I. Summary

SecReT6 ID	34
Strain	Yersinia pestis KIM10+
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_004088
Location	4055920..4092476
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

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	y3651 (tbpA)	4051616..4052608 [+], 993	161484745	thiamine transporter substrate binding subunit
2	y3652 (thiP)	4052572..4054191 [+], 1620	22127526	thiamine transporter membrane protein
3	y3653 (thiQ)	4054178..4054888 [+], 711	229013123	thiamine transporter ATP-binding subunit
4	y3654	4054957..4055724 [-], 768	22127528	hypothetical protein
5	y3655 (polB)	4055920..4058289 [+], 2370	22127529	DNA polymerase II
6	y3656 (hepA)	4058750..4061656 [+], 2907	22127530	ATP-dependent helicase HepA
7	y3657	4061912..4062271 [-], 360	22127531	hypothetical protein
8	y3658	4062287..4065781 [-], 3495	22127532	hypothetical protein	TssM
9	y3659	4065790..4067427 [-], 1638	22127533	hypothetical protein	TssL
10	y3660	4067397..4068770 [-], 1374	22127534	hypothetical protein	TssK
11	y3661	4068872..4069246 [-], 375	22127535	lipoprotein	TssJ
12	y3662	4069356..4069721 [-], 366	22127536	hypothetical protein	PAAR
13	y3663	4069727..4070344 [-], 618	22127537	hypothetical protein
14	y3664	4070337..4071440 [-], 1104	22127538	hypothetical protein
15	y3665	4071466..4073685 [-], 2220	22127539	hypothetical protein
16	y3668	4073698..4076046 [-], 2349	22127540	hypothetical protein	TssI
17	y3669	4076150..4078753 [-], 2604	22127543	ATP-dependent protease	TssH
18	y3670	4078756..4079778 [-], 1023	22127544	hypothetical protein	TssG
19	y3671	4079732..4081576 [-], 1845	22127545	hypothetical protein	TssF
20	y3672	4081609..4082052 [-], 444	22127546	hypothetical protein	TssE
21	y3673	4082126..4082644 [-], 519	22127547	hypothetical protein	TssD
22	y3674	4082807..4084318 [-], 1512	22127548	hypothetical protein	TssC
23	y3675	4084318..4084878 [-], 561	22127549	hypothetical protein	TssB
24	y3676	4084889..4085902 [-], 1014	22127550	hypothetical protein	TssA
25	y3677	4086232..4086975 [+], 744	22127551	hypothetical protein
26	y3678	4088198..4088818 [+], 621	22127552	ribosomal large subunit pseudouridine synthase A
27	y3679 (djlA)	4089116..4089949 [-], 834	22127553	Dna-J like membrane chaperone protein
28	y3680 (imp)	4090134..4092476 [+], 2343	161484744	organic solvent tolerance protein
29	y3681 (surA)	4092544..4093848 [+], 1305	22127555	peptidyl-prolyl cis-trans isomerase SurA
30	y3682 (pdxA)	4093820..4094827 [+], 1008	22127556	4-hydroxythreonine-4-phosphate dehydrogenase
31	y3683 (ksgA)	4094820..4095638 [+], 819	22127557	dimethyladenosine transferase
32	y3684 (apaG)	4095652..4096029 [+], 378	22127558	ApaG
33	y3685 (apaH)	4096046..4096915 [+], 870	22127559	diadenosine tetraphosphatase
34	y3686	4097005..4097469 [-], 465	22127560	hypothetical 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

YPK_3558 , YPK_3563

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	y3668	4073698..4076046 [-], 2349	22127540	hypothetical protein	YPK_3558
2	y3673	4082126..4082644 [-], 519	22127547	hypothetical protein	YPK_3563

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