Detailed information
Bioinformatically predicted
Overview
| Name | comB3 | Type | Machinery gene |
| Locus tag | D4I31_RS03330 | Genome accession | NZ_CP032908 |
| Coordinates | 688069..688332 (-) | Length | 87 a.a. |
| NCBI ID | WP_139534476.1 | Uniprot ID | - |
| Organism | Helicobacter pylori strain 23-A-EK1 | ||
| 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 | 604978..702982 | 688069..688332 | within | 0 |
Gene organization within MGE regions
Location: 604978..702982
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| D4I31_RS02985 | - | 605472..607103 (-) | 1632 | WP_139534393.1 | class I SAM-dependent DNA methyltransferase | - |
| D4I31_RS02990 | - | 607093..609372 (-) | 2280 | WP_236635759.1 | DEAD/DEAH box helicase family protein | - |
| D4I31_RS08380 | - | 609546..610232 (-) | 687 | WP_236635760.1 | type I restriction endonuclease | - |
| D4I31_RS02995 | - | 610280..612175 (-) | 1896 | WP_139534395.1 | motility associated factor glycosyltransferase family protein | - |
| D4I31_RS03000 | - | 612201..612968 (-) | 768 | WP_139534397.1 | TerB family tellurite resistance protein | - |
| D4I31_RS03005 | - | 612978..613292 (-) | 315 | WP_001861281.1 | hypothetical protein | - |
| D4I31_RS03010 | - | 613294..614781 (-) | 1488 | WP_139534398.1 | DUF5644 domain-containing protein | - |
| D4I31_RS03015 | - | 614793..615281 (-) | 489 | WP_139534400.1 | hypothetical protein | - |
| D4I31_RS03020 | - | 615266..617002 (-) | 1737 | WP_139534402.1 | M3 family oligoendopeptidase | - |
| D4I31_RS03025 | - | 617100..618350 (-) | 1251 | WP_139534404.1 | cation:proton antiporter | - |
| D4I31_RS08385 | - | 618505..618687 (-) | 183 | WP_139534405.1 | hypothetical protein | - |
| D4I31_RS03035 | - | 618671..619231 (-) | 561 | WP_000595783.1 | outer membrane beta-barrel protein | - |
| D4I31_RS08260 | - | 619347..619439 (-) | 93 | Protein_582 | orotate phosphoribosyltransferase | - |
| D4I31_RS03045 | modA | 619458..620198 (+) | 741 | WP_139534407.1 | molybdate ABC transporter substrate-binding protein | - |
| D4I31_RS03050 | modB | 620220..620894 (+) | 675 | WP_139534408.1 | molybdate ABC transporter permease subunit | - |
| D4I31_RS03055 | - | 620891..621688 (+) | 798 | WP_139534410.1 | sulfate/molybdate ABC transporter ATP-binding protein | - |
| D4I31_RS03060 | gltX | 621805..623196 (-) | 1392 | WP_139534412.1 | glutamate--tRNA ligase | - |
| D4I31_RS03065 | hopJ | 623313..624422 (+) | 1110 | WP_139534415.1 | Hop family outer membrane protein HopJ/HopK | - |
| D4I31_RS03070 | - | 624431..626068 (+) | 1638 | WP_139534417.1 | class I SAM-dependent methyltransferase | - |
| D4I31_RS03075 | - | 626034..626876 (+) | 843 | WP_139534419.1 | glycosyltransferase family 9 protein | - |
| D4I31_RS03080 | typA | 626922..628721 (+) | 1800 | WP_139534421.1 | translational GTPase TypA | - |
| D4I31_RS03085 | - | 628737..629132 (+) | 396 | Protein_591 | DNA adenine methylase | - |
| D4I31_RS03090 | - | 629511..630584 (+) | 1074 | WP_139534425.1 | site-specific integrase | - |
| D4I31_RS03095 | - | 630665..631348 (-) | 684 | WP_139534427.1 | CAAX protease | - |
| D4I31_RS03100 | - | 631421..632682 (-) | 1262 | Protein_594 | P-type conjugative transfer protein TrbL | - |
| D4I31_RS03105 | - | 632684..632962 (-) | 279 | WP_097681256.1 | hypothetical protein | - |
| D4I31_RS03110 | - | 633014..633460 (-) | 447 | Protein_596 | hypothetical protein | - |
| D4I31_RS03115 | - | 633456..634265 (-) | 810 | WP_236635761.1 | VirB8/TrbF family protein | - |
| D4I31_RS03120 | - | 634382..635434 (-) | 1053 | Protein_598 | DNA topoisomerase | - |
