Detailed information    

insolico Bioinformatically predicted

Overview

Name   comB10   Type   Machinery gene
Locus tag   HG579_RS05260 Genome accession   NZ_CP051493
Coordinates   1128657..1129865 (-) Length   402 a.a.
NCBI ID   WP_202133574.1    Uniprot ID   -
Organism   Helicobacter pylori strain LIM-006     
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 1116424..1173688 1128657..1129865 within 0


Gene organization within MGE regions


Location: 1116424..1173688
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HG579_RS05185 (HG579_05175) - 1116967..1117455 (-) 489 WP_202133565.1 hypothetical protein -
  HG579_RS05190 (HG579_05180) - 1117625..1118506 (-) 882 Protein_1028 molybdopterin dinucleotide binding domain-containing protein -
  HG579_RS05195 (HG579_05185) - 1118556..1119344 (+) 789 WP_202133567.1 integrase -
  HG579_RS05200 (HG579_05190) - 1119347..1119523 (+) 177 WP_202133568.1 hypothetical protein -
  HG579_RS05205 (HG579_05195) - 1119520..1120008 (+) 489 WP_202133569.1 hypothetical protein -
  HG579_RS05210 (HG579_05200) comB2 1119996..1120280 (+) 285 WP_000413637.1 TrbC/VirB2 family protein Machinery gene
  HG579_RS05215 (HG579_05205) comB3 1120292..1120555 (+) 264 WP_001177716.1 hypothetical protein Machinery gene
  HG579_RS05220 (HG579_05210) - 1120567..1120803 (+) 237 WP_001168532.1 hypothetical protein -
  HG579_RS05225 (HG579_05215) - 1120803..1122196 (+) 1394 Protein_1035 transporter -
  HG579_RS05230 (HG579_05220) - 1122255..1123583 (-) 1329 WP_202133570.1 RNA-guided endonuclease TnpB family protein -
  HG579_RS05235 (HG579_05225) tnpA 1123620..1124036 (+) 417 WP_202133571.1 IS200/IS605 family transposase -
  HG579_RS05240 (HG579_05230) - 1124217..1125161 (-) 945 WP_000362459.1 CpaF/VirB11 family protein -
  HG579_RS05245 (HG579_05235) - 1125166..1125441 (-) 276 WP_001278753.1 hypothetical protein -
  HG579_RS05250 (HG579_05240) - 1125458..1126420 (-) 963 WP_202133572.1 hypothetical protein -
  HG579_RS05255 (HG579_05245) - 1126433..1128673 (-) 2241 WP_202133573.1 collagen-like protein -
  HG579_RS05260 (HG579_05250) comB10 1128657..1129865 (-) 1209 WP_202133574.1 DNA type IV secretion system protein ComB10 Machinery gene
  HG579_RS05265 (HG579_05255) - 1129862..1131502 (-) 1641 WP_202133575.1 TrbG/VirB9 family P-type conjugative transfer protein -
  HG579_RS05270 (HG579_05260) - 1131499..1132635 (-) 1137 WP_202133576.1 VirB8/TrbF family protein -
  HG579_RS05275 (HG579_05265) - 1132628..1132762 (-) 135 WP_078265615.1 type IV secretion system protein VirB7 -
  HG579_RS05280 (HG579_05270) - 1132764..1133942 (-) 1179 Protein_1046 transporter -
  HG579_RS05285 (HG579_05275) tnpA 1134075..1134491 (-) 417 WP_202133571.1 IS200/IS605 family transposase -
  HG579_RS05290 (HG579_05280) - 1134528..1135856 (+) 1329 WP_202133570.1 RNA-guided endonuclease TnpB family protein -
  HG579_RS05295 (HG579_05285) - 1135915..1136379 (+) 465 Protein_1049 replication regulatory RepB family protein -
