YRHP - BACSU - GREMLIN Contacts

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YRHP - Uncharacterized membrane protein YrhP

UniProt:	O05406	Sequences: MHSLLAYIPIAAMMVIIPGADTMLVMKNTLRYGPKAGRYNILGLATGLSFWTVIAILGLSVVIAKSVILFTTIKYLGAAYLIYLGVKSFFAKSMFSLDDMQSQAKNMASSPKRYYKTSFMQGSLSNILNPKTVLVYVTIMPQFINLNGNINQQLIILASILTLLAVLWFLFLVYIIDYAKKWMKNSKFQKVFQKITGIILVGFGIKTGLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	210 (197)
Sequences:	12879 (9042)
Seq/√Len:	644.2

ECOLI - RHTC RHTB LEUE YAHN ARGO EAMB
BACSU - YRHP YISU YCGF
SULSO - Q97ZW7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_T	119_F	5.281	1.00
85_G	201_V	3.577	1.00
86_V	90_F	3.337	1.00
4_L	160_I	3.018	1.00
191_V	194_K	2.898	1.00
71_T	74_K	2.741	1.00
82_I	204_G	2.644	1.00
116_K	120_M	2.471	1.00
190_K	194_K	2.381	1.00
39_Y	115_Y	2.283	1.00
75_Y	79_A	2.233	1.00
50_F	123_S	2.199	1.00
83_Y	87_K	2.194	1.00
89_F	194_K	2.149	1.00
29_T	37_G	2.073	1.00
24_L	40_N	2.047	1.00
89_F	197_G	2.044	1.00
78_A	208_G	1.978	1.00
198_I	202_G	1.915	1.00
10_I	139_I	1.893	1.00
87_K	90_F	1.878	1.00
47_G	127_I	1.871	1.00
85_G	197_G	1.836	1.00
8_I	164_L	1.802	1.00
21_D	44_L	1.770	1.00
22_T	172_L	1.723	1.00
37_G	173_V	1.703	1.00
82_I	201_V	1.697	1.00
78_A	204_G	1.695	1.00
36_A	118_S	1.666	1.00
68_I	71_T	1.665	1.00
180_K	184_K	1.654	1.00
28_N	32_Y	1.636	1.00
92_K	194_K	1.613	1.00
70_F	74_K	1.612	1.00
15_V	164_L	1.566	1.00
16_I	168_W	1.563	1.00
71_T	75_Y	1.551	1.00
120_M	124_L	1.512	1.00
93_S	194_K	1.492	1.00
42_L	119_F	1.484	1.00
8_I	160_I	1.479	1.00
49_S	162_T	1.478	1.00
82_I	86_V	1.439	1.00
61_V	65_K	1.434	1.00
29_T	173_V	1.424	1.00
52_T	158_A	1.406	1.00
119_F	123_S	1.403	1.00
37_G	41_I	1.394	1.00
40_N	122_G	1.394	1.00
28_N	40_N	1.390	1.00
191_V	195_I	1.384	1.00
26_M	176_I	1.381	1.00
41_I	173_V	1.351	1.00
165_A	169_F	1.336	1.00
123_S	127_I	1.317	1.00
68_I	72_T	1.310	1.00
136_Y	161_L	1.304	1.00
114_Y	117_T	1.301	1.00
80_Y	84_L	1.282	1.00
38_R	174_Y	1.274	1.00
72_T	76_L	1.270	1.00
34_P	174_Y	1.267	1.00
188_F	191_V	1.251	1.00
75_Y	78_A	1.244	1.00
7_Y	157_L	1.242	1.00
185_N	188_F	1.230	1.00
178_Y	181_K	1.209	1.00
187_K	191_V	1.187	1.00
75_Y	208_G	1.180	1.00
117_T	120_M	1.174	1.00
21_D	126_N	1.171	1.00
53_V	57_L	1.157	1.00
28_N	121_Q	1.143	1.00
168_W	172_L	1.140	1.00
15_V	165_A	1.138	1.00
24_L	28_N	1.130	1.00
7_Y	11_A	1.128	1.00
24_L	125_S	1.123	1.00
197_G	201_V	1.122	1.00
171_F	175_I	1.119	1.00
85_G	204_G	1.118	1.00
201_V	205_I	1.112	1.00
3_S	6_A	1.111	1.00
45_A	166_V	1.107	1.00
32_Y	36_A	1.102	1.00
35_K	39_Y	1.101	1.00
45_A	162_T	1.098	1.00
21_D	165_A	1.087	1.00
