Detailed information    

insolico Bioinformatically predicted

Overview

Name   comB2   Type   Machinery gene
Locus tag   D4H43_RS06615 Genome accession   NZ_CP032911
Coordinates   1366824..1367108 (-) Length   94 a.a.
NCBI ID   WP_000736106.1    Uniprot ID   T0F3N0
Organism   Helicobacter pylori strain 19-A-EK3     
Function   transformation-associated type IV transport system (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 1289505..1369467 1366824..1367108 within 0


Gene organization within MGE regions


Location: 1289505..1369467
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  D4H43_RS06310 hopM 1290309..1292390 (+) 2082 WP_276567621.1 Hop family outer membrane protein HopM/HopN -
  D4H43_RS06315 - 1292603..1293436 (+) 834 WP_120998622.1 sulfite exporter TauE/SafE family protein -
  D4H43_RS06320 msrB 1293812..1294891 (-) 1080 WP_139544384.1 peptide-methionine (R)-S-oxide reductase MsrB -
  D4H43_RS06325 radA 1295015..1296361 (-) 1347 WP_201737145.1 DNA repair protein RadA -
  D4H43_RS06330 - 1296473..1296706 (-) 234 WP_000415833.1 ribbon-helix-helix domain-containing protein -
  D4H43_RS06335 - 1296862..1297842 (-) 981 WP_139544386.1 iron-sulfur cluster assembly scaffold protein -
  D4H43_RS06340 - 1297864..1299027 (-) 1164 WP_033744554.1 NifS family cysteine desulfurase -
  D4H43_RS06345 - 1299198..1299659 (-) 462 WP_139544387.1 helix-turn-helix domain-containing protein -
  D4H43_RS06350 - 1299725..1300356 (+) 632 Protein_1214 YbhB/YbcL family Raf kinase inhibitor-like protein -
  D4H43_RS06355 dxr 1300538..1301638 (-) 1101 WP_139544389.1 1-deoxy-D-xylulose-5-phosphate reductoisomerase -
  D4H43_RS06360 - 1301639..1302439 (-) 801 WP_139548828.1 phosphatidate cytidylyltransferase -
  D4H43_RS06365 - 1302452..1304110 (-) 1659 WP_139544391.1 DASS family sodium-coupled anion symporter -
  D4H43_RS06370 mnmG 1304206..1306071 (+) 1866 WP_139544392.1 tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG -
  D4H43_RS06375 dapE 1306082..1307233 (+) 1152 WP_139544393.1 succinyl-diaminopimelate desuccinylase -
  D4H43_RS06380 hcpA 1307690..1308442 (+) 753 WP_139544394.1 Sel1-like repeat protein HcpA -
  D4H43_RS06385 htpG 1308637..1310502 (-) 1866 WP_139544395.1 molecular chaperone HtpG -
  D4H43_RS06390 hofA 1310606..1311958 (-) 1353 WP_139544654.1 outer membrane beta-barrel protein HofA -
  D4H43_RS08550 - 1312118..1312271 (+) 154 Protein_1223 glycosyltransferase family 8 protein -
  D4H43_RS06395 - 1312258..1313361 (+) 1104 WP_236633633.1 glycosyltransferase -
  D4H43_RS06400 - 1313375..1314613 (-) 1239 WP_139544397.1 Mrp/NBP35 family ATP-binding protein -
  D4H43_RS06405 - 1314578..1317424 (+) 2847 WP_139544398.1 hypothetical protein -
  D4H43_RS06410 - 1318333..1320369 (+) 2037 WP_201737089.1 relaxase/mobilization nuclease domain-containing protein -
  D4H43_RS06415 - 1321454..1322521 (+) 1068 WP_139544399.1 tyrosine-type recombinase/integrase -
  D4H43_RS06420 - 1322834..1323631 (-) 798 WP_139544400.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  D4H43_RS06425 - 1323603..1323854 (-) 252 WP_120823133.1 hypothetical protein -
  D4H43_RS08655 - 1324101..1324773 (-) 673 Protein_1231 CAAX protease -
  D4H43_RS06445 - 1324953..1325967 (+) 1015 Protein_1232 hypothetical protein -
  D4H43_RS06450 - 1325972..1327249 (-) 1278 WP_139544403.1 hypothetical protein -
  D4H43_RS08560 - 1327246..1328506 (-) 1261 Protein_1234 P-type conjugative transfer protein TrbL -
  D4H43_RS06465 - 1328503..1329936 (-) 1434 WP_139544404.1 hypothetical protein -
  D4H43_RS06470 - 1329946..1331949 (-) 2004 Protein_1236 hypothetical protein -
  D4H43_RS06475 - 1331949..1333001 (-) 1053 WP_139544406.1 ArdC-like ssDNA-binding domain-containing protein -
  D4H43_RS08385 - 1333002..1333166 (-) 165 WP_000189763.1 hypothetical protein -
  D4H43_RS06480 - 1333803..1334471 (+) 669 WP_139544407.1 ParA family protein -
  D4H43_RS06485 - 1334518..1334895 (+) 378 WP_000365707.1 hypothetical protein -
  D4H43_RS06490 tnpA 1335080..1335547 (+) 468 WP_000063685.1 IS200/IS605 family transposase -
  D4H43_RS06495 - 1335516..1336664 (+) 1149 WP_139543879.1 RNA-guided endonuclease TnpB family protein -
  D4H43_RS06500 - 1336751..1337377 (+) 627 WP_139544408.1 hypothetical protein -
  D4H43_RS06505 - 1337451..1338254 (-) 804 WP_139544409.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  D4H43_RS06510 - 1338224..1338694 (-) 471 WP_000965788.1 hypothetical protein -
  D4H43_RS06515 - 1338749..1340809 (-) 2061 WP_139544410.1 type IA DNA topoisomerase -
  D4H43_RS06520 - 1340949..1341200 (-) 252 WP_108593827.1 hypothetical protein -
  D4H43_RS08600 - 1341211..1341333 (-) 123 WP_258222686.1 hypothetical protein -
  D4H43_RS06525 - 1341337..1341561 (-) 225 WP_139544411.1 hypothetical protein -
  D4H43_RS06530 - 1341554..1341751 (-) 198 WP_108593828.1 hypothetical protein -
  D4H43_RS06535 - 1342014..1343162 (-) 1149 WP_139543879.1 RNA-guided endonuclease TnpB family protein -
  D4H43_RS06540 tnpA 1343131..1343598 (-) 468 WP_000063685.1 IS200/IS605 family transposase -
  D4H43_RS06545 - 1343764..1349551 (-) 5788 Protein_1253 SNF2-related protein -
  D4H43_RS08660 - 1350130..1350939 (-) 810 WP_341845943.1 helicase -
  D4H43_RS06550 - 1352367..1354613 (-) 2247 WP_139544412.1 type IV secretory system conjugative DNA transfer family protein -
  D4H43_RS06555 - 1354610..1355128 (-) 519 WP_139544413.1 replication regulatory RepB family protein -
  D4H43_RS06560 - 1355125..1356069 (-) 945 WP_139544414.1 CpaF/VirB11 family protein -
  D4H43_RS06565 - 1356074..1356346 (-) 273 WP_201737090.1 hypothetical protein -
  D4H43_RS06570 - 1356364..1357322 (-) 959 Protein_1259 hypothetical protein -
  D4H43_RS06575 - 1357335..1359584 (-) 2250 WP_139544416.1 collagen-like protein -
  D4H43_RS06580 - 1359568..1360766 (-) 1199 Protein_1261 DNA type IV secretion system protein ComB10 -
  D4H43_RS06585 - 1360763..1362430 (-) 1668 WP_139544417.1 TrbG/VirB9 family P-type conjugative transfer protein -
  D4H43_RS06590 - 1362427..1363596 (-) 1170 WP_139544418.1 VirB8/TrbF family protein -
  D4H43_RS06595 - 1363589..1363723 (-) 135 WP_000738749.1 hypothetical protein -
  D4H43_RS06600 - 1363720..1366302 (-) 2583 WP_139544419.1 VirB4 family type IV secretion/conjugal transfer ATPase -
  D4H43_RS06605 - 1366302..1366538 (-) 237 WP_139544420.1 hypothetical protein -
  D4H43_RS06610 comB3 1366549..1366812 (-) 264 WP_128036898.1 competence protein ComB Machinery gene
  D4H43_RS06615 comB2 1366824..1367108 (-) 285 WP_000736106.1 TrbC/VirB2 family protein Machinery gene
  D4H43_RS06620 - 1367105..1367584 (-) 480 WP_033749032.1 hypothetical protein -
  D4H43_RS06625 - 1367577..1367807 (-) 231 WP_000189076.1 hypothetical protein -
  D4H43_RS06630 - 1367810..1368598 (-) 789 WP_139544421.1 integrase -
  D4H43_RS06635 - 1368734..1369117 (+) 384 WP_120957918.1 hypothetical protein -