  HG579_RS05300 (HG579_05290) - 1136376..1138619 (+) 2244 WP_108356317.1 type IV secretory system conjugative DNA transfer family protein -
  HG579_RS08430 - 1140053..1140850 (+) 798 WP_341848072.1 helicase -
  HG579_RS08435 - 1141966..1145583 (+) 3618 WP_341848073.1 SNF2-related protein -
  HG579_RS08440 - 1145589..1147301 (+) 1713 WP_341848039.1 helicase C-terminal domain-containing protein -
  HG579_RS05310 (HG579_05300) - 1147422..1147631 (+) 210 WP_000462384.1 hypothetical protein -
  HG579_RS05315 (HG579_05305) - 1147950..1148333 (+) 384 WP_000410259.1 hypothetical protein -
  HG579_RS05320 (HG579_05310) - 1148346..1150405 (+) 2060 Protein_1056 type IA DNA topoisomerase -
  HG579_RS05325 (HG579_05315) - 1150460..1150930 (+) 471 WP_000965792.1 hypothetical protein -
  HG579_RS05330 (HG579_05320) - 1150900..1151703 (+) 804 WP_187914228.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  HG579_RS05335 (HG579_05325) - 1151777..1152442 (-) 666 WP_202133577.1 hypothetical protein -
  HG579_RS05340 (HG579_05330) - 1152420..1152797 (-) 378 WP_077656947.1 hypothetical protein -
  HG579_RS05345 (HG579_05335) - 1152844..1153512 (-) 669 WP_097639550.1 ParA family protein -
  HG579_RS05350 (HG579_05340) - 1154151..1154315 (+) 165 WP_000189763.1 hypothetical protein -
  HG579_RS05355 (HG579_05345) - 1154316..1155368 (+) 1053 WP_202133578.1 ArdC family protein -
  HG579_RS05360 (HG579_05350) - 1155368..1157236 (+) 1869 WP_202133579.1 hypothetical protein -
  HG579_RS05365 (HG579_05355) - 1157246..1158679 (+) 1434 WP_000120427.1 hypothetical protein -
  HG579_RS05370 (HG579_05360) - 1158676..1159938 (+) 1263 WP_202133580.1 P-type conjugative transfer protein TrbL -
  HG579_RS05375 (HG579_05365) - 1159935..1161212 (+) 1278 WP_202133581.1 hypothetical protein -
  HG579_RS05380 (HG579_05370) - 1161217..1162230 (-) 1014 WP_097683352.1 hypothetical protein -
  HG579_RS05385 - 1162451..1163130 (+) 680 Protein_1069 CAAX protease -
  HG579_RS05390 (HG579_05385) - 1163262..1163513 (+) 252 WP_000006537.1 hypothetical protein -
  HG579_RS05395 (HG579_05390) - 1163485..1164288 (+) 804 WP_202133582.1 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
  HG579_RS05400 (HG579_05395) - 1164605..1165672 (-) 1068 WP_202133583.1 tyrosine-type recombinase/integrase -
  HG579_RS05405 (HG579_05400) - 1166827..1168860 (-) 2034 WP_202133584.1 relaxase/mobilization nuclease domain-containing protein -
  HG579_RS05410 (HG579_05405) - 1169837..1171357 (-) 1521 Protein_1074 molybdopterin-dependent oxidoreductase -
  HG579_RS05415 (HG579_05410) - 1171461..1172051 (-) 591 WP_000353118.1 DUF3972 domain-containing protein -
  HG579_RS05420 (HG579_05415) - 1172077..1173399 (-) 1323 WP_202133586.1 aminotransferase class V-fold PLP-dependent enzyme -

Sequence

Protein


Download         Length: 402 a.a.        Molecular weight: 44975.59 Da        Isoelectric Point: 9.9834