34_P	177_D	1.084	1.00
30_L	176_I	1.054	1.00
21_D	125_S	1.051	1.00
90_F	93_S	1.051	1.00
149_N	152_Q	1.050	1.00
22_T	169_F	1.049	1.00
5_L	9_P	1.043	1.00
150_I	153_Q	1.042	1.00
178_Y	182_W	1.037	1.00
6_A	9_P	1.035	1.00
91_A	193_Q	1.034	1.00
25_V	29_T	1.033	1.00
43_G	119_F	1.031	1.00
38_R	170_L	1.030	1.00
80_Y	83_Y	1.027	1.00
11_A	161_L	1.022	1.00
117_T	121_Q	1.021	1.00
25_V	169_F	1.020	1.00
27_K	31_R	1.016	1.00
151_N	154_L	1.016	1.00
202_G	206_K	1.013	1.00
48_L	126_N	1.011	1.00
31_R	35_K	0.996	1.00
187_K	190_K	0.986	1.00
47_G	123_S	0.979	1.00
21_D	48_L	0.971	1.00
50_F	127_I	0.967	1.00
93_S	96_S	0.960	1.00
48_L	132_T	0.958	1.00
6_A	10_I	0.957	1.00
194_K	198_I	0.942	1.00
113_R	117_T	0.941	1.00
34_P	170_L	0.926	1.00
184_K	188_F	0.925	1.00
51_W	133_V	0.914	1.00
195_I	198_I	0.914	1.00
145_N	153_Q	0.912	1.00
58_G	63_I	0.909	1.00
25_V	173_V	0.907	1.00
4_L	163_L	0.891	1.00
34_P	173_V	0.884	1.00
8_I	12_A	0.877	1.00
51_W	127_I	0.877	1.00
23_M	196_T	0.874	1.00
12_A	164_L	0.873	1.00
46_T	123_S	0.873	1.00
148_G	153_Q	0.871	1.00
124_L	128_L	0.867	1.00
48_L	51_W	0.863	1.00
35_K	115_Y	0.842	1.00
201_V	204_G	0.831	1.00
63_I	66_S	0.823	1.00
112_K	116_K	0.822	1.00
52_T	136_Y	0.819	1.00
10_I	13_M	0.819	1.00
38_R	173_V	0.813	1.00
76_L	79_A	0.813	1.00
87_K	91_A	0.811	1.00
58_G	65_K	0.810	1.00
21_D	169_F	0.807	1.00
43_G	123_S	0.806	1.00
22_T	168_W	0.805	1.00
23_M	27_K	0.804	1.00
189_Q	193_Q	0.804	1.00
138_T	142_Q	0.797	1.00
11_A	15_V	0.792	1.00
79_A	82_I	0.791	1.00
170_L	174_Y	0.787	1.00
41_I	170_L	0.784	1.00
192_F	196_T	0.769	1.00
83_Y	86_V	0.766	1.00
166_V	170_L	0.766	1.00
128_L	137_V	0.766	1.00
36_A	39_Y	0.756	1.00
89_F	201_V	0.750	1.00
45_A	165_A	0.743	1.00
78_A	82_I	0.741	1.00
88_S	197_G	0.738	1.00
90_F	94_M	0.735	1.00
69_L	72_T	0.732	1.00
22_T	26_M	0.732	1.00
9_P	13_M	0.729	1.00
182_W	188_F	0.729	1.00
66_S	69_L	0.727	1.00
51_W	132_T	0.726	1.00
118_S	121_Q	0.721	1.00
47_G	126_N	0.721	1.00
175_I	178_Y	0.716	1.00
60_S	64_A	0.715	1.00
51_W	126_N	0.711	1.00
44_L	48_L	0.710	1.00
57_L	61_V	0.708	1.00
169_F	172_L	0.704	1.00
26_M	172_L	0.701	1.00
13_M	17_I	0.701	1.00
95_F	98_D	0.698	1.00
15_V	169_F	0.697	1.00
51_W	137_V	0.696	1.00
25_V	40_N	0.695	1.00
39_Y	118_S	0.691	1.00
66_S	70_F	0.691	1.00
86_V	201_V	0.690	1.00
15_V	22_T	0.687	1.00
5_L	8_I	0.686	1.00
149_N	153_Q	0.685	1.00
52_T	169_F	0.685	1.00
51_W	55_A	0.678	1.00
4_L	8_I	0.677	1.00
44_L	126_N	0.675	1.00
25_V	44_L	0.675	1.00
182_W	185_N	0.673	1.00
48_L	165_A	0.671	1.00
32_Y	118_S	0.666	1.00
181_K	185_N	0.666	1.00
61_V	64_A	0.662	1.00
28_N	31_R	0.662	1.00
