YWJB - BACSU - GREMLIN Contacts

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YWJB - Uncharacterized protein YwjB

UniProt:	P45862	Sequences: MERKTVLYIAVSLDGMIAKEDGSIDWLDEFEGEGDNGYSDFYQTVDTVILGRSTYEHVKVLTPVFPYQDKTCYVFTGSPDSYQDEHVTFINEGARAFTARLKQEKGSNIWIAGGAELVNDFMKEDAIDEFIITVIPVVLGSGIPLFHELTNETKLRLKGTKQFGQAVQLHYVRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	174 (170)
Sequences:	5600 (3823)
Seq/√Len:	293.2

BACSU - YWJB YYAP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_V	169_L	4.128	1.00
52_R	56_E	3.555	1.00
122_M	130_F	3.193	1.00
156_R	172_V	3.165	1.00
7_L	118_V	2.975	1.00
71_T	88_T	2.550	1.00
93_G	96_A	2.547	1.00
158_K	172_V	2.388	1.00
129_E	170_H	2.380	1.00
17_I	115_A	2.375	1.00
75_F	117_L	2.373	1.00
116_E	120_D	2.315	1.00
3_R	106_G	2.314	1.00
47_T	73_Y	2.302	1.00
100_R	104_E	2.302	1.00
95_R	124_E	2.283	1.00
7_L	127_I	2.233	1.00
4_K	129_E	2.208	1.00
97_F	100_R	2.073	1.00
144_P	147_H	2.069	1.00
6_V	108_N	2.056	1.00
46_D	107_S	2.029	1.00
90_I	97_F	2.015	1.00
14_D	140_G	1.978	1.00
4_K	108_N	1.974	1.00
20_E	141_S	1.965	1.00
3_R	105_K	1.951	1.00
129_E	172_V	1.879	1.00
159_G	170_H	1.788	1.00
76_T	89_F	1.763	1.00
79_P	89_F	1.691	1.00
13_L	155_L	1.672	1.00
82_Y	89_F	1.651	1.00
100_R	103_Q	1.550	1.00
73_Y	90_I	1.509	1.00
44_T	108_N	1.481	1.00
19_K	23_S	1.477	1.00
127_I	130_F	1.456	1.00
76_T	79_P	1.419	1.00
131_I	170_H	1.412	1.00
92_E	96_A	1.398	1.00
47_T	71_T	1.386	1.00
18_A	143_I	1.386	1.00
95_R	99_A	1.346	1.00
99_A	103_Q	1.334	1.00
36_N	40_D	1.314	1.00
138_V	155_L	1.296	1.00
80_D	91_N	1.285	1.00
144_P	148_E	1.279	1.00
19_K	152_E	1.258	1.00
54_T	113_G	1.254	1.00
75_F	97_F	1.252	1.00
157_L	169_L	1.250	1.00
23_S	26_W	1.242	1.00
56_E	60_V	1.242	1.00
39_S	43_Q	1.238	1.00
31_E	34_G	1.220	1.00
35_D	39_S	1.218	1.00
5_T	98_T	1.201	1.00
71_T	104_E	1.192	1.00
53_S	116_E	1.189	1.00
47_T	109_I	1.182	1.00
75_F	90_I	1.169	1.00
4_K	172_V	1.165	1.00
9_I	17_I	1.151	1.00
157_L	167_V	1.132	1.00
96_A	100_R	1.126	1.00
16_M	144_P	1.107	1.00
57_H	61_L	1.100	1.00
92_E	100_R	1.096	1.00
131_I	168_Q	1.084	1.00
130_F	155_L	1.082	1.00
11_V	134_V	1.081	1.00
10_A	135_I	1.074	1.00
157_L	160_T	1.070	1.00
119_N	123_K	1.069	1.00
5_T	102_K	1.055	1.00
96_A	99_A	1.041	1.00
