I. Summary

SecReT6 ID	62
Strain	Yersinia pseudotuberculosis IP32953
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_006155
Location	752607..789182
Comment
Function	N/A
T6SS Type	Type i; subtype i3
Bioinformatics investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	1	1	1	1	1	1	1	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	1

13

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	YPTB0630	747614..748078 [+], 465	51594981	hypothetical protein
2	YPTB0631 (apaH)	748168..749037 [-], 870	51594982	diadenosine tetraphosphatase
3	YPTB0632 (apaG)	749054..749431 [-], 378	51594983	ApaG protein
4	YPTB0633 (ksgA)	749445..750263 [-], 819	51594984	dimethyladenosine transferase
5	YPTB0634 (pdxA)	750256..751251 [-], 996	51594985	4-hydroxythreonine-4-phosphate dehydrogenase
6	YPTB0635 (surA)	751235..752539 [-], 1305	51594986	peptidyl-prolyl cis-trans isomerase SurA
7	YPTB0636 (imp)	752607..754949 [-], 2343	51594987	organic solvent tolerance protein
8	YPTB0637 (djlA)	755134..755967 [+], 834	51594988	Dna-J like membrane chaperone protein
9	YPTB0638 (rluA)	756284..756904 [-], 621	51594989	23S rRNA pseudouridylate 746 synthase
10	YPTB0639	758127..758870 [-], 744	51594990	hypothetical protein
11	YPTB0640	759200..760213 [+], 1014	51594991	hypothetical protein	TssA
12	YPTB0641	760224..760784 [+], 561	51594992	hypothetical protein	TssB
13	YPTB0642	760784..762295 [+], 1512	51594993	hypothetical protein	TssC
14	YPTB0643	762458..762976 [+], 519	51594994	hypothetical protein	TssD
15	YPTB0644	763050..763493 [+], 444	51594995	hypothetical protein	TssE
16	YPTB0645	763526..765370 [+], 1845	51594996	hypothetical protein	TssF
17	YPTB0646	765363..766346 [+], 984	51594997	hypothetical protein	TssG
18	YPTB0647 (clpB)	766349..768952 [+], 2604	51594998	ATP-dependent protease, Hsp 100, part of novel multi-chaperone system with DnaK, DnaJ, and GrpE	TssH
19	YPTB0648	769056..771404 [+], 2349	51594999	hypothetical protein	TssI
20	YPTB0649	771417..773636 [+], 2220	51595000	hypothetical protein
21	YPTB0650	773662..774765 [+], 1104	51595001	hypothetical protein
22	YPTB0651	774758..775375 [+], 618	51595002	hypothetical protein
23	YPTB0652	775381..775746 [+], 366	51595003	hypothetical protein	PAAR
24	YPTB0653	775739..776230 [+], 492	51595004	lipoprotein	TssJ
25	YPTB0654	776350..777705 [+], 1356	51595005	hypothetical protein	TssK
26	YPTB0655	777702..779312 [+], 1611	51595006	hypothetical protein	TssL
27	YPTB0656	779321..782815 [+], 3495	51595007	hypothetical protein	TssM
28	YPTB0657	782837..783190 [+], 354	51595008	hypothetical protein
29	YPTB0658 (rapA)	783446..786352 [-], 2907	51595009	ATP-dependent helicase HepA
30	YPTB0659 (polB)	786813..789182 [-], 2370	51595010	DNA polymerase II
31	YPTB0660	789378..790145 [+], 768	51595011	DedA family membrane protein
32	YPTB0661 (thiQ)	790214..790924 [-], 711	229310105	thiamine transporter ATP-binding subunit
33	YPTB0662 (thiP)	790911..792518 [-], 1608	51595013	thiamine transporter membrane protein
34	YPTB0663 (tbpA)	792494..793486 [-], 993	51595014	thiamine transporter substrate binding subunit

 Genes in the 5-kb flanking regions if available, or non-core components encoded by the T6SS gene cluster if any. In the 'Note' column,if available, '(e)' denotes effector while '(i)' for immunity protein

Download FASTA format files

Proteins        Genes

V. Investigation of the genomic context of the T6SS gene cluster.

1. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the mobile genetic elements database, ACLAME.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

2. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against the virulence factor database, VFDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

3. BLASTp searches of the proteins encoded by T6SS gene cluster and its flanking regions against against the antibiotic resistance database, ARDB.

Job_id: Replicon RefSeq: T6SS Region Start (bp): T6SS Region End (bp): Upstream Region (kb): Downstream Region (kb):

Homology Effector list

YPK_3563 , YPK_3558

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	YPTB0643	762458..762976 [+], 519	51594994	hypothetical protein	YPK_3563
2	YPTB0648	769056..771404 [+], 2349	51594999	hypothetical protein	YPK_3558

Download FASTA format files

Proteins        Genes

N/A

(1) Boyer F et al. (2009). Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources. BMC Genomics. 10:104. [PudMed:19284603]

This literature contains bioinformatics investigation