ICEberg

ICE
Gene list
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References

I. Information of ICE

ICEberg ID	39
Name	ICESpuPO1
ICEO ID	ICEO_0000007
Organism	Shewanella putrefaciens W3-18-1
Size (bp)	111191
GC content [Genome] (%)	48.28[44.63]
Insertion site	prfC (Sputw3181_1184)
Function	Zn/Co/Cd efflux system; restriction modification system
Species that ICE can be transferred to	Shewanella putrefaciens
Nucleotide Sequence	CP000503 (complete ICE sequence in this genome)
Replicon	chromosome (4708380 bp, BioProject:13902) [NC_008750]
Genome coordinates	1224492..1335682
Putative oriT region	-
Putative relaxase	coordinates: 1248113..1250263; Locus tag: Sputw3181_1098; Family: MOB_H

II. ICE interaction with IME/CIME/

The interaction information of ICESpuPO1 is not available.

The graph information of ICESpuPO1 components from CP000503

Complete gene list of ICESpuPO1 from CP000503
#	Gene	Coordinates [+/-], size (bp)	Product (GenBank annotation)	*Reannotation
1	Sputw3181_1073	1219611..1219880 [+], 270	SSU ribosomal protein S15P
2	Sputw3181_1074	1219957..1222005 [-], 2049	diguanylate cyclase/phosphodiesterase
3	Sputw3181_1075	1222201..1224300 [+], 2100	Polyribonucleotide nucleotidyltransferase
4	Sputw3181_1076	1224492..1225397 [+], 906	TPR repeat-containing protein
5	Sputw3181_1077	1226232..1227473 [-], 1242	phage integrase family protein
6	Sputw3181_1078	1227475..1227744 [-], 270	hypothetical protein
7	Sputw3181_1079	1227747..1228721 [-], 975	hypothetical protein
8	Sputw3181_1080	1228826..1229104 [-], 279	hypothetical protein
9	Sputw3181_1081	1229186..1229629 [+], 444	hypothetical protein
10	Sputw3181_1082	1229640..1230908 [-], 1269	DNA-directed DNA polymerase
11	Sputw3181_1083	1230916..1231365 [-], 450	UmuD protein. Serine peptidase. MEROPS family S24
12	Sputw3181_1084	1232005..1232910 [+], 906	Exonuclease, RNase T and DNA polymerase III
13	Sputw3181_1085	1232998..1233297 [+], 300	hypothetical protein
14	Sputw3181_1086	1233619..1234542 [+], 924	conserved hypothetical protein
15	Sputw3181_1087	1234656..1237079 [+], 2424	N-6 DNA methylase
16	Sputw3181_1088	1237086..1238375 [+], 1290	putative type I site-specific restriction-modification system, S subunit
17	Sputw3181_1089	1238385..1239548 [+], 1164	hypothetical protein
18	Sputw3181_1090	1239563..1242580 [+], 3018	type III restriction enzyme, res subunit
19	Sputw3181_1091	1242603..1243688 [+], 1086	ATP-binding region, ATPase-like protein
20	Sputw3181_1092	1243711..1244262 [+], 552	conserved hypothetical protein
21	Sputw3181_1093	1244391..1244564 [+], 174	conserved hypothetical protein
22	Sputw3181_1094	1244566..1244934 [+], 369	membrane-bound metal-dependent hydrolase
23	Sputw3181_1095	1244944..1246098 [+], 1155	conserved hypothetical protein
24	Sputw3181_1096	1246091..1247281 [+], 1191	conserved hypothetical protein
25	Sputw3181_1097	1247282..1247995 [+], 714	conserved hypothetical protein
26	Sputw3181_1098	1248113..1250263 [+], 2151	metal dependent phosphohydrolase	Relaxase, MOB_H Family
27	Sputw3181_1099	1250312..1252135 [+], 1824	conserved hypothetical protein	TraD_F, T4SS component
28	Sputw3181_1100	1252145..1252705 [+], 561	hypothetical protein
29	Sputw3181_1101	1252692..1253327 [+], 636	hypothetical protein
30	Sputw3181_1102	1253354..1253941 [-], 588	hypothetical protein
31	Sputw3181_1103	1253955..1254194 [-], 240	hypothetical protein
32	Sputw3181_1104	1254230..1254511 [+], 282	hypothetical protein	TraL_F, T4SS component
33	Sputw3181_1105	1254508..1255134 [+], 627	hypothetical protein	TraE_F, T4SS component
