YQII - BACSU - GREMLIN Contacts

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YQII - Uncharacterized protein YqiI

UniProt:	P54525	Sequences: MRMLWRSLALCGLALTLAPCAQAAEPIEGKTVYIDAGHGGEDSGAVGNGLFEKDINLAVSEHVTDKLKEEGANPVASRSDDHFLTLEERVAKASANQADLFVSIHVNSGVASASGTETYFQSDYEGENSRRLASDIQSQLVSSLQTRDRGVKESDFYVITYSQMPSVLAELGFITNSSDADKLGSEEYQQKAADAIVNGIDSYYDQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	206 (179)
Sequences:	6510 (4799)
Seq/√Len:	358.7

ECOLI - AMIC AMIB AMIA
BACSU - YQII YRVJ CWLC CWLD LYTC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_T	68_K	2.934	1.00
62_H	190_Q	2.928	1.00
64_T	76_A	2.658	1.00
34_I	60_S	2.580	1.00
139_Q	202_S	2.551	1.00
66_K	194_D	2.524	1.00
31_T	73_N	2.523	1.00
107_N	117_E	2.489	1.00
59_V	171_L	2.455	1.00
36_A	60_S	2.416	1.00
136_I	167_V	2.399	1.00
58_A	189_Q	2.284	1.00
75_V	96_N	2.149	1.00
51_F	54_D	2.123	1.00
33_Y	98_A	2.019	1.00
33_Y	77_S	1.937	1.00
70_E	201_D	1.813	1.00
56_N	106_V	1.792	1.00
157_Y	161_Y	1.742	1.00
50_L	184_G	1.726	1.00
48_N	180_A	1.725	1.00
118_T	137_Q	1.722	1.00
88_E	91_A	1.715	1.00
60_S	104_I	1.713	1.00
85_T	88_E	1.685	1.00
139_Q	198_N	1.657	1.00
101_F	158_V	1.623	1.00
58_A	62_H	1.614	1.00
169_A	196_I	1.601	1.00
137_Q	148_D	1.600	1.00
94_S	163_Q	1.582	1.00
53_K	81_D	1.575	1.00
182_K	188_Y	1.548	1.00
70_E	197_V	1.537	1.00
33_Y	92_K	1.534	1.00
109_G	113_A	1.533	1.00
47_G	180_A	1.530	1.00
66_K	197_V	1.520	1.00
66_K	190_Q	1.518	1.00
108_S	175_T	1.499	1.00
55_I	106_V	1.491	1.00
32_V	72_A	1.478	1.00
60_S	76_A	1.465	1.00
62_H	186_E	1.429	1.00
90_V	157_Y	1.418	1.00
50_L	180_A	1.412	1.00
91_A	95_A	1.409	1.00
93_A	164_M	1.399	1.00
100_L	132_L	1.383	1.00
75_V	92_K	1.382	1.00
72_A	201_D	1.343	1.00
130_R	134_S	1.342	1.00
62_H	189_Q	1.326	1.00
87_E	157_Y	1.315	1.00
102_V	200_I	1.314	1.00
62_H	66_K	1.314	1.00
31_T	75_V	1.314	1.00
63_V	196_I	1.306	1.00
59_V	106_V	1.303	1.00
45_A	174_I	1.283	1.00
66_K	70_E	1.278	1.00
135_D	202_S	1.246	1.00
117_E	152_K	1.245	1.00
29_G	72_A	1.231	1.00
100_L	200_I	1.224	1.00
117_E	149_R	1.217	1.00
27_I	72_A	1.217	1.00
139_Q	142_S	1.216	1.00
185_S	188_Y	1.214	1.00
120_F	130_R	1.196	1.00
63_V	197_V	1.187	1.00
135_D	199_G	1.179	1.00
114_S	178_S	1.173	1.00
30_K	99_D	1.168	1.00
63_V	193_A	1.164	1.00
30_K	204_Y	1.159	1.00
106_V	183_L	1.145	1.00
41_E	83_F	1.143	1.00
68_K	74_P	1.143	1.00
43_S	51_F	1.131	1.00
92_K	96_N	1.129	1.00
