YCAC - ECOLI - GREMLIN Contacts

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YCAC - Uncharacterized protein YcaC

UniProt:	P21367	Sequences: MTKPYVRLDKNDAAVLLVDHQAGLLSLVRDIEPDKFKNNVLALGDLAKYFNLPTILTTSFETGPNGPLVPELKAQFPDTPYIARPGNINAWDNEDFVKAVKATGKKQLIIAGVVTEVCVAFPALSAIEEGFDVFVVTDASGTFNEITRHSAWDRLSQAGAQLMTWFGVACELHRDWRNDIEGLATLFSNHIPDYRNLMTSYDTLTKQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11241
Length:	208 (162)
Sequences:	7961 (5406)
Seq/√Len:	424.7

ECOLI - YCAC RUTB YECD PNCA
BACSU - YWOC YAAI YRDC YDDQ PNCA
HALSA - Q9HMH5 Q9HQL7
SULSO - Q97YW7 Q97VZ5

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
97_V	101_K	3.235	1.00
89_N	125_S	2.917	1.00
107_Q	132_D	2.657	1.00
12_D	106_K	2.622	1.00
110_I	123_A	2.540	1.00
20_H	40_V	2.539	1.00
155_L	160_A	2.503	1.00
47_A	52_L	2.462	1.00
145_E	149_H	2.375	1.00
136_V	168_V	2.341	1.00
97_V	131_F	2.324	1.00
46_L	169_A	2.297	1.00
39_N	165_W	2.217	1.00
43_L	136_V	2.187	1.00
40_V	111_A	2.076	1.00
97_V	129_E	2.046	1.00
164_T	167_G	2.040	1.00
108_L	126_A	1.920	1.00
14_A	105_K	1.914	1.00
58_T	83_A	1.894	1.00
137_T	162_L	1.850	1.00
107_Q	134_F	1.835	1.00
126_A	133_V	1.760	1.00
39_N	42_A	1.738	1.00
46_L	50_F	1.713	1.00
95_D	99_A	1.673	1.00
90_A	122_P	1.654	1.00
48_K	79_T	1.651	1.00
138_D	165_W	1.643	1.00
42_A	166_F	1.638	1.00
22_A	70_P	1.608	1.00
23_G	65_N	1.594	1.00
15_V	47_A	1.567	1.00
139_A	165_W	1.559	1.00
116_E	142_T	1.538	1.00
137_T	164_T	1.523	1.00
115_T	148_R	1.508	1.00
17_L	111_A	1.504	1.00
13_A	107_Q	1.501	1.00
120_A	124_L	1.490	1.00
13_A	109_I	1.457	1.00
80_P	99_A	1.448	1.00
153_D	156_S	1.431	1.00
41_L	45_D	1.428	1.00
82_I	99_A	1.412	1.00
98_K	102_A	1.379	1.00
109_I	168_V	1.366	1.00
99_A	103_T	1.351	1.00
119_V	135_V	1.349	1.00
17_L	44_G	1.335	1.00
55_I	99_A	1.329	1.00
25_L	69_V	1.323	1.00
9_D	12_D	1.321	1.00
115_T	140_S	1.304	1.00
22_A	64_P	1.291	1.00
47_A	109_I	1.289	1.00
41_L	71_E	1.275	1.00
18_V	118_C	1.253	1.00
149_H	153_D	1.249	1.00
53_P	103_T	1.247	1.00
146_I	149_H	1.236	1.00
91_W	126_A	1.214	1.00
58_T	68_L	1.202	1.00
36_F	40_V	1.185	1.00
22_A	67_P	1.179	1.00
123_A	155_L	1.178	1.00
136_V	163_M	1.156	1.00
57_T	90_A	1.155	1.00
127_I	160_A	1.153	1.00
166_F	170_C	1.117	1.00
120_A	151_A	1.110	1.00
43_L	111_A	1.090	1.00
44_G	48_K	1.083	1.00
61_E	83_A	1.074	1.00
17_L	20_H	1.062	1.00
67_P	73_K	1.054	1.00
134_F	163_M	1.044	1.00
60_F	83_A	1.044	1.00
135_V	140_S	1.043	1.00
17_L	40_V	1.041	1.00
46_L	49_Y	1.039	1.00
110_I	122_P	1.018	1.00
16_L	110_I	1.013	1.00
60_F	66_G	1.005	1.00
123_A	135_V	0.998	1.00
101_K	131_F	0.990	1.00
137_T	152_W	0.979	1.00
121_F	124_L	0.969	1.00
39_N	139_A	0.965	1.00
163_M	168_V	0.963	1.00
39_N	138_D	0.950	1.00
110_I	119_V	0.947	1.00
73_K	76_F	0.946	1.00
123_A	160_A	0.944	1.00
14_A	55_I	0.938	1.00
144_N	147_T	0.921	1.00
92_D	129_E	0.916	1.00
125_S	129_E	0.915	1.00
56_L	79_T	0.913	1.00
45_D	76_F	0.903	1.00
64_P	67_P	0.895	1.00
19_D	84_R	0.895	1.00
163_M	167_G	0.887	1.00
15_V	111_A	0.870	1.00
125_S	128_E	0.870	1.00
152_W	162_L	0.865	1.00
42_A	165_W	0.863	1.00
20_H	113_V	0.859	1.00
99_A	102_A	0.848	1.00
43_L	168_V	0.847	1.00
12_D	107_Q	0.845	1.00
115_T	152_W	0.844	1.00
140_S	152_W	0.842	1.00
95_D	98_K	0.841	1.00
45_D	49_Y	0.836	1.00
91_W	97_V	0.833	1.00
140_S	148_R	0.830	1.00
48_K	78_D	0.829	1.00
15_V	43_L	0.826	1.00
