PHOT - BACSU - GREMLIN Contacts

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PHOT - Blue-light photoreceptor

UniProt:	O34627	Sequences: MASFQSFGIPGQLEVIKKALDHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLEDSLTEITALSTPIVPIRNGISALPLVGNLTEERFNSIVCTLTNILSTSKDDYLIIDLSGLAQVNEQTADQIFKLSHLLKLTGTELIITGIKPELAMKMNKLDANFSSLKTYSNVKDAVKVLPIM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	261 (243)
Sequences:	45658 (38508)
Seq/√Len:	2470.3

ECOLI - ARCB EVGS RCSD RCSC ATOS NTRB DCUS DPIB PHOR NARX NARQ ZRAS BARA
BACSU - PHOT KINA KINE YYCG PHOR KINC RESE DCTS CITS MALK DEGS RSBP
HALSA - Q9HQ16 O51970 Q9HRE4 BAT Q9HR10 Q9HNM2 Q9HQG5 Q9HRG1 Q9HQB9 Q9HNA6 Q9HP91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_V	124_N	3.634	1.00
164_G	178_L	3.010	1.00
96_K	100_T	2.675	1.00
28_V	121_G	2.507	1.00
91_Q	130_K	2.404	1.00
31_D	36_D	2.339	1.00
45_G	48_Q	2.322	1.00
26_G	49_M	2.296	1.00
130_K	133_E	2.291	1.00
93_Q	103_W	2.263	1.00
20_L	41_Y	2.234	1.00
142_E	145_A	2.198	1.00
105_E	124_N	2.162	1.00
89_T	105_E	2.148	1.00
167_T	171_F	2.135	1.00
26_G	123_Q	2.071	1.00
168_E	171_F	2.065	1.00
140_L	143_I	2.065	1.00
161_P	182_L	2.042	1.00
140_L	144_T	2.040	1.00
95_Y	101_M	2.039	1.00
129_Q	133_E	2.031	1.00
213_H	244_S	2.022	1.00
93_Q	101_M	2.007	1.00
13_L	17_K	1.998	1.00
12_Q	15_V	1.958	1.00
96_K	102_F	1.898	1.00
163_V	174_I	1.885	1.00
42_V	46_F	1.866	1.00
29_I	118_Y	1.853	1.00
31_D	38_P	1.849	1.00
52_Y	97_K	1.845	1.00
105_E	129_Q	1.843	1.00
47_V	54_T	1.806	1.00
218_T	248_Y	1.768	1.00
103_W	130_K	1.762	1.00
161_P	185_S	1.742	1.00
106_L	123_Q	1.723	1.00
17_K	21_D	1.671	1.00
135_L	139_S	1.648	1.00
28_V	46_F	1.646	1.00
92_I	106_L	1.625	1.00
60_K	64_F	1.624	1.00
188_D	192_I	1.621	1.00
239_D	242_F	1.607	1.00
40_V	118_Y	1.605	1.00
23_V	27_V	1.592	1.00
44_Q	48_Q	1.580	1.00
179_T	185_S	1.573	1.00
192_I	195_S	1.546	1.00
137_E	141_T	1.545	1.00
163_V	177_T	1.539	1.00
42_V	47_V	1.512	1.00
31_D	35_E	1.484	1.00
113_I	116_K	1.481	1.00
137_E	140_L	1.474	1.00
131_E	135_L	1.469	1.00
146_L	150_I	1.463	1.00
38_P	61_N	1.460	1.00
136_L	139_S	1.456	1.00
31_D	40_V	1.452	1.00
28_V	39_I	1.451	1.00
136_L	140_L	1.449	1.00
164_G	179_T	1.447	1.00
21_D	44_Q	1.443	1.00
29_I	120_V	1.433	1.00
53_E	56_E	1.430	1.00
238_L	243_S	1.413	1.00
80_T	84_N	1.389	1.00
147_S	150_I	1.355	1.00
29_I	41_Y	1.352	1.00
219_G	223_I	1.350	1.00
133_E	137_E	1.348	1.00
222_L	255_V	1.344	1.00
67_G	70_T	1.344	1.00
244_S	248_Y	1.335	1.00
30_T	121_G	1.332	1.00
221_E	224_I	1.329	1.00
252_K	256_K	1.327	1.00
139_S	142_E	1.315	1.00
141_T	144_T	1.296	1.00
