Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103852
Name   oriT_HM006|psymA in_silico
Organism   Sinorhizobium meliloti strain HM006
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021830 (402747..402775 [-], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_HM006|psymA
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2863 GenBank   WP_088202563
Name   traA_CDO22_RS20195_HM006|psymA insolico UniProt ID   _
Length   1539 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1539 a.a.        Molecular weight: 170146.87 Da        Isoelectric Point: 9.4212

>WP_088202563.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
RSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMTSDELVLLKPQQVDAETGKAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWEMAWESGREQLQRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARRERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AILHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMTLSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFTY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAAVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKDALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMPVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRIQSSQEIISERQRRVIDRARGVTR

  Protein domains


Predicted by InterproScan.

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(1309-1400)

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-578)


  Protein structure



No available structure.




T4CP

ID   2698 GenBank   WP_027991006
Name   traG_CDO22_RS20210_HM006|psymA insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70399.34 Da        Isoelectric Point: 9.2422

>WP_027991006.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLLILLPVAVTAFAIYVVGWRWPGLAAGMSGNTAYWFLRASPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVAGFYALREFGRLSPSVESGLLSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMSAAGKLFPPDGEIVVGERYRVDKDIVHELPFDPDDPATWGKGGKAP
LLTYSQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVLEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSSGAYFQNQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSQSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSTDIVTGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAIP

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(165-635)

  Protein structure



No available structure.



ID   2699 GenBank   WP_088202258
Name   virD4_CDO22_RS20875_HM006|psymA insolico UniProt ID   _
Length   563 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 563 a.a.        Molecular weight: 63019.32 Da        Isoelectric Point: 9.1751

>WP_088202258.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLFQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILAMPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPTPLMIADERF
SHV

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(97-537)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 273909..283487

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDO22_RS19505 (CDO22_19510) 270796..271644 + 849 WP_017264156 alpha/beta fold hydrolase -
CDO22_RS19510 (CDO22_19515) 271694..272341 + 648 WP_017264157 dihydrofolate reductase family protein -
CDO22_RS19515 (CDO22_19520) 272460..272663 + 204 WP_017264158 hypothetical protein -
CDO22_RS19520 (CDO22_19525) 272922..273290 - 369 WP_017264159 transcriptional regulator -
CDO22_RS36315 (CDO22_19530) 273387..273905 + 519 WP_017264160 hypothetical protein -
CDO22_RS19530 (CDO22_19535) 273909..274580 + 672 WP_017264161 lytic transglycosylase domain-containing protein virB1
CDO22_RS19535 (CDO22_19540) 274577..274876 + 300 WP_003526741 TrbC/VirB2 family protein virB2
CDO22_RS19540 (CDO22_19545) 274881..275222 + 342 WP_017264162 type IV secretion system protein VirB3 virB3
CDO22_RS19545 (CDO22_19550) 275197..277593 + 2397 WP_017264163 VirB4 family type IV secretion system protein virb4
CDO22_RS19550 (CDO22_19555) 277593..278294 + 702 WP_017264164 P-type DNA transfer protein VirB5 virB5
CDO22_RS19555 (CDO22_19560) 278291..278506 + 216 WP_014531545 EexN family lipoprotein -
CDO22_RS19560 (CDO22_19565) 278529..279464 + 936 WP_014531546 type IV secretion system protein virB6
CDO22_RS19565 (CDO22_19570) 279461..279775 + 315 WP_017264165 hypothetical protein -
CDO22_RS19570 (CDO22_19575) 279780..280451 + 672 WP_010967689 virB8 family protein virB8
CDO22_RS19575 (CDO22_19580) 280451..281305 + 855 WP_014528658 P-type conjugative transfer protein VirB9 virB9
CDO22_RS19580 (CDO22_19585) 281315..282487 + 1173 WP_014990096 type IV secretion system protein VirB10 virB10
CDO22_RS19585 (CDO22_19590) 282498..283487 + 990 WP_010967686 P-type DNA transfer ATPase VirB11 virB11
CDO22_RS19590 (CDO22_19595) 283799..285025 - 1227 WP_010967685 MFS transporter -
CDO22_RS19595 (CDO22_19600) 285060..285671 - 612 WP_017264166 TetR/AcrR family transcriptional regulator -
CDO22_RS19600 (CDO22_19605) 285923..286600 + 678 WP_017264167 YoaK family protein -
CDO22_RS19605 (CDO22_19610) 286848..287870 + 1023 WP_010967682 alcohol dehydrogenase AdhP -