43_S	46_V	1.126	1.00
104_I	171_L	1.124	1.00
143_S	195_A	1.118	1.00
57_L	61_E	1.106	1.00
29_G	73_N	1.103	1.00
87_E	91_A	1.095	1.00
119_Y	154_S	1.088	1.00
67_L	197_V	1.082	1.00
98_A	164_M	1.078	1.00
66_K	69_E	1.061	1.00
64_T	74_P	1.057	1.00
188_Y	192_A	1.055	1.00
64_T	79_S	1.043	1.00
34_I	63_V	1.038	1.00
36_A	77_S	1.035	1.00
35_D	89_R	1.031	1.00
67_L	72_A	1.029	1.00
114_S	147_R	1.020	1.00
194_D	198_N	1.018	1.00
137_Q	141_V	1.010	1.00
93_A	101_F	1.003	1.00
38_H	105_H	0.998	1.00
180_A	184_G	0.990	1.00
171_L	196_I	0.982	1.00
190_Q	194_D	0.981	1.00
46_V	51_F	0.980	1.00
63_V	104_I	0.979	1.00
171_L	192_A	0.971	1.00
114_S	182_K	0.970	1.00
62_H	65_D	0.965	1.00
33_Y	75_V	0.950	1.00
106_V	174_I	0.944	1.00
50_L	55_I	0.942	1.00
57_L	78_R	0.937	1.00
131_R	135_D	0.933	1.00
119_Y	156_F	0.922	1.00
65_D	68_K	0.918	1.00
172_G	179_D	0.917	1.00
67_L	200_I	0.913	1.00
134_S	138_S	0.911	1.00
94_S	164_M	0.907	1.00
62_H	193_A	0.906	1.00
132_L	167_V	0.896	1.00
155_D	160_T	0.893	1.00
138_S	202_S	0.887	1.00
29_G	71_G	0.882	1.00
94_S	162_S	0.880	1.00
65_D	69_E	0.876	1.00
197_V	201_D	0.873	1.00
128_N	131_R	0.862	1.00
110_V	175_T	0.856	1.00
139_Q	195_A	0.851	1.00
61_E	64_T	0.845	1.00
90_V	161_Y	0.842	1.00
143_S	198_N	0.841	1.00
90_V	94_S	0.839	1.00
156_F	168_L	0.836	1.00
177_S	181_D	0.828	1.00
187_E	191_K	0.824	1.00
38_H	170_E	0.823	1.00
132_L	203_Y	0.821	1.00
33_Y	96_N	0.814	1.00
90_V	162_S	0.809	1.00
116_T	144_L	0.806	1.00
120_F	133_A	0.804	1.00
178_S	182_K	0.801	1.00
149_R	173_F	0.787	1.00
86_L	157_Y	0.781	1.00
111_A	175_T	0.776	1.00
66_K	193_A	0.772	1.00
93_A	98_A	0.754	1.00
156_F	159_I	0.748	1.00
116_T	172_G	0.744	1.00
101_F	166_S	0.739	1.00
39_G	53_K	0.738	1.00
39_G	42_D	0.737	1.00
174_I	180_A	0.731	1.00
34_I	64_T	0.730	1.00
133_A	151_V	0.723	0.99
105_H	170_E	0.718	0.99
27_I	30_K	0.714	0.99
116_T	140_L	0.712	0.99
59_V	104_I	0.711	0.99
182_K	191_K	0.709	0.99
149_R	152_K	0.706	0.99
113_A	175_T	0.705	0.99
118_T	169_A	0.703	0.99
157_Y	160_T	0.703	0.99
140_L	195_A	0.697	0.99
144_L	195_A	0.693	0.99
106_V	171_L	0.692	0.99
31_T	99_D	0.692	0.99
120_F	153_E	0.691	0.99
119_Y	152_K	0.689	0.99
32_V	67_L	0.688	0.99
134_S	151_V	0.686	0.99
42_D	83_F	0.686	0.99
195_A	199_G	0.686	0.99
141_V	148_D	0.676	0.99
32_V	100_L	0.676	0.99
102_V	167_V	0.669	0.99
31_T	96_N	0.667	0.99
116_T	146_T	0.665	0.99
119_Y	168_L	0.660	0.99
109_G	175_T	0.655	0.99