152_P	156_G	1.279	1.00
135_L	138_D	1.270	1.00
14_E	18_K	1.265	1.00
134_K	137_E	1.259	1.00
91_Q	105_E	1.235	1.00
242_F	245_L	1.234	1.00
89_T	107_N	1.228	1.00
16_I	20_L	1.227	1.00
132_Y	135_L	1.221	1.00
128_K	131_E	1.215	1.00
165_N	179_T	1.210	1.00
61_N	64_F	1.209	1.00
189_Y	241_N	1.206	1.00
240_A	244_S	1.194	1.00
75_V	79_R	1.184	1.00
15_V	29_I	1.182	1.00
47_V	53_E	1.163	1.00
41_Y	54_T	1.161	1.00
215_L	219_G	1.158	1.00
139_S	143_I	1.147	1.00
217_L	248_Y	1.134	1.00
185_S	188_D	1.133	1.00
173_S	177_T	1.118	1.00
130_K	134_K	1.114	1.00
160_L	182_L	1.112	1.00
15_V	41_Y	1.108	1.00
134_K	138_D	1.102	1.00
138_D	142_E	1.097	1.00
10_P	13_L	1.096	1.00
44_Q	47_V	1.088	1.00
213_H	240_A	1.086	1.00
218_T	251_V	1.072	1.00
159_A	181_I	1.072	1.00
46_F	50_T	1.071	1.00
212_S	215_L	1.069	1.00
79_R	83_Q	1.063	1.00
108_I	121_G	1.061	1.00
212_S	231_L	1.060	1.00
161_P	179_T	1.059	1.00
176_C	180_N	1.058	1.00
177_T	181_I	1.045	1.00
25_V	122_I	1.044	1.00
167_T	170_R	1.042	1.00
54_T	58_L	1.041	1.00
215_L	231_L	1.041	1.00
127_T	131_E	1.031	1.00
162_L	166_L	1.029	1.00
164_G	175_V	1.026	1.00
104_N	123_Q	1.026	1.00
70_T	93_Q	1.025	1.00
146_L	149_P	1.023	1.00
28_V	123_Q	1.021	1.00
162_L	165_N	1.018	1.00
52_Y	56_E	1.015	1.00
63_R	75_V	1.014	1.00
151_V	155_N	1.007	1.00
214_L	244_S	1.003	1.00
113_I	117_T	1.002	1.00
11_G	15_V	1.000	1.00
56_E	97_K	0.999	1.00
10_P	14_E	0.993	1.00
94_N	104_N	0.989	1.00
42_V	57_I	0.986	1.00
67_G	101_M	0.986	1.00
217_L	244_S	0.985	1.00
161_P	165_N	0.977	1.00
73_A	77_N	0.976	1.00
26_G	46_F	0.957	1.00
177_T	180_N	0.949	1.00
108_I	119_F	0.946	1.00
168_E	172_N	0.943	1.00
247_T	251_V	0.937	1.00
131_E	134_K	0.935	1.00
107_N	124_N	0.926	1.00
159_A	163_V	0.923	1.00
102_F	125_D	0.921	1.00
111_M	118_Y	0.919	1.00
152_P	155_N	0.916	1.00
128_K	132_Y	0.915	1.00
18_K	22_H	0.912	1.00
44_Q	54_T	0.912	1.00
109_D	120_V	0.906	1.00
129_Q	132_Y	0.906	1.00
112_E	117_T	0.903	1.00
73_A	76_D	0.900	1.00
216_K	219_G	0.898	1.00
103_W	127_T	0.889	1.00
138_D	141_T	0.888	1.00
132_Y	136_L	0.886	1.00
35_E	117_T	0.886	1.00
29_I	40_V	0.883	1.00
12_Q	16_I	0.878	1.00
160_L	178_L	0.874	1.00
16_I	19_A	0.873	1.00
161_P	188_D	0.868	1.00
191_I	195_S	0.864	1.00
172_N	176_C	0.856	1.00
154_R	188_D	0.851	1.00
212_S	216_K	0.849	1.00
200_V	203_Q	0.845	1.00
170_R	173_S	0.842	1.00
227_I	255_V	0.841	1.00
164_G	182_L	0.840	1.00
111_M	120_V	0.837	1.00
30_T	78_I	0.818	1.00
63_R	71_D	0.814	1.00
181_I	186_K	0.806	1.00
186_K	244_S	0.805	1.00
13_L	16_I	0.804	1.00
30_T	39_I	0.790	1.00
74_E	77_N	0.789	1.00
19_A	120_V	0.787	1.00
171_F	174_I	0.787	1.00