12_S	139_L	1.030	1.00
11_V	132_I	1.026	1.00
11_V	17_I	1.007	1.00
98_T	121_F	1.001	1.00
159_G	162_Q	1.001	1.00
40_D	43_Q	0.986	1.00
52_R	77_G	0.972	1.00
133_T	168_Q	0.968	1.00
73_Y	104_E	0.954	1.00
82_Y	87_V	0.950	1.00
122_M	127_I	0.949	1.00
77_G	116_E	0.948	1.00
123_K	149_L	0.938	1.00
163_F	166_A	0.937	1.00
22_G	53_S	0.936	1.00
117_L	120_D	0.927	1.00
6_V	131_I	0.921	1.00
102_K	109_I	0.919	1.00
60_V	63_P	0.912	1.00
50_L	58_V	0.911	1.00
41_F	44_T	0.911	1.00
158_K	170_H	0.902	1.00
94_A	124_E	0.900	1.00
9_I	115_A	0.898	1.00
29_E	154_K	0.897	1.00
26_W	29_E	0.894	1.00
49_I	75_F	0.893	1.00
52_R	79_P	0.877	1.00
19_K	25_D	0.869	1.00
141_S	148_E	0.865	1.00
119_N	147_H	0.861	1.00
49_I	98_T	0.853	1.00
37_G	40_D	0.850	1.00
42_Y	70_K	0.849	1.00
73_Y	88_T	0.847	1.00
120_D	124_E	0.844	1.00
167_V	171_Y	0.843	1.00
37_G	41_F	0.840	1.00
40_D	44_T	0.840	1.00
55_Y	59_K	0.839	1.00
157_L	171_Y	0.835	1.00
41_F	45_V	0.824	1.00
3_R	47_T	0.824	1.00
46_D	108_N	0.824	1.00
123_K	148_E	0.809	1.00
115_A	119_N	0.808	1.00
7_L	114_G	0.806	1.00
41_F	131_I	0.802	1.00
45_V	110_W	0.799	0.99
77_G	120_D	0.796	0.99
5_T	121_F	0.795	0.99
111_I	127_I	0.790	0.99
37_G	168_Q	0.787	0.99
161_K	168_Q	0.787	0.99
50_L	114_G	0.786	0.99
123_K	150_T	0.784	0.99
46_D	105_K	0.781	0.99
125_D	153_T	0.778	0.99
22_G	143_I	0.770	0.99
26_W	30_F	0.764	0.99
31_E	165_Q	0.759	0.99
8_Y	131_I	0.748	0.99
97_F	101_L	0.745	0.99
81_S	89_F	0.739	0.99
123_K	151_N	0.735	0.99
163_F	168_Q	0.732	0.99
135_I	166_A	0.728	0.99
40_D	161_K	0.728	0.99
52_R	78_S	0.723	0.99
76_T	80_D	0.723	0.99
118_V	127_I	0.721	0.99
132_I	145_L	0.715	0.99
13_L	138_V	0.710	0.99
27_L	30_F	0.709	0.99
48_V	70_K	0.704	0.99
31_E	164_G	0.697	0.99
3_R	46_D	0.695	0.99
5_T	111_I	0.688	0.98
154_K	157_L	0.687	0.98
73_Y	97_F	0.681	0.98
9_I	118_V	0.677	0.98
129_E	158_K	0.672	0.98
8_Y	41_F	0.672	0.98
33_E	36_N	0.670	0.98
49_I	121_F	0.670	0.98
24_I	57_H	0.668	0.98
19_K	22_G	0.666	0.98
8_Y	38_Y	0.665	0.98
92_E	97_F	0.664	0.98
160_T	167_V	0.662	0.98
7_L	111_I	0.660	0.98
18_A	23_S	0.651	0.98
75_F	94_A	0.651	0.98
102_K	106_G	0.648	0.98
46_D	106_G	0.643	0.98
162_Q	167_V	0.642	0.98
53_S	56_E	0.640	0.98
83_Q	87_V	0.637	0.97
58_V	112_A	0.636	0.97
46_D	109_I	0.636	0.97
