Detailed information
Bioinformatically predicted
Overview
| Name | comB3 | Type | Machinery gene |
| Locus tag | D4H43_RS06610 | Genome accession | NZ_CP032911 |
| Coordinates | 1366549..1366812 (-) | Length | 87 a.a. |
| NCBI ID | WP_128036898.1 | Uniprot ID | A0AB37V0S2 |
| 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 | 1366549..1366812 | 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: 87 a.a. Molecular weight: 10018.89 Da Isoelectric Point: 5.7206
>NTDB_id=320312 D4H43_RS06610 WP_128036898.1 1366549..1366812(-) (comB3) [Helicobacter pylori strain 19-A-EK3]
MQLVGISVSNLKEISSKEKFLWLNAKSFLLSGFIPFVMIPWLDFLNSLMLYVCFLLVFSIAEFFDEDISDILIAHSKIKT
KTNSFYA
MQLVGISVSNLKEISSKEKFLWLNAKSFLLSGFIPFVMIPWLDFLNSLMLYVCFLLVFSIAEFFDEDISDILIAHSKIKT
KTNSFYA
Nucleotide
Download Length: 264 bp
>NTDB_id=320312 D4H43_RS06610 WP_128036898.1 1366549..1366812(-) (comB3) [Helicobacter pylori strain 19-A-EK3]
ATGCAATTAGTTGGTATTTCAGTTTCTAATCTCAAAGAAATCAGCTCCAAAGAAAAATTTCTTTGGCTCAATGCTAAGAG
CTTTTTACTCTCAGGATTTATTCCTTTTGTAATGATACCTTGGCTAGATTTTTTAAATTCTTTAATGCTGTATGTGTGCT
TTTTATTGGTTTTTAGCATAGCGGAGTTCTTTGATGAAGATATAAGCGACATTTTAATCGCCCATTCTAAAATTAAAACC
AAAACTAATTCATTTTATGCTTAA
ATGCAATTAGTTGGTATTTCAGTTTCTAATCTCAAAGAAATCAGCTCCAAAGAAAAATTTCTTTGGCTCAATGCTAAGAG
CTTTTTACTCTCAGGATTTATTCCTTTTGTAATGATACCTTGGCTAGATTTTTTAAATTCTTTAATGCTGTATGTGTGCT
TTTTATTGGTTTTTAGCATAGCGGAGTTCTTTGATGAAGATATAAGCGACATTTTAATCGCCCATTCTAAAATTAAAACC
AAAACTAATTCATTTTATGCTTAA
Domains
No domain identified.
3D structure
| Source | ID | Structure |
|---|
Similar proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| comB3 | Helicobacter pylori 26695 |
59.77 |
100 |
0.598 |