34	Sputw3181_1106	1255115..1256014 [+], 900	hypothetical protein	TraK_F, T4SS component
35	Sputw3181_1107	1256017..1257306 [+], 1290	TraB pilus assembly family protein	TraB_F, T4SS component
36	Sputw3181_1108	1257303..1257953 [+], 651	hypothetical protein	TraV_F, T4SS component
37	Sputw3181_1109	1257950..1258339 [+], 390	hypothetical protein	TraA_F, T4SS component
38	Sputw3181_1110	1258748..1261243 [+], 2496	heavy metal translocating P-type ATPase
39	Sputw3181_1111	1261269..1261733 [+], 465	putative transcriptional regulator, MerR family
40	Sputw3181_1113	1262840..1263595 [-], 756	IstB domain protein ATP-binding protein
41	Sputw3181_1114	1263607..1265148 [-], 1542	Integrase, catalytic region
42	Sputw3181_1115	1265250..1265513 [+], 264	hypothetical protein
43	Sputw3181_1116	1265548..1267053 [+], 1506	Integrase, catalytic region
44	Sputw3181_1117	1267046..1267801 [+], 756	IstB domain protein ATP-binding protein	TrbB, T4SS component
45	Sputw3181_1118	1267824..1268675 [-], 852	Integrase, catalytic region	Integrase
46	Sputw3181_1119	1268690..1268974 [-], 285	transposase IS3/IS911 family protein
47	Sputw3181_1120	1269595..1270020 [+], 426	transcriptional regulator, MerR family
48	Sputw3181_1122	1270783..1271136 [+], 354	transcriptional regulator, ArsR family
49	Sputw3181_1124	1272501..1273529 [+], 1029	cation diffusion facilitator family transporter
50	Sputw3181_1125	1273574..1273852 [+], 279	regulatory protein, ArsR
51	Sputw3181_1126	1274449..1277103 [+], 2655	heavy metal translocating P-type ATPase
52	Sputw3181_1127	1277356..1278207 [-], 852	Integrase, catalytic region	Integrase
53	Sputw3181_1128	1278222..1278506 [-], 285	transposase IS3/IS911 family protein
54	Sputw3181_1129	1278712..1280022 [+], 1311	efflux transporter, RND family, MFP subunit
55	Sputw3181_1130	1280019..1283210 [+], 3192	transporter, hydrophobe/amphiphile efflux-1 (HAE1) family
56	Sputw3181_1131	1283212..1284705 [+], 1494	RND efflux system, outer membrane lipoprotein, NodT family
57	Sputw3181_1135	1285681..1285902 [+], 222	hydrophobe/amphiphile efflux-1 HAE1
58	Sputw3181_1136	1286021..1286191 [+], 171	putative Copper chaperone
59	Sputw3181_1138	1287161..1287415 [+], 255	hypothetical protein
60	Sputw3181_1139	1287626..1288318 [+], 693	hypothetical protein	TrbB_I, T4SS component
61	Sputw3181_1140	1288318..1290717 [+], 2400	sex pilus assembly protein	TraC_F, T4SS component
62	Sputw3181_1141	1290710..1291057 [+], 348	hypothetical protein
63	Sputw3181_1142	1291041..1291553 [+], 513	hypothetical protein	TraF, T4SS component
64	Sputw3181_1143	1291564..1292688 [+], 1125	hypothetical protein	TraW_F, T4SS component
65	Sputw3181_1144	1292672..1293700 [+], 1029	TraU family protein	TraU_F, T4SS component
66	Sputw3181_1145	1293703..1297395 [+], 3693	Mating pair stabilisation TraN	TraN_F, T4SS component
67	Sputw3181_1146	1297637..1297885 [+], 249	hypothetical protein
68	Sputw3181_1147	1297895..1300168 [+], 2274	hypothetical protein
69	Sputw3181_1148	1300188..1300706 [+], 519	hypothetical protein
70	Sputw3181_1149	1300765..1301439 [-], 675	Deoxyribonuclease I
71	Sputw3181_1150	1301548..1302150 [-], 603	hypothetical protein
72	Sputw3181_1151	1302518..1302844 [+], 327	hypothetical protein
73	Sputw3181_1152	1302860..1303279 [+], 420	single-strand binding protein
74	Sputw3181_1153	1303359..1304177 [+], 819	phage recombination protein Bet
75	Sputw3181_1154	1304464..1305480 [+], 1017	predicted endonuclease-like phage-related protein
76	Sputw3181_1155	1305573..1306649 [+], 1077	ATPase associated with various cellular activities, AAA_5
