGCTGGAAAGACAGAAATGATTTATCAAGTAG
TAGCTAAAGTGATCAATGCGGGTGGTGCAGTATGCTTGGCTAGTCCTCGCATAGATGTTTGTTTGGAGCTGTACAAGCGC
CTGCAAGATGATTTTGCTTGCGAGATATCTTTACTATACGGAGAATCAGAGCCGTATTTTCGAACACCACTAGTTGTTTC
GACGACCCATCAGTTATTGAAGTTTTATCAAGCTTTTGATTTGCTGATAGTGGATGAAGTAGATGCCTTTCCTTATGTTG
ATAATCCCATGCTTTACCATGCTGTCAAGAATAGTGTAAAGGAGAATGGCTTGAGAATCTTTTTAACAGCAACTTCGACT
GATGAGTTAGATAGGAAGGTTCGCATAGGAGAACTAAAACGATTGAGTTTGCCAAGACGATTTCATGGAAATCCGTTGAT
TATTCCTAAACCTGTCTGGTTATCCGATTTTAATCGCTATTTAGAGAAGAAGTGTTTGTCACCAAAGTTAAAGTCTTATA
TTGAGAAGCAGAGAAAGACAGGTTATCCGTTACTCATTTTTGCTTCAGAAATTAAGAAAGGGGAGCAGTTAAAAGAAATC
TTACAGAAGGAATTTCCGCATGAGAAAATTGGCTTTGTATCTTCTGTAACAGAGGATCGATTAGAGCAGGTACAAGCTTT
TCGAGATGGAGAACTGACAATACTGATCAGTACGACGATATTGGAGCGTGGAGTTACTTTCCCTTGTGTGGACGTTTTCG
TAGTAGAGGCCAATCATCGTCTTTTTACCAAGTCTAGTTTAATACAGATTGGAGGACGTGTCGGTCGGAGTATGGACAGA
CCGACAGGAGATTTGCTTTTTTTCCATGATGGGTTAAATACTTCAATCAAGAAGGCAATTAAGGAAATTCAGCAGATGAA
TAAGGAGGCGGGGCTATGA

Domains

Predicted by InterproScan.

Helicase conserved C-terminal domain (Helicase_C)

(293-396)

Type III restriction enzyme, res subunit (ResIII)

(94-238)


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
  comFA/cflA Streptococcus mitis NCTC 12261

93.75

100

0.938
  comFA/cflA Streptococcus pneumoniae Rx1

92.361

100

0.924
  comFA/cflA Streptococcus pneumoniae D39

92.361

100

0.924
  comFA/cflA Streptococcus pneumoniae R6

92.361

100

0.924
  comFA/cflA Streptococcus pneumoniae TIGR4

92.13

100

0.921
  comFA Lactococcus lactis subsp. cremoris KW2

50.228

100

0.512
  comFA Latilactobacillus sakei subsp. sakei 23K

38.621

100

0.389
  comFA Bacillus subtilis subsp. subtilis str. 168

39.303

93.056

0.366

Multiple sequence alignment    



References

[1] G Salvadori et al. (2018) High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes. BMC Genomics 19(1):453. [PMID: 29898666]