38_R	41_I	0.658	1.00
15_V	168_W	0.657	1.00
46_T	50_F	0.655	1.00
41_I	45_A	0.654	1.00
145_N	148_G	0.653	1.00
195_I	199_I	0.648	1.00
174_Y	178_Y	0.646	1.00
29_T	176_I	0.646	1.00
93_S	190_K	0.645	1.00
10_I	14_M	0.643	1.00
76_L	128_L	0.642	1.00
18_P	131_K	0.641	1.00
67_V	71_T	0.636	1.00
155_I	158_A	0.636	1.00
176_I	179_A	0.635	1.00
79_A	83_Y	0.634	1.00
36_A	115_Y	0.633	1.00
48_L	162_T	0.633	1.00
92_K	95_F	0.633	1.00
72_T	75_Y	0.633	1.00
126_N	132_T	0.630	1.00
22_T	125_S	0.629	1.00
48_L	136_Y	0.627	1.00
20_A	129_N	0.627	1.00
40_N	118_S	0.622	1.00
48_L	161_L	0.621	1.00
136_Y	165_A	0.620	1.00
77_G	134_L	0.617	1.00
17_I	22_T	0.616	1.00
188_F	192_F	0.615	1.00
163_L	167_L	0.615	1.00
148_G	152_Q	0.614	1.00
11_A	160_I	0.613	1.00
156_I	160_I	0.604	1.00
126_N	169_F	0.604	1.00
56_I	158_A	0.598	1.00
162_T	166_V	0.594	1.00
73_I	77_G	0.589	1.00
152_Q	156_I	0.589	1.00
85_G	89_F	0.589	1.00
50_F	53_V	0.589	1.00
55_A	60_S	0.587	1.00
21_D	132_T	0.582	1.00
55_A	133_V	0.581	1.00
182_W	186_S	0.577	1.00
152_Q	155_I	0.577	1.00
55_A	136_Y	0.571	1.00
12_A	16_I	0.567	1.00
167_L	171_F	0.566	1.00
51_W	60_S	0.564	1.00
42_L	45_A	0.563	1.00
15_V	48_L	0.560	1.00
44_L	132_T	0.558	1.00
132_T	169_F	0.557	1.00
27_K	193_Q	0.556	1.00
115_Y	119_F	0.556	1.00
202_G	205_I	0.555	1.00
34_P	178_Y	0.552	1.00
133_V	137_V	0.551	1.00
203_F	206_K	0.549	1.00
180_K	183_M	0.547	1.00
132_T	165_A	0.546	1.00
40_N	125_S	0.544	1.00
53_V	158_A	0.542	1.00
17_I	193_Q	0.537	1.00
116_K	119_F	0.537	1.00
108_A	111_P	0.535	0.99
139_I	161_L	0.534	0.99
175_I	179_A	0.533	0.99
37_G	40_N	0.532	0.99
155_I	159_S	0.531	0.99
34_P	37_G	0.531	0.99
38_R	42_L	0.529	0.99
20_A	88_S	0.528	0.99
52_T	162_T	0.526	0.99
161_L	165_A	0.521	0.99
14_M	135_V	0.521	0.99
135_V	139_I	0.519	0.99
183_M	186_S	0.518	0.99
121_Q	125_S	0.517	0.99
169_F	173_V	0.516	0.99
109_S	112_K	0.513	0.99
66_S	71_T	0.513	0.99
33_G	36_A	0.513	0.99
159_S	163_L	0.506	0.99
36_A	114_Y	0.506	0.99
45_A	169_F	0.506	0.99
7_Y	160_I	0.505	0.99
112_K	115_Y	0.504	0.99
172_L	176_I	0.504	0.99
151_N	155_I	0.500	0.99

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
3o7qA	1	0.9238	50.9	0.914	Contact Map
3wdoA	1	0.8619	39.5	0.92	Contact Map
4m64A	1	0.9524	33.9	0.922	Contact Map
2cfqA	1	0.9048	23.4	0.929	Contact Map
4ikvA	1	0.5095	20	0.931	Contact Map
2gfpA	2	0.9286	19	0.931	Contact Map
1pw4A	1	0.519	18	0.932	Contact Map
4w6vA	1	0.4762	17.9	0.932	Contact Map
3j1zP	8	0.8143	12.6	0.937	Contact Map
4c7rA	3	0.3095	12.4	0.937	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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