I. Summary

SecReT6 ID	90
Strain	Shigella sonnei Ss046
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_007384
Location	250465..285696
Comment
Function	N/A
T6SS Type	Type i; subtype i1
Bioinformatics investigation has been performed on this T6SS.

II. T6SS components

Component	TssH	TssD	TssL	TssI	TssA	TssB	TssC	TssE	TssF
Number	1	2	1	1	2	1	2	0	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	2	3

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	SSON_0221 (dkgB)	245604..246407 [+], 804	74310822	2,5-diketo-D-gluconate reductase B
2	SSON_0222 (yafC)	246404..247318 [-], 915	74310823	LysR family transcriptional regulator
3	SSON_0223 (yafD)	247559..248359 [+], 801	74310824	hypothetical protein
4	SSON_0224 (yafE)	248363..248986 [+], 624	74310825	biotin synthesis protein
5	SSON_0225 (mltD)	249035..250393 [-], 1359	74310826	membrane-bound lytic murein transglycosylase D
6	SSON_0226 (gloB)	250465..251220 [-], 756	74310827	hydroxyacylglutathione hydrolase
7	SSON_0227 (yafS)	251236..251976 [+], 741	74310828	hypothetical protein
8	SSON_0228 (rnhA)	251973..252440 [-], 468	74310829	ribonuclease H
9	SSON_0229 (dnaQ)	252505..253236 [+], 732	74310830	DNA polymerase III subunit epsilon
10	SSON_0231 (yafT)	253775..254560 [+], 786	74310831	aminopeptidase
11	SSON_0232 (yafU)	255186..255524 [-], 339	74310832	hypothetical protein
12	SSON_0233	256165..256647 [-], 483	74310833	Hcp-like protein	TssD
13	SSON_0234	256671..258023 [-], 1353	74310834	hypothetical protein	TssA
14	SSON_0235	258034..258720 [-], 687	74310835	hypothetical protein	TssM
15	SSON_0236	258757..259932 [-], 1176	74310836	hypothetical protein	TssM
16	SSON_0237	259945..260850 [-], 906	161986585	insertion element IS2 transposase InsD
17	SSON_0238	260808..261173 [-], 366	74310838	insertion sequence 2 OrfA protein
18	SSON_0239	261215..262894 [-], 1680	74310839	hypothetical protein	TssM
19	SSON_0240	262913..264325 [-], 1413	74310840	hypothetical protein	TssA
20	SSON_0241	264330..265022 [-], 693	74310841	hypothetical protein
21	SSON_0242	265070..267529 [-], 2460	74310842	ATP-dependent Clp proteinase ATP-binding chain	TssH
22	SSON_0243	267548..267847 [-], 300	74310843	hypothetical protein
23	SSON_0244	267856..268617 [-], 762	74310844	hypothetical protein	TssL
24	SSON_0245	268622..269410 [-], 789	74310845	cytoplasmic protein	TssK
25	SSON_0246	269403..269912 [-], 510	74310846	hypothetical protein	TssK
26	SSON_0247	269954..270478 [-], 525	74310847	lipoprotein	TssJ
27	SSON_0248	270475..271755 [-], 1281	74310848	hypothetical protein	Fha
28	SSON_0249	271780..272862 [-], 1083	74310849	hypothetical protein	TssG
29	SSON_0250	272826..274676 [-], 1851	74310850	hypothetical protein	TssF
30	SSON_0251	275100..275648 [-], 549	74310851	hypothetical protein	TssC
31	SSON_0252	275685..276575 [-], 891	74310852	cytoplasmic protein	TssC
32	SSON_0253	276626..276850 [-], 225	74310853	hypothetical protein
33	SSON_0254	276885..277385 [-], 501	74310854	hypothetical protein	TssB
34	SSON_0255	278082..278600 [+], 519	74310855	hemolysin co-regulated protein	TssD
35	SSON_0256 (vgrG)	278810..280951 [+], 2142	74310856	Rhs element protein	TssI
36	SSON_0257	281027..285235 [+], 4209	74310857	rhs core protein with extension	PAAR
37	SSON_0258	285247..285696 [+], 450	74310858	hypothetical protein
38	SSON_0259 (ybfL)	286237..287094 [+], 858	74310859	receptor protein
39	SSON_0260 (yhhI)	288388..289524 [+], 1137	74310860	receptor
40	SSON_0261 (yafV)	289566..290336 [-], 771	74310861	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

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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

ECA4275

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	SSON_0255	278082..278600 [+], 519	74310855	hemolysin co-regulated protein	ECA4275

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