Plasmid (Source) orf



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Table S1 - Summary of pTRACA18, pTRACA20, pTRACA22, and pTRACA30 open reading frames and putative functions.


Plasmid

(Source)

ORF

Location1

Length of amino acid sequence2

Putative product/function3

Alignment

and identity4


This study




pTRACA18




















ORF18-1

4-201

65aa

Unknown function.


NSH





ORF18-2

272-544 c

90aa

Unknown function. Similar to hypothetical protein HMPREF0577_1032 from Mobiluncus mulieris ATCC 35243. NCD.


57% (49/85)





ORF18-3

550-810 c

86aa

Unknown function. Similar to hypothetical protein COLINT_03765 Collinsella intestinalis DSM 13280. NCD.


33% (29/86)





ORF18-4

1165-2571

468aa

Putative replication protein. Similar to EUBIFOR_02271 Eubacterium biforme DSM 3989 and putative replication protein from Staphylococcus sciuri plasmid PSCFS1. Conserved domains of HTH_Hin_like (Helix-turn-helix domain of Hin, cd00569,) DNA-binding proteins detected*.


45% (203/444)





ORF18-5

2748-3083

111aa

Unknown function.

NSH





ORF18-6

3050-3418

122aa

Unknown function.

NSH





ORF18-7

3530-3832 c

100aa

Unknown function.

NSH





ORF18-8

4090-4302 c

70aa

Unknown function.

NSH





ORF18-9

4279-5796

505aa

Putative MobA_MobL type plasmid mobilization protein. Similar to Anaerotruncus colihominis DSM 17241 predicted MobA/MobL protein (ANACOL_03249). Conserved domains detected from MobA_MobL superfamily (pfam03389), and the TraA_Ti, Ti-type conjugative transfer relaxase TraA (TIGR02768)M.


37% (94/251)


pTRACA20




















ORF20-1

102-1223 c

373aa

Putative plasmid mobilization/recombination protein. Similar to a mobilization protein from Geobacillus stearothermophilus. Mob_Pre superfamily (pfam01076) conserved domains detected.


42% (96/2228)





ORF20-2

1633-1749 c

38aa

Unknown function.

NSH





ORF20-3

1712-2005 c

97aa

Unknown function.

NSH





ORF20-4

2034-2216 c

60aa

Unknown function.

NSH





ORF20-5

2275-3657 c

460aa

Putative RepA type replication protein similar to RepA from Campylobacter jejuni pTet37, pCC31, and pTet. DNA_Primase_S (pfam01896), eukaryotic and archaeal DNA primase small subunit superfamily conserved domains detected.



69% (312/448)


pTRACA22




















ORF22-1

180-800 c

206aa

Putative plasmid recombination protein. Similar to RUMHYD_01660 putative plasmid recombination protein from Blautia hydrogenotrophica DSM 10507. NCD.



99% (186/187)





ORF22-2

832 - 1416 c

194aa

Putative plasmid mobilization/recombination protein. Similar to predicted Mob_Pre type protein RUMHYD_01660 from Blautia hydrogenotrophica DSM 10507. Mob_Pre superfamily (pfam01076) conserved domains detected.


98% (170/172)





ORF22-3

1659-2555 c

298aa

Unknown function. Putative toxin protein. Similar to putative entericidin protein RUMHYD_01665 from Blautia hydrogenotrophica DSM 10507. NCD.


100% (248/248)





ORF22-4

2610-3077 c

155aa

Unknown function. Identical to hypothetical protein RUMHYD_01666 from Blautia hydrogenotrophica DSM 10507. NCD.



100% (155/155)





ORF22-5

3074-3322 c

82aa

Unknown function. Putative thiamine-phosphate pyrophosphorylase, similar to RUMHYD_01667 Blautia hydrogenotrophica DSM 10507. NCD.


100% (82/82)




ORF22-6

3341-3613 c

90aa

Putative addiction module toxin component. Similar to RUMHYD_01668 from Blautia hydrogenotrophica DSM 10507. Conserved domains of COG3041, TIGR02385, RelE_StbE, and pfam_05016 plasmid stability protein superfamilies detected.


100% (90/90)





ORF22-7

3606-3887 c

93aa

Putative addiction module anti-toxin component. Similar to RUMHYD_01669 from Blautia hydrogenotrophica DSM 10507. Conserved domains from RelB superfamily detected including RelB_DinJ antitoxin family (TIGR02384), RelB (pfam04221), and DNA damage inducible protein DinJ (COG3077).


100% (93/93)






ORF22-8

4132-5658 c

508aa

Putative plasmid replication protein. Similar to putative ATP-dependent DNA ligase RUMHYD_01670 from Blautia hydrogenotrophica DSM 10507, putative replication protein SmonDRAFT_14340 from Streptobacillus moniliformis DSM 12112and Rep protein from Treponema denticola plasmid pTS1_p1. NCD.


99% (507/508)





ORF22-9

5662-5841 c

59aa

Unknown function. Similar to hypothetical protein RUMHYD_01671 from Blautia hydrogenotrophica DSM 10507. NCD.


99% (56/57)


pTRACA30




















ORF30-1

2-568 c

188aa

Putative ATPase involved in plasmid partitioning. Similar to ParA plasmid segregation protein from Lawsonia intracellularis plasmid 2. Conserved domains detected from ParA chromosome segregation proteins (cd02042)*, and partial domains from ArsA ATPase efflux proteins (cd02035)*, and Soj ATPasesM (COG1192).


58% (101/174)





ORF30-2

565-711 c

48aa

Unknown function.