>NTDB_id=439034 HG579_RS05260 WP_202133574.1 1128657..1129865(-) (comB10) [Helicobacter pylori strain LIM-006]
MKQSLLKKIGLGVGGFVVLMALGLLANKGSNNNNKEEIFQVSESKFPLSDYFFEEVKEEPKEKAKETPEVTTQEPTTQTS
PNPSVSANPNIKDYSHLNNNLNQQNNTITHLQQVLQNPSKIKPKPKHTKEQLEFLNTRLKPLEPTKPATKPEMEYGVDSF
TNLKYKDIGTNEHKLLRTITADRMIPAFLITPISSQIAGKVTAQVESDIFASMGRAVLIPKGSKVIGYYNNNNQIGQYRL
NIAWTRIITPQGINIMLTNARGADVKGYNGLVGKYISRNFQRYGIPLLTNTLSNGLLIGITSALANNQNKKGDGNPFFGD
YLLMQLTRNTGMGINQVINQMLRQYGAQNPIIIIREGSRVFISPNLDIFIPKPKDGEVLAEFFKEKKPPIKTKEEINNEE
EI

Nucleotide


Download         Length: 1209 bp        

>NTDB_id=439034 HG579_RS05260 WP_202133574.1 1128657..1129865(-) (comB10) [Helicobacter pylori strain LIM-006]
ATGAAACAATCCTTGCTTAAAAAGATAGGCTTAGGTGTTGGGGGCTTTGTTGTTTTAATGGCATTAGGATTGCTTGCTAA
TAAAGGCTCAAACAATAACAATAAAGAAGAAATCTTTCAAGTAAGTGAGAGTAAATTCCCTTTAAGTGATTATTTCTTTG
AAGAAGTCAAAGAAGAGCCAAAAGAAAAAGCCAAAGAAACACCAGAAGTAACTACCCAAGAGCCTACAACACAAACTAGC
CCCAATCCTAGTGTTTCAGCTAATCCTAACATTAAAGATTATAGTCATCTTAACAACAATCTTAATCAGCAAAATAATAC
TATCACGCATTTACAACAAGTTTTACAAAACCCCTCTAAAATAAAGCCTAAACCAAAGCATACTAAAGAGCAATTAGAAT
TTTTAAACACACGCCTTAAACCTTTAGAACCAACTAAACCAGCCACTAAGCCTGAGATGGAATACGGCGTGGATAGTTTT
ACTAATTTAAAATATAAAGACATTGGCACTAATGAGCATAAGCTCTTAAGAACTATAACCGCTGATAGAATGATACCAGC
CTTTTTGATCACGCCTATTAGCTCTCAAATTGCTGGAAAAGTAACCGCTCAAGTAGAGAGCGATATTTTTGCCTCTATGG
GTAGAGCGGTGCTAATCCCTAAAGGCTCTAAGGTTATAGGCTATTACAACAACAATAATCAAATCGGACAATACCGCTTA
AACATTGCTTGGACTAGAATTATCACCCCTCAAGGTATCAATATCATGCTCACTAATGCAAGAGGGGCTGATGTGAAAGG
CTATAATGGCTTAGTAGGCAAATACATTAGCCGAAATTTTCAACGCTATGGTATCCCCTTACTCACTAACACGCTTTCTA
ATGGGCTTTTAATAGGAATTACTTCAGCCTTAGCTAATAACCAAAACAAAAAAGGTGATGGCAACCCTTTTTTTGGGGAT
TACTTGCTTATGCAACTCACTAGAAATACAGGCATGGGCATCAATCAAGTTATCAATCAAATGCTAAGACAATATGGAGC
GCAAAACCCCATTATCATCATTAGAGAGGGGAGCAGAGTGTTTATTAGCCCTAATTTAGACATCTTTATCCCTAAACCAA
AAGATGGGGAGGTTTTAGCGGAGTTCTTTAAAGAGAAAAAACCCCCAATCAAAACAAAAGAGGAAATTAACAATGAAGAA
GAAATCTAA

Domains

Predicted by InterproScan.

Bacterial conjugation TrbI-like protein (TrbI)

(178-368)


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
  comB10 Helicobacter pylori P1

52.685

97.264

0.512