YQCA - ECOLI - GREMLIN Contacts

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YQCA - Uncharacterized protein YqcA

UniProt:	P65367	Sequences: MAEIGIFVGTMYGNSLLVAEEAEAILTAQGHKATVFEDPELSDWLPYQDKYVLVVTSTTGQGDLPDSIVPLFQGIKDSLGFQPNLRYGVIALGDSSYVNFCNGGKQFDALLQEQSAQRVGEMLLIDASENPEPETESNPWVEQWGTLLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13170
Length:	149 (140)
Sequences:	4022 (2703)
Seq/√Len:	228.4

ECOLI - YQCA CYSJ MIOC FLAV FLAW
BACSU - CYSJ FLAV FLAW CYPD CYPE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_D	118_R	3.951	1.00
91_A	104_G	3.774	1.00
105_K	124_L	3.408	1.00
11_M	66_D	2.930	1.00
86_R	117_Q	2.665	1.00
112_Q	118_R	2.623	1.00
102_N	106_Q	2.501	1.00
110_L	113_E	2.449	1.00
110_L	114_Q	2.270	1.00
87_Y	108_D	2.187	1.00
90_I	125_I	2.139	1.00
4_I	26_L	2.024	1.00
64_L	103_G	1.976	1.00
23_E	35_V	1.966	1.00
87_Y	112_Q	1.958	1.00
41_L	49_D	1.946	1.00
26_L	145_G	1.932	1.00
7_F	38_D	1.799	1.00
9_G	68_I	1.799	1.00
51_Y	86_R	1.771	1.00
89_V	104_G	1.762	1.00
6_I	23_E	1.745	1.00
54_V	107_F	1.714	1.00
120_G	143_Q	1.673	1.00
3_E	32_K	1.590	1.00
15_S	55_V	1.579	1.00
108_D	112_Q	1.578	1.00
38_D	71_L	1.568	1.00
16_L	20_E	1.562	1.00
56_T	107_F	1.540	1.00
54_V	111_L	1.526	1.00
87_Y	118_R	1.525	1.00
53_L	144_W	1.478	1.00
10_T	67_S	1.475	1.00
87_Y	116_A	1.435	1.00
108_D	122_M	1.431	1.00
18_V	137_S	1.413	1.00
7_F	41_L	1.411	1.00
105_K	122_M	1.398	1.00
23_E	33_A	1.393	1.00
72_F	107_F	1.373	1.00
9_G	56_T	1.368	1.00
60_G	63_D	1.351	1.00
23_E	27_T	1.326	1.00
15_S	92_L	1.319	1.00
111_L	116_A	1.316	1.00
18_V	92_L	1.313	1.00
72_F	106_Q	1.280	1.00
76_K	110_L	1.275	1.00
90_I	137_S	1.266	1.00
52_V	85_L	1.263	1.00
101_C	124_L	1.229	1.00
71_L	107_F	1.220	1.00
53_L	88_G	1.195	1.00
88_G	120_G	1.157	1.00
91_A	101_C	1.116	1.00
118_R	121_E	1.106	1.00
22_A	55_V	1.105	1.00
25_I	141_V	1.104	1.00
57_S	65_P	1.096	1.00
109_A	113_E	1.080	1.00
90_I	123_L	1.068	1.00
7_F	52_V	1.059	1.00
56_T	103_G	1.053	1.00
5_G	36_F	1.050	1.00
38_D	68_I	1.042	1.00
22_A	141_V	1.027	1.00
37_E	67_S	1.026	1.00
64_L	68_I	1.025	1.00
64_L	72_F	1.015	1.00
125_I	137_S	1.002	1.00
9_G	67_S	0.999	1.00
120_G	144_W	0.986	1.00
20_E	35_V	0.983	1.00
88_G	144_W	0.975	1.00
56_T	65_P	0.974	1.00
72_F	110_L	0.971	1.00
58_T	101_C	0.969	1.00
56_T	68_I	0.969	1.00
72_F	103_G	0.965	1.00
84_N	117_Q	0.958	1.00
36_F	40_E	0.949	1.00
102_N	105_K	0.933	1.00
142_E	146_T	0.910	0.99
26_L	33_A	0.899	0.99
82_Q	116_A	0.894	0.99
8_V	16_L	0.875	0.99
118_R	122_M	0.870	0.99
49_D	52_V	0.867	0.99
3_E	50_K	0.859	0.99
74_G	78_S	0.840	0.99
18_V	55_V	0.838	0.99
101_C	104_G	0.830	0.99
25_I	29_Q	0.829	0.99
10_T	15_S	0.819	0.99
42_S	45_L	0.812	0.99
88_G	119_V	0.811	0.99
37_E	40_E	0.810	0.99
31_H	51_Y	0.810	0.99
139_P	143_Q	0.798	0.99
39_P	67_S	0.795	0.99
66_D	69_V	0.794	0.99
121_E	143_Q	0.794	0.99
125_I	129_E	0.789	0.99