109_I	136_V	0.824	1.00
58_T	81_Y	0.816	1.00
38_N	71_E	0.813	1.00
16_L	96_F	0.805	1.00
120_A	154_R	0.797	1.00
146_I	150_S	0.797	1.00
22_A	26_S	0.797	1.00
68_L	81_Y	0.797	1.00
116_E	143_F	0.797	1.00
43_L	165_W	0.796	1.00
70_P	73_K	0.789	1.00
41_L	74_A	0.788	1.00
76_F	79_T	0.788	1.00
56_L	74_A	0.784	1.00
87_N	130_G	0.774	1.00
135_V	155_L	0.774	1.00
148_R	152_W	0.767	1.00
13_A	52_L	0.761	1.00
63_G	66_G	0.758	1.00
37_K	69_V	0.758	1.00
47_A	172_L	0.754	1.00
119_V	140_S	0.750	1.00
98_K	101_K	0.750	1.00
90_A	96_F	0.747	1.00
36_F	141_G	0.741	1.00
116_E	154_R	0.737	1.00
82_I	95_D	0.737	1.00
48_K	76_F	0.729	1.00
56_L	68_L	0.726	1.00
38_N	41_L	0.724	1.00
74_A	79_T	0.722	1.00
156_S	162_L	0.722	1.00
35_K	38_N	0.719	1.00
55_I	103_T	0.715	1.00
44_G	56_L	0.706	1.00
87_N	93_N	0.705	1.00
142_T	148_R	0.701	1.00
60_F	63_G	0.700	1.00
111_A	139_A	0.698	1.00
92_D	125_S	0.696	1.00
137_T	148_R	0.692	1.00
116_E	147_T	0.679	1.00
132_D	161_Q	0.678	1.00
161_Q	171_E	0.677	1.00
123_A	133_V	0.676	1.00
101_K	129_E	0.675	1.00
37_K	41_L	0.675	1.00
36_F	113_V	0.661	0.99
135_V	160_A	0.661	0.99
70_P	74_A	0.659	0.99
136_V	139_A	0.655	0.99
165_W	169_A	0.645	0.99
108_L	133_V	0.642	0.99
43_L	139_A	0.641	0.99
87_N	92_D	0.640	0.99
24_L	118_C	0.639	0.99
135_V	152_W	0.631	0.99
121_F	159_G	0.629	0.99
91_W	129_E	0.623	0.99
24_L	114_V	0.621	0.99
167_G	170_C	0.619	0.99
44_G	54_T	0.617	0.99
25_L	37_K	0.615	0.99
42_A	45_D	0.612	0.99
40_V	139_A	0.612	0.99
147_T	153_D	0.611	0.99
94_E	98_K	0.606	0.99
42_A	46_L	0.606	0.99
14_A	108_L	0.606	0.99
37_K	71_E	0.602	0.99
150_S	153_D	0.599	0.99
93_N	98_K	0.599	0.99
38_N	42_A	0.598	0.99
20_H	72_L	0.594	0.99
114_V	143_F	0.591	0.99
124_L	158_A	0.584	0.99
41_L	73_K	0.583	0.99
13_A	172_L	0.583	0.99
53_P	105_K	0.582	0.99
124_L	159_G	0.581	0.99
22_A	25_L	0.579	0.99
113_V	141_G	0.578	0.99
114_V	142_T	0.575	0.99
82_I	96_F	0.572	0.99
42_A	169_A	0.570	0.98
14_A	103_T	0.566	0.98
88_I	122_P	0.566	0.98
15_V	54_T	0.559	0.98
110_I	133_V	0.555	0.98
134_F	161_Q	0.550	0.98
89_N	128_E	0.546	0.98
152_W	156_S	0.545	0.98
62_T	67_P	0.543	0.98
59_S	114_V	0.540	0.98
64_P	70_P	0.539	0.98
146_I	153_D	0.538	0.98
69_V	72_L	0.536	0.98
52_L	172_L	0.535	0.98
28_V	31_I	0.535	0.98
14_A	100_V	0.528	0.98
106_K	132_D	0.524	0.97
26_S	64_P	0.522	0.97
9_D	107_Q	0.521	0.97
20_H	36_F	0.520	0.97
100_V	131_F	0.517	0.97
22_A	69_V	0.513	0.97
58_T	67_P	0.513	0.97
88_I	127_I	0.512	0.97
150_S	164_T	0.512	0.97
24_L	113_V	0.511	0.97
114_V	117_V	0.508	0.97
25_L	113_V	0.508	0.97
127_I	133_V	0.507	0.97
88_I	117_V	0.506	0.97
18_V	90_A	0.506	0.97
34_D	38_N	0.506	0.97
62_T	65_N	0.505	0.97
147_T	150_S	0.504	0.97
80_P	103_T	0.503	0.97
137_T	156_S	0.503	0.97
43_L	169_A	0.502	0.97
133_V	136_V	0.501	0.97
124_L	128_E	0.500	0.97
44_G	79_T	0.500	0.97

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1yacA	5	0.976	100	0.187	Contact Map
2b34A	8	0.9087	100	0.234	Contact Map
2fq1A	2	0.9904	100	0.255	Contact Map
3tg2A	2	0.8221	100	0.26	Contact Map
3mcwA	2	0.8462	100	0.262	Contact Map
1x9gA	3	0.8942	100	0.263	Contact Map
3kl2A	4	0.8269	100	0.263	Contact Map
3irvA	2	0.8365	100	0.263	Contact Map
1nf9A	2	0.8077	100	0.264	Contact Map
4l07A	4	0.8413	100	0.266	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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