93_G	97_F	0.634	0.97
84_D	114_G	0.632	0.97
77_G	92_E	0.630	0.97
57_H	60_V	0.626	0.97
84_D	87_V	0.625	0.97
90_I	93_G	0.625	0.97
25_D	29_E	0.624	0.97
120_D	123_K	0.620	0.97
79_P	82_Y	0.617	0.97
9_I	145_L	0.614	0.97
9_I	114_G	0.609	0.97
8_Y	110_W	0.608	0.97
59_K	63_P	0.607	0.97
47_T	106_G	0.601	0.96
149_L	152_E	0.599	0.96
38_Y	48_V	0.598	0.96
91_N	97_F	0.598	0.96
155_L	171_Y	0.592	0.96
10_A	38_Y	0.591	0.96
40_D	159_G	0.591	0.96
149_L	153_T	0.590	0.96
37_G	133_T	0.588	0.96
78_S	82_Y	0.587	0.96
115_A	143_I	0.587	0.96
73_Y	106_G	0.583	0.96
121_F	126_A	0.583	0.96
141_S	150_T	0.583	0.96
56_E	79_P	0.577	0.96
33_E	164_G	0.576	0.95
48_V	67_Y	0.571	0.95
94_A	120_D	0.570	0.95
38_Y	41_F	0.570	0.95
116_E	119_N	0.568	0.95
31_E	39_S	0.560	0.95
8_Y	133_T	0.556	0.95
151_N	154_K	0.553	0.94
65_F	72_C	0.552	0.94
37_G	131_I	0.552	0.94
88_T	97_F	0.551	0.94
8_Y	112_A	0.551	0.94
18_A	22_G	0.550	0.94
83_Q	89_F	0.550	0.94
59_K	62_T	0.548	0.94
27_L	135_I	0.546	0.94
42_Y	45_V	0.542	0.94
78_S	81_S	0.541	0.94
56_E	59_K	0.540	0.94
101_L	105_K	0.537	0.93
51_G	54_T	0.537	0.93
138_V	153_T	0.535	0.93
72_C	86_H	0.533	0.93
12_S	27_L	0.532	0.93
58_V	63_P	0.532	0.93
58_V	67_Y	0.531	0.93
41_F	110_W	0.530	0.93
59_K	84_D	0.529	0.93
93_G	99_A	0.527	0.93
99_A	124_E	0.525	0.93
90_I	94_A	0.522	0.93
18_A	115_A	0.522	0.93
72_C	84_D	0.520	0.92
16_M	143_I	0.516	0.92
138_V	146_F	0.513	0.92
10_A	27_L	0.511	0.92
33_E	163_F	0.510	0.92
134_V	167_V	0.509	0.92
90_I	100_R	0.507	0.91
17_I	143_I	0.507	0.91
119_N	122_M	0.506	0.91
3_R	102_K	0.505	0.91
34_G	37_G	0.504	0.91
101_L	109_I	0.503	0.91
125_D	155_L	0.503	0.91
10_A	114_G	0.503	0.91
12_S	138_V	0.503	0.91
38_Y	42_Y	0.502	0.91
48_V	112_A	0.500	0.91

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
3jtwA	2	0.9885	100	0.306	Contact Map
2gd9A	2	0.9655	100	0.334	Contact Map
2xw7A	2	0.9713	100	0.349	Contact Map
3kgyA	2	0.9828	100	0.356	Contact Map
3ky8A	2	0.9885	100	0.356	Contact Map
3qg2A	2	0.954	100	0.358	Contact Map
3zpgA	2	0.977	100	0.379	Contact Map
3ix9A	2	0.908	100	0.381	Contact Map
3hj3A	2	0.9425	100	0.385	Contact Map
3nrrA	2	0.931	100	0.385	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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