12_Y	61_Q	0.788	0.99
21_E	138_N	0.783	0.98
139_P	142_E	0.783	0.98
61_Q	99_N	0.773	0.98
89_V	108_D	0.770	0.98
5_G	34_T	0.770	0.98
109_A	112_Q	0.768	0.98
22_A	53_L	0.763	0.98
9_G	38_D	0.763	0.98
72_F	76_K	0.762	0.98
80_G	83_P	0.755	0.98
17_L	21_E	0.753	0.98
4_I	51_Y	0.748	0.98
5_G	50_K	0.742	0.98
104_G	122_M	0.740	0.98
120_G	123_L	0.740	0.98
4_I	31_H	0.735	0.98
41_L	74_G	0.730	0.98
24_A	27_T	0.725	0.98
25_I	142_E	0.721	0.97
95_S	128_S	0.711	0.97
137_S	141_V	0.708	0.97
92_L	127_A	0.703	0.97
55_V	90_I	0.701	0.97
34_T	49_D	0.695	0.97
76_K	106_Q	0.694	0.97
58_T	104_G	0.688	0.97
3_E	34_T	0.686	0.97
80_G	114_Q	0.678	0.96
123_L	136_E	0.678	0.96
12_Y	127_A	0.672	0.96
54_V	65_P	0.670	0.96
11_M	15_S	0.670	0.96
56_T	104_G	0.669	0.96
7_F	54_V	0.663	0.96
85_L	111_L	0.660	0.96
6_I	26_L	0.657	0.96
25_I	145_G	0.655	0.95
62_G	65_P	0.651	0.95
24_A	28_A	0.650	0.95
10_T	17_L	0.647	0.95
99_N	102_N	0.645	0.95
136_E	139_P	0.642	0.95
5_G	49_D	0.642	0.95
6_I	19_A	0.635	0.95
3_E	49_D	0.634	0.95
16_L	67_S	0.632	0.95
143_Q	146_T	0.630	0.94
27_T	33_A	0.624	0.94
15_S	57_S	0.624	0.94
8_V	35_V	0.611	0.93
81_F	114_Q	0.608	0.93
73_Q	77_D	0.604	0.93
59_T	127_A	0.603	0.93
9_G	65_P	0.598	0.93
4_I	53_L	0.596	0.93
75_I	114_Q	0.596	0.93
44_W	79_L	0.595	0.93
45_L	48_Q	0.589	0.92
6_I	34_T	0.586	0.92
87_Y	111_L	0.585	0.92
138_N	142_E	0.581	0.92
7_F	36_F	0.580	0.92
135_T	139_P	0.578	0.91
135_T	138_N	0.572	0.91
82_Q	85_L	0.570	0.91
29_Q	120_G	0.564	0.90
61_Q	98_V	0.562	0.90
104_G	124_L	0.560	0.90
17_L	20_E	0.560	0.90
36_F	41_L	0.559	0.90
94_D	97_Y	0.558	0.90
64_L	106_Q	0.558	0.90
6_I	35_V	0.557	0.90
93_G	97_Y	0.553	0.90
39_P	70_P	0.553	0.90
90_I	144_W	0.551	0.89
105_K	109_A	0.550	0.89
64_L	107_F	0.546	0.89
43_D	74_G	0.545	0.89
100_F	122_M	0.545	0.89
24_A	29_Q	0.545	0.89
58_T	65_P	0.544	0.89
8_V	37_E	0.544	0.89
8_V	55_V	0.533	0.88
79_L	114_Q	0.530	0.88
15_S	134_E	0.529	0.88
63_D	106_Q	0.529	0.88
97_Y	101_C	0.524	0.87
9_G	103_G	0.523	0.87
94_D	128_S	0.522	0.87
129_E	135_T	0.517	0.86
16_L	66_D	0.516	0.86
25_I	138_N	0.515	0.86
14_N	17_L	0.512	0.86
61_Q	69_V	0.511	0.86
95_S	126_D	0.510	0.86
19_A	35_V	0.510	0.86
48_Q	84_N	0.508	0.85
12_Y	59_T	0.507	0.85
6_I	53_L	0.505	0.85
63_D	134_E	0.502	0.85
91_A	122_M	0.501	0.85
78_S	114_Q	0.501	0.85
18_V	65_P	0.500	0.84
53_L	119_V	0.500	0.84

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
1tllA	2	0.9732	100	0.154	Contact Map
2bpoA	1	0.9933	100	0.213	Contact Map
3qe2A	1	0.9866	100	0.215	Contact Map
3hr4A	2	0.9799	100	0.286	Contact Map
1bvyF	1	0.9732	100	0.362	Contact Map
4h2dA	1	0.9933	100	0.384	Contact Map
1ykgA	1	0.953	100	0.392	Contact Map
4oxxA	1	0.9866	100	0.397	Contact Map
2m6rA	1	0.9866	100	0.401	Contact Map
2hnaA	1	0.9866	100	0.406	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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