I. Summary

SecReT6 ID	130
Strain	Yersinia pestis Nepal516
Replicon	chromosome [Browse all T6SS(s) in this replicon]
Accession	NC_008149
Location	1622569..1653017
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	0	1	1	1	0	1
Component	TssG	TssJ	TssK	TssM
Number	1	1	1	0

III. genome coordinates of the T6SS gene cluster
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Note
1	YPN_1423	1617901..1618920 [-], 1020	108811586	iron(III)-binding periplasmic protein
2	YPN_1424	1619249..1620343 [+], 1095	108811587	murein hydrolase B
3	YPN_1425	1621609..1622211 [+], 603	108811588	LuxR family regulatory protein
4	YPN_1426	1622569..1623051 [-], 483	108811589	hypothetical protein
5	YPN_1427	1623048..1624730 [-], 1683	108811590	hypothetical protein	TagL
6	YPN_1428	1624731..1625483 [-], 753	108811591	hypothetical protein
7	YPN_1429	1625429..1626766 [-], 1338	108811592	hypothetical protein
8	YPN_1430	1626806..1627837 [-], 1032	108811593	fimbrial protein
9	YPN_1431	1627844..1629025 [-], 1182	108811594	hypothetical protein	TssA
10	YPN_1432	1629124..1630149 [-], 1026	108811595	hypothetical protein	TssG
11	YPN_1433	1630149..1632029 [-], 1881	108811596	hypothetical protein	TssF
12	YPN_1434	1632812..1635487 [+], 2676	108811597	Clp ATPase	TssH
13	YPN_1435	1635688..1636233 [+], 546	108811598	frimbrial protein
14	YPN_1436	1636390..1637151 [+], 762	108811599	pili chaperone protein
15	YPN_1437	1637279..1638829 [+], 1551	108811600	hypothetical protein
16	YPN_1438	1638851..1639291 [-], 441	108811601	transposase
17	YPN_1439	1639336..1640058 [-], 723	108811602	transposase
18	YPN_1440	1640083..1641273 [+], 1191	108811603	outer membrane fimbrial usher porin
19	YPN_1441	1641258..1641866 [+], 609	108811604	fimbrial protein
20	YPN_1442	1641971..1642495 [+], 525	108811605	hypothetical protein	TssB
21	YPN_1443	1642519..1644021 [+], 1503	108811606	hypothetical protein	TssC
22	YPN_1444	1644263..1644832 [+], 570	108811607	hypothetical protein	TssD
23	YPN_1445	1645085..1645645 [+], 561	108811608	hypothetical protein	TssJ
24	YPN_1446	1645649..1646998 [+], 1350	108811609	hypothetical protein	TssK
25	YPN_1447	1646995..1647663 [+], 669	108811610	hypothetical protein	TssL
26	YPN_1448	1647677..1648699 [+], 1023	108811611	transposase for insertion sequence IS100
27	YPN_1449	1648699..1649478 [+], 780	108811612	transposase/IS protein
28	YPN_1450	1649606..1649758 [+], 153	108811613	outer membrane protein C2, porin
29	YPN_1451	1650023..1650829 [-], 807	108811614	N-formylglutamate amidohydrolase
30	YPN_1452	1650826..1652046 [-], 1221	108811615	imidazolonepropionase
31	YPN_1453	1652250..1653017 [-], 768	108811616	GntR family transcriptional regulator
32	YPN_1454	1653165..1654535 [+], 1371	108811617	N-formimino-L-glutamate deiminase
33	YPN_1455	1654535..1655107 [+], 573	108811618	hypothetical protein
34	YPN_1456	1655285..1656889 [-], 1605	108811619	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

ROD_27741

Effector identified
#	Locus tag (Gene)	Coordinates [+/-], size (bp)	Protein GI	Product	Homolog
1	YPN_1444	1644263..1644832 [+], 570	108811607	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