198_N	202_S	0.652	0.99
121_Q	159_I	0.651	0.99
37_G	170_E	0.649	0.99
100_L	204_Y	0.648	0.99
35_D	103_S	0.644	0.99
100_L	203_Y	0.642	0.99
135_D	139_Q	0.642	0.99
144_L	172_G	0.642	0.99
178_S	181_D	0.638	0.99
133_A	167_V	0.636	0.99
40_G	53_K	0.630	0.99
36_A	76_A	0.630	0.99
70_E	198_N	0.630	0.99
59_V	193_A	0.629	0.99
88_E	92_K	0.628	0.99
107_N	173_F	0.628	0.99
67_L	74_P	0.627	0.99
76_A	79_S	0.625	0.99
140_L	192_A	0.623	0.99
40_G	78_R	0.616	0.98
172_G	183_L	0.612	0.98
159_I	166_S	0.610	0.98
139_Q	143_S	0.608	0.98
140_L	169_A	0.606	0.98
176_N	179_D	0.599	0.98
118_T	133_A	0.598	0.98
132_L	136_I	0.596	0.98
84_L	88_E	0.595	0.98
121_Q	160_T	0.593	0.98
37_G	105_H	0.593	0.98
59_V	189_Q	0.592	0.98
61_E	79_S	0.588	0.98
116_T	137_Q	0.587	0.98
114_S	179_D	0.587	0.98
135_D	138_S	0.585	0.98
60_S	63_V	0.585	0.98
50_L	174_I	0.579	0.98
77_S	92_K	0.570	0.97
53_K	78_R	0.568	0.97
123_D	126_G	0.567	0.97
88_E	95_A	0.566	0.97
143_S	191_K	0.565	0.97
120_F	129_S	0.564	0.97
58_A	186_E	0.563	0.97
115_G	179_D	0.563	0.97
130_R	153_E	0.561	0.97
116_T	141_V	0.560	0.97
139_Q	199_G	0.560	0.97
93_A	162_S	0.560	0.97
45_A	108_S	0.557	0.97
135_D	203_Y	0.556	0.97
58_A	61_E	0.555	0.97
146_T	179_D	0.553	0.97
127_E	130_R	0.552	0.97
118_T	167_V	0.552	0.97
78_R	81_D	0.551	0.97
117_E	173_F	0.551	0.97
186_E	189_Q	0.548	0.97
158_V	168_L	0.547	0.97
34_I	74_P	0.547	0.97
35_D	77_S	0.547	0.97
119_Y	173_F	0.545	0.97
198_N	201_D	0.544	0.97
114_S	176_N	0.543	0.96
54_D	58_A	0.542	0.96
40_G	81_D	0.542	0.96
57_L	79_S	0.539	0.96
131_R	134_S	0.537	0.96
68_K	73_N	0.533	0.96
42_D	53_K	0.530	0.96
111_A	177_S	0.529	0.96
136_I	196_I	0.528	0.96
120_F	151_V	0.527	0.96
172_G	188_Y	0.525	0.96
72_A	204_Y	0.523	0.96
47_G	55_I	0.519	0.95
154_S	159_I	0.518	0.95
63_V	200_I	0.511	0.95
118_T	136_I	0.510	0.95
146_T	172_G	0.507	0.95
158_V	166_S	0.501	0.95
113_A	173_F	0.500	0.94

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
3ne8A	2	0.8689	100	0.114	Contact Map
4rn7A	1	0.8641	100	0.115	Contact Map
1jwqA	1	0.8447	100	0.127	Contact Map
4binA	1	0.9612	100	0.131	Contact Map
4lq6A	1	0.8592	100	0.141	Contact Map
1xovA	1	0.8447	100	0.149	Contact Map
3czxA	2	0.8301	100	0.164	Contact Map
3qayA	1	0.8301	100	0.189	Contact Map
3nh4A	2	0.801	88.5	0.907	Contact Map
4axvA	2	0.8592	85.7	0.911	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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