Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200479
Name   oriT_ICEAciJS42-1 in_silico
Organism   Acidovorax sp. JS42
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP000539 (93496..93813 [+], 318 nt)
oriT length   318 nt
IRs (inverted repeats)      199..206, 215..222  (TAAAAGGC..GCCTTTTA)
 197..202, 207..212  (TTTAAA..TTTAAA)
 71..76, 86..91  (TTCCAC..GTGGAA)
 34..39, 41..46  (GGAACG..CGTTCC)
 20..26, 29..35  (CCTGCGC..GCGCAGG)
Location of nic site      19..20
Conserved sequence flanking the
  nic site    		  TCGTGCCTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 318 nt

>oriT_ICEAciJS42-1
CCATGGCCGAGCGGTCGTGCCTGCGCCAGCGCAGGAACGTCGTTCCCGCGCCAGTGGTCTGCTGGGCCAGTTCCACGGGCAGCAGGTGGAAGGGATGCCCACTGGCCTGTTGCAGCACTTGTCGCTGCGCCAAGCCGATCAACTCGTCGCGCATGGCGAAGCACTGGCCGGCCCAGGCCTCCAAGTCCCCTTTACCTTTAAAAGGCTTTAAAAGGCCTTTTAGAGAGGCCGCGTGTTCCAGGCGCATGAAGGCTCCCGGTTGCAGGCCCCGGAAGTAGCGGGTCGGCTGGTTCAGATCGCTCATGCGGATTCGTCCTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14516 GenBank   ABM41469
Name   TraI_2_Ajs_1245_ICEAciJS42-1 insolico UniProt ID   _
Length   627 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 627 a.a.        Molecular weight: 68988.32 Da        Isoelectric Point: 6.8415

>ABM41469.1 Relaxase [Acidovorax sp. JS42]
MLSLFQRKRPAVAAAPTPPSVTDLPKGLMRPESAASLLATPRRQKLLEHIWQRTSLSRKQFATLYRAPLE
RYAELVQAFPASEAHHHAYPGGMLDHGLEIVAYSLKLRQSHLLPIGASPEDQAAQSEAWTAAVAYAALLH
DIGKIAVDLHVELADGSLWHPWHGPLHQPYRFRYRDDREYRLHSAATGLLYRQLLDRDALDWLSGYPDLW
GPLLYVLAGQYEHAGVLGELVVQADRASVAQELGGDPARAMAAPKHALQRKLLDGLRYLLKEQLKLNQPE
ASDGWLTEDALWLVSKTVSDKLRAHLLSQGIDGIPANNTAVFNVLQDHGMLQPTSDGKAVWRATVTSTTG
WSHSFTLLRLTPTLIWEPRERPAPFPGTVAIDVAPTDKEADVFTTISTAGPLAAPEGQEDPPGEGGRSSS
APSSKFQTLPDVMEDMLSMVGIGDLPAIGQDAAVLSEQVPAARPEIPTLPASLPSSPAPAPSIAHPSGEH
FMAWLKQGILSRRLIINDAKALVHTVSGTTYLVSPGVFQRYAQEHPQVGAQAKQESQQDWQWIQKRFERL
QLHRKQPNGLNIWTCKVTGPRKSRHLHGYLLEDSSLLFLETPPNNPYLSLLCETTGSGLHESNEGQH

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(27-340)

Putative conjugal transfer nickase/helicase TraI C-term (TraI_2_C)

(487-609)


  Protein structure



No available structure.




T4CP

ID   17132 GenBank   ABM41498
Name   t4cp2_Ajs_1274_ICEAciJS42-1 insolico UniProt ID   _
Length   730 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 730 a.a.        Molecular weight: 80698.34 Da        Isoelectric Point: 7.3316

>ABM41498.1 conserved hypothetical protein [Acidovorax sp. JS42]
MSGKQPVEVLLRPAVELYTVAACAGAAFLSLVAPWSLALSPAMGVGSALAFGAYGAIRYRDARVILRYRR
NIRRLPRYVMTSRDVPVSQQRLFVGRGFLWEQKHTHRLMQTYRPEFRRYAEPTPAYRLARRLEERLEFAP
LPLSRLPKLTGWDVPFNPVRPLPPVGGLPRLHGIEPDEVDVSLPLGERVGHSLVLGTTRVGKTRLAELFV
TQDIRRRNAAGEHEVVIVIDPKGDADLLKRMYVEAQRAGREGEFYVFHLGWPDISARYNAVGRFGRISEV
ATRVAGQLSGEGNSAAFREFAWRFVNIIARALVELGQRPDYMLIQRHVINIDALFIEYAQHYFAKTEPKA
WEVIVQIEAKLNEKNIPRNMIGREKRVVALEQYLSQARNYDPVLDGLRSAVRYDKTYFDKIVASLLPLLE
KLTSGKIAQLLAPNYSDLADPRPIFDWMQVIRKRAVVYVGLDALSDAEVAAAVGNSMFSDLVSVAGHIYK
HGIDDGLPGASAGARVPINVHADEFNELMGDEFIPLINKGGGAGLQVTAYTQTLSDIEARIGNRAKAGQV
IGNFNNLFMLRVRETATAELLTRQLPKVEVYTTTIVSGATDSSDIRGATDFTSNTQDRISMSSVPMIEPS
HVVGLPKGQCFALLQGGQLWKVRMPLPAPDPDEVMPADLQQLAGYMRQSYSEATQWWEFTSSSALQDAAL
PDDLLDDAAAAEPGAVATGADDGAGNEAVP