| D4I31_RS03125 | - | 635500..635739 (+) | 240 | Protein_599 | DNA adenine methylase | - |
| D4I31_RS03130 | - | 635742..636365 (+) | 624 | WP_139534428.1 | GIY-YIG nuclease family protein | - |
| D4I31_RS03135 | - | 636456..637046 (+) | 591 | WP_139534430.1 | DNA cytosine methyltransferase | - |
| D4I31_RS03140 | - | 637052..637996 (-) | 945 | WP_139534432.1 | catalase | - |
| D4I31_RS03145 | hofC | 638272..639858 (+) | 1587 | WP_050839967.1 | outer membrane beta-barrel protein HofC | - |
| D4I31_RS03150 | hofD | 639929..641326 (+) | 1398 | WP_201738165.1 | outer membrane beta-barrel protein HofD | - |
| D4I31_RS03155 | - | 641557..641757 (-) | 201 | WP_139534435.1 | hypothetical protein | - |
| D4I31_RS03160 | - | 641726..644179 (+) | 2454 | WP_139534437.1 | DUF3519 domain-containing protein | - |
| D4I31_RS03165 | - | 645167..647200 (+) | 2034 | WP_201738166.1 | relaxase/mobilization nuclease domain-containing protein | - |
| D4I31_RS03170 | - | 648319..649386 (+) | 1068 | WP_139534439.1 | tyrosine-type recombinase/integrase | - |
| D4I31_RS03175 | - | 649703..650505 (-) | 803 | Protein_609 | nucleotidyl transferase AbiEii/AbiGii toxin family protein | - |
| D4I31_RS03180 | - | 650477..650728 (-) | 252 | WP_000006537.1 | hypothetical protein | - |
| D4I31_RS08540 | - | 650860..651512 (-) | 653 | Protein_611 | CAAX protease | - |
| D4I31_RS03195 | - | 651762..652409 (+) | 648 | WP_104707240.1 | hypothetical protein | - |
| D4I31_RS03200 | - | 652413..653654 (-) | 1242 | WP_139534442.1 | hypothetical protein | - |
| D4I31_RS03205 | - | 653666..654904 (-) | 1239 | WP_139534445.1 | type IV secretion system protein | - |
| D4I31_RS03210 | - | 654904..656337 (-) | 1434 | WP_139534447.1 | toprim domain-containing protein | - |
| D4I31_RS03215 | - | 656347..658302 (-) | 1956 | WP_139534448.1 | hypothetical protein | - |
| D4I31_RS03220 | - | 658302..659369 (-) | 1068 | WP_139534450.1 | ArdC-like ssDNA-binding domain-containing protein | - |
| D4I31_RS08265 | - | 659370..659534 (-) | 165 | WP_000189755.1 | hypothetical protein | - |
| D4I31_RS03225 | - | 660171..660839 (+) | 669 | WP_021301015.1 | ParA family protein | - |
| D4I31_RS03230 | - | 660886..661263 (+) | 378 | WP_000365702.1 | hypothetical protein | - |
| D4I31_RS03235 | - | 661241..661813 (+) | 573 | WP_139534452.1 | hypothetical protein | - |
| D4I31_RS03240 | - | 661936..662739 (-) | 804 | WP_139534454.1 | nucleotidyl transferase AbiEii/AbiGii toxin family protein | - |
| D4I31_RS03245 | - | 662709..663179 (-) | 471 | WP_000965792.1 | hypothetical protein | - |
| D4I31_RS03250 | - | 663234..665294 (-) | 2061 | WP_139534456.1 | type IA DNA topoisomerase | - |
| D4I31_RS03255 | - | 665324..665548 (-) | 225 | WP_001043180.1 | hypothetical protein | - |
| D4I31_RS03260 | - | 665541..665795 (-) | 255 | WP_000732628.1 | hypothetical protein | - |
| D4I31_RS03265 | - | 665931..673943 (-) | 8013 | WP_139534458.1 | SNF2-related protein | - |
| D4I31_RS03270 | - | 673963..676227 (-) | 2265 | WP_139534460.1 | type IV secretory system conjugative DNA transfer family protein | - |
| D4I31_RS03275 | - | 676224..676742 (-) | 519 | WP_139534461.1 | replication regulatory RepB family protein | - |
| D4I31_RS03280 | - | 676739..677683 (-) | 945 | WP_006564526.1 | CpaF/VirB11 family protein | - |
| D4I31_RS03285 | - | 677688..677960 (-) | 273 | WP_015427688.1 | hypothetical protein | - |
| D4I31_RS03290 | - | 677978..678955 (-) | 978 | WP_139534463.1 | hypothetical protein | - |