NSH





ORF30-3

708-941 c

77aa

Unknown function. Similar to COPEUT_02663 hypothetical protein from Coprococcus eutactus ATCC 27759. Conserved domains from COG4443 and DUF2128 superfamily detected, comprising uncharacterized proteins conserved in bacteria.


53% (36/67)





ORF30-4

922-1065 c

47aa

Unknown function.

NSH





ORF30-5

1058-1996 c

312aa

Putative tyrosine site specific integrase. Similar to Streptococcus thermophilus plasmid SMQ308 integrase. Conserved domains detected from XerC and XerD tyrosine site specific recombinase (PRK00236)M and the DNA_BRE_C superfamily of DNA breaking-rejoining enzymes.


53% (169/314)





ORF30-6

2256-2885 c

209aa

Hypothetical protein, similar to hypothetical protein CLOSTMETH_01823 from Clostridium methylpentosum DSM 5476. NCD.


38% (67/172)





ORF30-7

2897-4862 c

654aa

Putative DNA primase/helicase. Similar to putative primase/helicase of Streptococcus thermophilus plasmid SMQ308. Conserved domains from TOPRIM primases (cd01029)*, ABC_ATPase superfamily ATP binding cassette with A and B walker domains, and P-loop nucleoside triphosphate hydrolases (cl09099).


50% (276/543)





ORF30-8

4934-5254 c

106aa

Putative DNA primase/helicase. Similar to primase/helicase predicted to be encoded by Streptococcus thermophilus plasmids pSMQ-316 and pSMQ308. NCD.


42% (39/92)





ORF30-9

5251-5478 c

75aa

Unknown function.

NSH





ORF30-10

5755-5940 c

61aa

Unknown function.

NSH





ORF30-11

6006-6254 c

82aa

Unknown function.

NSH





ORF30-12

6251-7390 c

379aa

Unknown function.


NSH




ORF30-13

7390-9234 c

614aa

Unknown function. Similar to hypothetical protein from Streptococcus themophilus pSMQ308. NCD.


24% (49/202)





ORF30-14

9289-9786 c

165aa

Unknown function. Similar to hypothetical protein WS2053 from Wolinella succinogenes DSM 1740. NCD.


31% (28/90)





30-ORF15

9802-9921 c

39aa

Unknown function.

NSH





30-ORF16

10074-10307 c

77aa

Putative excisionase. Similar to hypothetical protein from Streptococcus thermophilus plasmid pSMQ308, Enterococcus faecium TX1330, and Acholeplasma laidlawii PG-8A putative excisionase. Conserved domains form the HTH_MerR-SF superfamily of excisionase proteins detected (TIGR01764).


51% (27/52)





30-ORF17

10313-10609 c

98aa

Hypothetical protein.

NSH





30-ORF18

10615-10827 c

70aa

Putative ATPase. Similar to ATPase from Lawsonia intracellularis plasmid 2. Conserved domains from Soj ATPases detectedM.



54% (33/61)


Jones & Marchesi (2007) [13]




















pTRACA10





































ORF10-1


1089-2600

503aa

Putative plasmid mobilisation protein. Similar to MobB mobilization protein from Bifidobacterium longum plasmid pKJ36. MobA/MobL conserved domains detected.


43% (50/144)




ORF10-2

2597-3403 c

268aa

Hypothetical protein. Unknown function.

-






















ORF10-3

3331-4044 c

237aa

Putative phophoesterase/phosphohydrolase. COG4168 conserved domains detected. Similar to putative phosphoesterase from Aurantimonas spp.

33% (59/177)






















ORF10-4

4681-6579

632aa

Putative plasmid replication protein. Similar to replication protein form Treponema denticola plasmid pTS1. No conserved domains detected.

35% (145/413)





































pTRACA17




















ORF17-1

36-713 c

225aa

Putative plasmid mobilisation protein. Similar to Mob protein form Bacillus thuringiensis plasmid. Pre_Mob conserved domains detected


46% (81/174)




ORF17-2

1632-2129

165aa

Putative plasmid replication protein. Similar to replication protein form Bacillus subtilis plasmid pIM13. Conserved domains from RepL firmicute plasmid replication proteins detected.

35% (47/131)




















The putative product/function of plasmid encoded ORFs were predicted using BlastP and conserved domain searches. As well as plasmids newly characterised in this study (pTRACA18,20,22,30), plasmids characterised previously by Jones & Marchesi (2007) (pTRACA10 and pTRACA17;) are also represented [13].

1) Provides the location of each predicted ORF in bp, c indicates ORF encoded on complementary strand.

2) Length of the predicted amino acid sequence from annotated ORFs, given as number of amino acid residues. 3) Summary of Blast searches and predicted product/function of ORF. For rpsBlast searches: * denotes a specific hit, and M denotes hits to computationally detected multi-domains. Non-specific hits are reported as hits to the overall protein superfamily. Specific hits provide a very high confidence level in the association of query sequence and detected conserved domain(s) and high confidence level in inferred protein function. Non-specific hits are statistically significant and general protein function can be inferred from the protein superfamily. For non-specific-hits and multidomain hits inferred function is less certain. For rpsBlast conserved domain searches all e-values were 1e-04 or lower. NCD - no conserved domains detected. 4) % identity of plasmid ORF amino acid sequences to homologous sequences in public databases identified in BlastP searches (e values = 1e-02 or lower). NSH - No significant hits generated. For plasmids characterised previously (pTRACA10 and pTRACA17) predicted functions and results of Blast are as described in the original publication [13].


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