Region 2: 527760..537173

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDO22_RS20880 (CDO22_20895) 523003..523728 - 726 WP_014528527 response regulator -
CDO22_RS36360 (CDO22_20910) 524747..525052 - 306 WP_011971014 hypothetical protein -
CDO22_RS20900 (CDO22_20915) 525052..526617 - 1566 WP_011971015 IS66 family transposase -
CDO22_RS20905 (CDO22_20920) 526689..527036 - 348 WP_011971016 IS66 family insertion sequence element accessory protein TnpB -
CDO22_RS20910 (CDO22_20925) 527033..527416 - 384 WP_011971017 transposase -
CDO22_RS20915 (CDO22_20930) 527760..528800 - 1041 WP_014528525 P-type DNA transfer ATPase VirB11 virB11
CDO22_RS20920 (CDO22_20935) 528840..529958 - 1119 WP_014528524 type IV secretion system protein VirB10 virB10
CDO22_RS20925 (CDO22_20940) 529955..530836 - 882 WP_014528523 TrbG/VirB9 family P-type conjugative transfer protein virB9
CDO22_RS20930 (CDO22_20945) 530833..531546 - 714 WP_014528522 type IV secretion system protein VirB8 virB8
CDO22_RS20935 (CDO22_20950) 531533..531700 - 168 WP_011970875 type IV secretion system lipoprotein VirB7 -
CDO22_RS20940 (CDO22_20955) 531733..532620 - 888 WP_014528521 type IV secretion system protein virB6
CDO22_RS20945 (CDO22_20960) 532701..533384 - 684 WP_014528520 pilin minor subunit VirB5 traI
CDO22_RS20950 (CDO22_20965) 533398..535767 - 2370 WP_014528519 VirB4 family type IV secretion/conjugal transfer ATPase virb4
CDO22_RS20955 (CDO22_20970) 535767..536093 - 327 WP_003537077 type IV secretion system protein VirB3 virB3
CDO22_RS20960 (CDO22_20975) 536090..536452 - 363 WP_014528518 pilin major subunit VirB2 virB2
CDO22_RS20965 (CDO22_20980) 536466..537173 - 708 WP_014528517 type IV secretion system lytic transglycosylase VirB1 virB1
CDO22_RS35890 537382..537540 + 159 WP_170849885 hypothetical protein -
CDO22_RS20975 (CDO22_20990) 537692..537883 - 192 Protein_515 Lrp/AsnC ligand binding domain-containing protein -
CDO22_RS20980 (CDO22_20995) 537867..538442 + 576 WP_153428644 type IV secretory system conjugative DNA transfer family protein -
CDO22_RS20985 (CDO22_21000) 538526..539637 + 1112 Protein_517 IS256-like element ISRm5 family transposase -
CDO22_RS20990 (CDO22_21005) 539657..539925 + 269 Protein_518 hypothetical protein -
CDO22_RS20995 (CDO22_21010) 540255..541708 - 1454 Protein_519 PLP-dependent aminotransferase family protein -

Host bacterium

ID   4292 GenBank   NZ_CP021830
Plasmid name   HM006|psymA Incompatibility group   -
Plasmid size   1484605 bp Coordinate of oriT [Strand]   402747..402775 [-]
Host baterium   Sinorhizobium meliloti strain HM006

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixN, fixO, fixG, fixS, nodM, nifN, nodD, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, nifX, nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifB, fixU, nifT
Anti-CRISPR   -