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(508-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1327178..1354704

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Ajs_1243 1322310..1323404 + 1095 ABM41468 signal peptidase II -
Ajs_1245 1323801..1325684 - 1884 ABM41469 Relaxase -
Ajs_1246 1325914..1326300 + 387 ABM41470 transcriptional regulator, AbrB family -
Ajs_1247 1326300..1326758 + 459 ABM41471 conserved hypothetical protein -
Ajs_1248 1326785..1327162 + 378 ABM41472 conserved hypothetical protein -
Ajs_1249 1327178..1328695 - 1518 ABM41473 conserved hypothetical protein tfc19
Ajs_1250 1328710..1329069 - 360 ABM41474 conserved hypothetical protein tfc18
Ajs_1251 1329066..1330460 - 1395 ABM41475 conserved hypothetical protein tfc22
Ajs_1252 1330470..1331417 - 948 ABM41476 protein of unknown function DUF1527 tfc23
Ajs_1253 1331414..1331860 - 447 ABM41477 protein of unknown function DUF1525 tfc24
Ajs_1254 1332024..1332518 - 495 ABM41478 DNA repair protein RadC -
Ajs_1255 1332698..1333462 - 765 ABM41479 conserved hypothetical protein -
Ajs_1256 1333487..1336378 - 2892 ABM41480 conserved hypothetical protein virb4
Ajs_1257 1336378..1336827 - 450 ABM41481 putative secreted protein tfc15
Ajs_1258 1336808..1338238 - 1431 ABM41482 putative secreted protein tfc14
Ajs_1259 1338228..1339136 - 909 ABM41483 putative secreted protein tfc13
Ajs_1260 1339133..1339825 - 693 ABM41484 putative secreted protein tfc12
Ajs_1261 1339822..1340220 - 399 ABM41485 conserved hypothetical protein tfc11
Ajs_1262 1340232..1340591 - 360 ABM41486 conserved hypothetical protein tfc10
Ajs_1263 1340608..1340841 - 234 ABM41487 conserved hypothetical protein tfc9
Ajs_1264 1340838..1341221 - 384 ABM41488 plasmid conserved hypothetical protein, RAQPRD tfc8
Ajs_1265 1341425..1341895 + 471 ABM41489 DNA binding domain, excisionase family -
Ajs_1266 1341892..1342467 + 576 ABM41490 conserved hypothetical protein -
Ajs_1267 1342485..1343399 + 915 ABM41491 AAA ATPase, central domain protein -
Ajs_1268 1343396..1343866 + 471 ABM41492 conserved hypothetical protein -
Ajs_1269 1343863..1344363 + 501 ABM41493 conserved hypothetical protein -
Ajs_1270 1344363..1345265 + 903 ABM41494 conserved hypothetical protein -
Ajs_1271 1345304..1346029 + 726 ABM41495 conserved hypothetical protein -
Ajs_1272 1346039..1348663 + 2625 ABM41496 conserved hypothetical protein -
Ajs_1273 1348704..1349453 - 750 ABM41497 conserved hypothetical protein tfc7
Ajs_1274 1349450..1351642 - 2193 ABM41498 conserved hypothetical protein -
Ajs_1275 1351647..1352195 - 549 ABM41499 putative secreted protein tfc5
Ajs_1276 1352192..1352782 - 591 ABM41500 Lytic transglycosylase, catalytic virB1
Ajs_1277 1352764..1353489 - 726 ABM41501 putative secreted protein tfc3
Ajs_1278 1353506..1354141 - 636 ABM41502 conserved hypothetical protein -
Ajs_1279 1354138..1354704 - 567 ABM41503 putative secreted protein tfc2
Ajs_1280 1354831..1355193 + 363 ABM41504 transcriptional regulator, ArsR family -
Ajs_1281 1355196..1355690 + 495 ABM41505 protein tyrosine phosphatase -
Ajs_1282 1355701..1356777 + 1077 ABM41506 arsenical-resistance protein -
Ajs_1283 1356794..1357216 + 423 ABM41507 arsenate reductase -
Ajs_1284 1357200..1357931 + 732 ABM41508 NADPH-dependent FMN reductase -

Host bacterium

ID   424 Element type   ICE (Integrative and conjugative element)
Element name   ICEAciJS42-1 GenBank   CP000539
Element size   4448856 bp Coordinate of oriT [Strand]   93496..93813 [+]
Host bacterium   Acidovorax sp. JS42 Coordinate of element   1287924..1407821

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   cusA/ybdE, copA, copR, pbrT, pbrA, pbrB/pbrC, arsC, arsH, merA, merT, merR2
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -