I. Summary

SecReT6 ID	59
Strain	Yersinia pestis biovar Microtus str. 91001
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_005810
Location	4163085..4199623
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	YP_3657 (tbpA)	4158781..4159773 [+], 993	45443389	thiamine transporter substrate binding subunit
2	YP_3658 (thiP)	4159737..4161356 [+], 1620	45443390	thiamine transporter membrane protein
3	YP_3659 (thiQ)	4161343..4162053 [+], 711	229220776	thiamine transporter ATP-binding subunit
4	YP_3660 (dedA5)	4162122..4162889 [-], 768	45443392	DedA family membrane protein
5	YP_3661 (polB)	4163085..4165454 [+], 2370	45443393	DNA polymerase II
6	YP_3662 (hepA)	4165915..4168821 [+], 2907	45443394	ATP-dependent helicase HepA
7	YP_3663	4169077..4169436 [-], 360	45443395	hypothetical protein
8	YP_3664 (icmF3)	4169452..4172946 [-], 3495	45443396	hypothetical protein	TssM
9	YP_3665	4172955..4174592 [-], 1638	45443397	hypothetical protein	TssL
10	YP_3666	4174562..4175935 [-], 1374	45443398	hypothetical protein	TssK
11	YP_3667	4176019..4176510 [-], 492	45443399	lipoprotein	TssJ
12	YP_3668	4176503..4176868 [-], 366	45443400	hypothetical protein	PAAR
13	YP_3669	4176874..4177491 [-], 618	45443401	hypothetical protein
14	YP_3670	4177484..4178587 [-], 1104	45443402	hypothetical protein
15	YP_3671	4178613..4180832 [-], 2220	45443403	hypothetical protein
16	YP_3672 (vgrG5)	4180845..4183193 [-], 2349	45443404	hypothetical protein	TssI
17	YP_3673 (clpB2)	4183297..4185900 [-], 2604	45443405	Clp ATPase	TssH
18	YP_3674	4185903..4186925 [-], 1023	45443406	hypothetical protein	TssG
19	YP_3675	4186879..4188723 [-], 1845	45443407	hypothetical protein	TssF
20	YP_3676	4188756..4189199 [-], 444	45443408	hypothetical protein	TssE
21	YP_3677	4189273..4189791 [-], 519	45443409	hypothetical protein	TssD
22	YP_3678	4189954..4191465 [-], 1512	45443410	hypothetical protein	TssC
23	YP_3679	4191465..4192025 [-], 561	45443411	hypothetical protein	TssB
24	YP_3680	4192036..4193049 [-], 1014	45443412	hypothetical protein	TssA
25	YP_3681	4193379..4194122 [+], 744	45443413	hypothetical protein
26	YP_3682 (rluA3)	4195345..4195965 [+], 621	45443414	ribosomal large subunit pseudouridine synthase A
27	YP_3683 (djlA)	4196263..4197096 [-], 834	45443415	Dna-J like membrane chaperone protein
28	YP_3684 (imp)	4197281..4199623 [+], 2343	45443416	organic solvent tolerance protein
29	YP_3685 (surA)	4199691..4200995 [+], 1305	45443417	peptidyl-prolyl cis-trans isomerase SurA
30	YP_3686 (pdxA)	4200967..4201974 [+], 1008	45443418	4-hydroxythreonine-4-phosphate dehydrogenase
31	YP_3687 (ksgA)	4201967..4202785 [+], 819	45443419	dimethyladenosine transferase
32	YP_3688 (apaG)	4202799..4203176 [+], 378	45443420	ApaG protein
33	YP_3689 (apaH)	4203193..4204062 [+], 870	45443421	diadenosine tetraphosphatase
34	YP_3690	4204152..4204616 [-], 465	45443422	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	YP_3672(vgrG5)	4180845..4183193 [-], 2349	45443404	hypothetical protein	YPK_3558
2	YP_3677	4189273..4189791 [-], 519	45443409	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