77	Sputw3181_1156	1306649..1307416 [+], 768	hypothetical protein
78	Sputw3181_1157	1307516..1308469 [+], 954	conserved hypothetical protein
79	Sputw3181_1158	1308531..1308971 [+], 441	hypothetical protein
80	Sputw3181_1159	1309041..1310696 [+], 1656	von Willebrand factor, type A
81	Sputw3181_1160	1310780..1311277 [+], 498	DNA repair protein RadC
82	Sputw3181_1161	1311277..1311618 [+], 342	hypothetical protein
83	Sputw3181_1162	1311710..1312783 [+], 1074	Phage P4 alpha, zinc-binding domain protein
84	Sputw3181_1163	1312873..1313580 [+], 708	hypothetical protein
85	Sputw3181_1164	1313953..1314363 [+], 411	conserved hypothetical protein
86	Sputw3181_1165	1314429..1317551 [-], 3123	heavy metal efflux pump, CzcA family
87	Sputw3181_1166	1317561..1318580 [-], 1020	biotin/lipoyl attachment domain-containing protein
88	Sputw3181_1167	1318659..1319903 [-], 1245	outer membrane efflux protein
89	Sputw3181_1168	1319955..1320320 [-], 366	hypothetical protein
90	Sputw3181_1169	1320363..1321268 [-], 906	cation efflux system permease, putative
91	Sputw3181_1170	1321291..1321755 [+], 465	putative transcriptional regulator, MerR family
92	Sputw3181_1171	1321777..1322694 [+], 918	cation diffusion facilitator family transporter
93	Sputw3181_1172	1322696..1323022 [+], 327	protein of unknown function UPF0060
94	Sputw3181_1173	1323458..1324402 [+], 945	sex pilus assembly protein	TraF_F, T4SS component
95	Sputw3181_1174	1324405..1325793 [+], 1389	TraH family protein	TraH_F, T4SS component
96	Sputw3181_1175	1325797..1329366 [+], 3570	TraG domain protein	TraG_F, T4SS component
97	Sputw3181_1176	1329399..1329830 [-], 432	hypothetical protein
98	Sputw3181_1177	1329888..1330421 [-], 534	hypothetical protein
99	Sputw3181_1178	1330418..1330717 [-], 300	hypothetical protein
100	Sputw3181_1179	1330714..1331262 [-], 549	Lytic transglycosylase, catalytic	Orf169_F, T4SS component
101	Sputw3181_1180	1331249..1331911 [-], 663	conserved hypothetical protein
102	Sputw3181_1181	1331898..1332767 [-], 870	hypothetical protein
103	Sputw3181_1182	1332823..1333074 [-], 252	hypothetical protein
104	Sputw3181_1183	1333192..1333839 [+], 648	phage lambda repressor protein. Serine peptidase. MEROPS family S24
105	Sputw3181_1184	1334096..1335682 [+], 1587	bacterial peptide chain release factor 3 (bRF-3)
106	Sputw3181_1185	1335765..1335950 [+], 186	conserved hypothetical protein
107	Sputw3181_1186	1335961..1336725 [+], 765	TatD-related deoxyribonuclease
108	Sputw3181_1187	1336902..1338161 [+], 1260	nucleoside transporter
109	Sputw3181_1188	1338521..1339378 [+], 858	nucleoside-specific channel-forming protein, Tsx
110	Sputw3181_1189	1339785..1340555 [+], 771	deoxyribose-phosphate aldolase

Flanking regions

Element	No. of sequences	Download
Nucleotide sequences	1	Fasta
Proteins	102	Fasta

(1) Wozniak RA; Fouts DE; Spagnoletti M; Colombo MM; Ceccarelli D; Garriss G; Dery C; Burrus V; Waldor MK (2009). Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 5(12):e1000786. [PubMed:20041216]

(2) Ceccarelli D; Daccord A; Rene M; Burrus V (2008). Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 190(15):5328-38. [PubMed:18539733]

(3) Marrero J; Waldor MK (2007). The SXT/R391 family of integrative conjugative elements is composed of two exclusion groups. J Bacteriol. 189(8):3302-5. [PubMed:17307849]

(4) Pembroke JT; Piterina AV (2006). A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements. FEMS Microbiol Lett. 264(1):80-8. [PubMed:17020552]

experimental literature

in silico analysis literature