I. Summary

SecReT6 ID	64
Strain	Yersinia pseudotuberculosis IP32953
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_006155
Location	3128417..3167344
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	YPTB2645 (ccmE)	3125049..3125543 [-], 495	51596964	cytochrome c-type biogenesis protein CcmE
2	YPTB2646 (ccmD)	3125540..3125890 [-], 351	51596965	heme exporter protein D
3	YPTB2647 (ccmC)	3125887..3126624 [-], 738	51596966	ABC type heme exporter, permease subunit ccmC
4	YPTB2648 (ccmB)	3126687..3127346 [-], 660	51596967	heme ABC transporter permease subunit CcmB
5	YPTB2649 (ccmA)	3127316..3127972 [-], 657	51596968	cytochrome c biogenesis protein CcmA
6	YPTB2650	3128417..3128884 [-], 468	51596969	hypothetical protein
7	YPTB2651 (lemA)	3129501..3130043 [+], 543	51596970	hypothetical protein
8	YPTB2652	3129988..3132087 [+], 2100	51596971	hypothetical protein
9	YPTB2653	3132463..3132804 [+], 342	51596972	hypothetical protein
10	YPTB2654	3132879..3133244 [-], 366	51596973	hypothetical protein
11	YPTB2655	3133251..3133730 [-], 480	51596974	hypothetical protein	TssE
12	YPTB2656	3133795..3134601 [-], 807	51596975	hypothetical protein	TagJ
13	YPTB2657	3134621..3135469 [-], 849	51596976	hypothetical protein
14	YPTB2658	3135469..3135729 [-], 261	51596977	hypothetical protein	PAAR
15	YPTB2659	3135809..3138721 [-], 2913	51596978	hypothetical protein	TssI
16	YPTB2660	3139015..3142842 [-], 3828	51596979	hypothetical protein	TssM
17	YPTB2661	3142851..3144227 [-], 1377	51596980	OmpA/MotB family protein	TssL
18	YPTB2662	3144224..3145573 [-], 1350	51596981	hypothetical protein	TssK
19	YPTB2663	3145577..3146137 [-], 561	51596982	hypothetical protein	TssJ
20	YPTB2664	3146390..3146959 [-], 570	51596983	hypothetical protein	TssD
21	YPTB2665	3147208..3148710 [-], 1503	51596984	hypothetical protein	TssC
22	YPTB2666	3148734..3149258 [-], 525	51596985	hypothetical protein	TssB
23	YPTB2667	3149364..3149972 [-], 609	51596986	fimbrial protein
24	YPTB2668	3149957..3152668 [-], 2712	51596987	outer membrane fimbrial usher porin
25	YPTB2669	3152757..3153518 [-], 762	51596988	pili chaperone protein
26	YPTB2670	3153675..3154220 [-], 546	51596989	frimbrial protein
27	YPTB2671 (clpB5)	3154431..3157088 [-], 2658	51596990	Clp ATPase	TssH
28	YPTB2672	3157872..3159752 [+], 1881	51596991	hypothetical protein	TssF
29	YPTB2673	3159752..3160777 [+], 1026	51596992	hypothetical protein	TssG
30	YPTB2674	3160876..3162069 [+], 1194	51596993	hypothetical protein	TssA
31	YPTB2675	3162076..3163107 [+], 1032	51596994	fimbrial protein
32	YPTB2676	3163147..3164484 [+], 1338	51596995	hypothetical protein
33	YPTB2677	3164481..3165182 [+], 702	51596996	hypothetical protein
34	YPTB2678	3165183..3166865 [+], 1683	51596997	OMPA family outer membrane porin	TagL
35	YPTB2679	3166862..3167344 [+], 483	51596998	hypothetical protein
36	YPTB2680	3167717..3168319 [-], 603	51596999	LuxR family transcriptional regulator
37	YPTB2681 (mltB)	3169588..3170682 [-], 1095	51597000	murein hydrolase B
38	YPTB2682 (sfuA)	3171011..3172030 [+], 1020	51597001	iron(III)-ABC transporter substrate-binding protein

 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

ROD_27741

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	YPTB2664	3146390..3146959 [-], 570	51596983	hypothetical protein	ROD_27741

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