| D4I31_RS03295 | - | 678968..681202 (-) | 2235 | WP_139534465.1 | collagen-like protein | - |
| D4I31_RS03300 | comB10 | 681186..682385 (-) | 1200 | WP_139534467.1 | DNA type IV secretion system protein ComB10 | Machinery gene |
| D4I31_RS03305 | - | 682382..683986 (-) | 1605 | WP_139534469.1 | TrbG/VirB9 family P-type conjugative transfer protein | - |
| D4I31_RS03310 | - | 683983..685116 (-) | 1134 | WP_139534471.1 | VirB8/TrbF family protein | - |
| D4I31_RS03315 | - | 685109..685243 (-) | 135 | WP_000738749.1 | hypothetical protein | - |
| D4I31_RS03320 | - | 685240..687822 (-) | 2583 | WP_139534473.1 | VirB4 family type IV secretion/conjugal transfer ATPase | - |
| D4I31_RS03325 | - | 687822..688058 (-) | 237 | WP_139534474.1 | hypothetical protein | - |
| D4I31_RS03330 | comB3 | 688069..688332 (-) | 264 | WP_139534476.1 | competence protein ComB | Machinery gene |
| D4I31_RS03335 | comB2 | 688343..688627 (-) | 285 | WP_000736478.1 | TrbC/VirB2 family protein | Machinery gene |
| D4I31_RS03340 | - | 688624..689103 (-) | 480 | WP_139534478.1 | hypothetical protein | - |
| D4I31_RS03345 | - | 689207..689995 (-) | 789 | WP_139534480.1 | integrase | - |
| D4I31_RS03350 | - | 690069..690488 (+) | 420 | WP_236635762.1 | hypothetical protein | - |
| D4I31_RS03355 | - | 690576..691010 (+) | 435 | WP_139534482.1 | hypothetical protein | - |
| D4I31_RS03360 | - | 691010..692131 (+) | 1122 | WP_201738180.1 | DUF1542 domain-containing protein | - |
| D4I31_RS03370 | - | 692347..693483 (-) | 1137 | WP_139534486.1 | NAD-binding protein | - |
| D4I31_RS03380 | rpmB | 693665..693853 (-) | 189 | WP_001118998.1 | 50S ribosomal protein L28 | - |
| D4I31_RS03385 | - | 693953..694789 (-) | 837 | WP_139534488.1 | HpaA family protein | - |
| D4I31_RS03390 | mraY | 694915..695976 (+) | 1062 | WP_101022463.1 | phospho-N-acetylmuramoyl-pentapeptide- transferase | - |
| D4I31_RS03395 | murD | 695978..697246 (+) | 1269 | WP_139534490.1 | UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase | - |
| D4I31_RS03400 | - | 697243..697503 (-) | 261 | WP_139534492.1 | DUF493 family protein | - |
| D4I31_RS03405 | ybgC | 697493..697894 (-) | 402 | WP_139534494.1 | acyl-CoA thioesterase YbgC | - |
| D4I31_RS03410 | - | 698122..699450 (+) | 1329 | WP_139534496.1 | sodium-dependent transporter | - |
| D4I31_RS03415 | - | 699461..700789 (+) | 1329 | WP_139534498.1 | sodium-dependent transporter | - |
| D4I31_RS03420 | - | 700804..701871 (+) | 1068 | WP_139534500.1 | phospholipase A | - |
Sequence
Protein
Download Length: 87 a.a. Molecular weight: 9984.86 Da Isoelectric Point: 5.7206
>NTDB_id=320254 D4I31_RS03330 WP_139534476.1 688069..688332(-) (comB3) [Helicobacter pylori strain 23-A-EK1]
MQLVGISVSNLKEISSKEKFLWLNAKSFLIAGFIPFVMIPWLDFLNSLILYVCFLLVFSIAEFFDEDISDILIAHSKIKT
KTNSFYA
MQLVGISVSNLKEISSKEKFLWLNAKSFLIAGFIPFVMIPWLDFLNSLILYVCFLLVFSIAEFFDEDISDILIAHSKIKT
KTNSFYA
Nucleotide
Download Length: 264 bp
>NTDB_id=320254 D4I31_RS03330 WP_139534476.1 688069..688332(-) (comB3) [Helicobacter pylori strain 23-A-EK1]
ATGCAATTAGTCGGAATTTCAGTTTCTAATCTCAAAGAAATCAGTTCTAAAGAAAAGTTTCTTTGGCTCAATGCTAAGAG
CTTTTTAATCGCAGGATTTATTCCTTTTGTAATGATACCTTGGCTAGATTTTTTAAATTCTTTAATACTGTATGTGTGCT
TTTTATTGGTTTTTAGCATAGCGGAGTTCTTTGATGAAGATATAAGCGACATTTTAATCGCCCATTCTAAGATTAAAACC
AAAACTAATTCATTTTATGCTTAA
ATGCAATTAGTCGGAATTTCAGTTTCTAATCTCAAAGAAATCAGTTCTAAAGAAAAGTTTCTTTGGCTCAATGCTAAGAG
CTTTTTAATCGCAGGATTTATTCCTTTTGTAATGATACCTTGGCTAGATTTTTTAAATTCTTTAATACTGTATGTGTGCT
TTTTATTGGTTTTTAGCATAGCGGAGTTCTTTGATGAAGATATAAGCGACATTTTAATCGCCCATTCTAAGATTAAAACC
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 |