Sequence

Protein


Download         Length: 94 a.a.        Molecular weight: 10752.11 Da        Isoelectric Point: 11.1589

>NTDB_id=320313 D4H43_RS06615 WP_000736106.1 1366824..1367108(-) (comB2) [Helicobacter pylori strain 19-A-EK3]
MKKLRHFRKLIAFLGFSPLLLQADMTTFFNSIEQQLTSPTAKGILMVIFLGLAIFIWKNLDRWKEILMTVLAIAIGAAIF
FKAPALANWFMSIF

Nucleotide


Download         Length: 285 bp        

>NTDB_id=320313 D4H43_RS06615 WP_000736106.1 1366824..1367108(-) (comB2) [Helicobacter pylori strain 19-A-EK3]
ATGAAAAAATTAAGGCATTTTAGAAAGCTTATCGCCTTTTTAGGTTTTTCACCTCTTTTATTACAAGCGGATATGACTAC
CTTTTTTAATTCCATTGAACAACAGCTCACTAGCCCTACGGCTAAAGGCATTTTAATGGTTATTTTTTTAGGACTTGCTA
TTTTTATATGGAAAAACTTAGATAGATGGAAAGAAATTTTAATGACCGTGCTTGCTATTGCAATTGGTGCTGCAATCTTT
TTTAAAGCCCCAGCCTTAGCTAACTGGTTTATGAGTATTTTTTAA

Domains

Predicted by InterproScan.

TrbC/VIRB2 pilin (TrbC)

(4-90)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB T0F3N0

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
  comB2 Helicobacter pylori 26695

57.778

95.745

0.553

Multiple sequence alignment