193_D	242_F	0.786	1.00
76_D	80_T	0.785	1.00
30_T	119_F	0.785	1.00
158_S	162_L	0.782	1.00
113_I	118_Y	0.780	1.00
154_R	192_I	0.778	1.00
77_N	80_T	0.776	1.00
23_V	122_I	0.774	1.00
210_K	240_A	0.773	1.00
209_F	237_K	0.772	1.00
50_T	94_N	0.772	1.00
25_V	45_G	0.771	1.00
169_E	172_N	0.767	1.00
222_L	227_I	0.763	1.00
153_I	187_D	0.754	1.00
221_E	252_K	0.749	1.00
217_L	221_E	0.746	1.00
207_Q	210_K	0.745	1.00
47_V	57_I	0.743	1.00
50_T	123_Q	0.736	1.00
66_Q	71_D	0.734	1.00
81_A	119_F	0.731	1.00
216_K	220_T	0.731	1.00
186_K	191_I	0.728	1.00
60_K	65_L	0.727	1.00
159_A	162_L	0.725	1.00
214_L	251_V	0.722	1.00
30_T	62_C	0.719	1.00
218_T	221_E	0.718	1.00
77_N	90_V	0.718	1.00
185_S	189_Y	0.717	1.00
67_G	93_Q	0.715	1.00
182_L	188_D	0.710	1.00
189_Y	193_D	0.710	1.00
29_I	111_M	0.708	1.00
167_T	172_N	0.704	1.00
191_I	194_L	0.702	1.00
24_R	45_G	0.701	1.00
70_T	74_E	0.698	1.00
220_T	223_I	0.696	1.00
110_P	119_F	0.695	1.00
110_P	117_T	0.695	1.00
72_P	76_D	0.695	1.00
27_V	122_I	0.690	1.00
46_F	57_I	0.686	1.00
68_K	71_D	0.684	1.00
176_C	179_T	0.683	1.00
190_L	195_S	0.681	1.00
94_N	102_F	0.681	1.00
220_T	224_I	0.679	1.00
213_H	217_L	0.676	1.00
166_L	174_I	0.675	1.00
215_L	229_P	0.673	1.00
186_K	193_D	0.665	1.00
225_T	255_V	0.664	1.00
81_A	84_N	0.664	1.00
211_L	214_L	0.661	1.00
158_S	161_P	0.661	1.00
20_L	27_V	0.658	1.00
214_L	218_T	0.658	1.00
188_D	191_I	0.657	1.00
12_Q	17_K	0.655	1.00
243_S	247_T	0.655	1.00
218_T	255_V	0.654	1.00
74_E	92_I	0.654	1.00
155_N	159_A	0.653	1.00
26_G	45_G	0.650	1.00
153_I	156_G	0.648	1.00
45_G	49_M	0.646	1.00
242_F	246_K	0.645	1.00
139_S	144_T	0.644	1.00
171_F	175_V	0.643	1.00
103_W	126_I	0.642	1.00
214_L	248_Y	0.641	1.00
163_V	178_L	0.640	1.00
249_S	252_K	0.638	1.00
31_D	118_Y	0.636	1.00
156_G	160_L	0.633	1.00
222_L	226_G	0.632	1.00
228_K	231_L	0.631	1.00
174_I	177_T	0.630	1.00
241_N	244_S	0.630	1.00
227_I	231_L	0.629	1.00
17_K	41_Y	0.628	1.00
66_Q	70_T	0.622	1.00
140_L	145_A	0.620	1.00
67_G	95_Y	0.618	1.00
189_Y	192_I	0.616	1.00
27_V	120_V	0.612	1.00
211_L	247_T	0.610	1.00
35_E	38_P	0.609	1.00
18_K	120_V	0.608	1.00
103_W	134_K	0.605	1.00
30_T	108_I	0.603	1.00
126_I	130_K	0.595	1.00
92_I	95_Y	0.594	1.00
51_G	98_D	0.593	1.00
173_S	176_C	0.593	1.00
214_L	217_L	0.593	1.00
37_N	79_R	0.592	1.00
106_L	121_G	0.591	1.00
112_E	116_K	0.590	1.00
72_P	75_V	0.590	1.00
153_I	157_I	0.589	1.00
70_T	73_A	0.588	1.00
174_I	178_L	0.586	1.00
37_N	119_F	0.584	1.00
192_I	196_G	0.582	1.00
218_T	222_L	0.581	1.00
141_T	145_A	0.578	1.00
71_D	74_E	0.576	1.00
52_Y	57_I	0.574	1.00
151_V	156_G	0.574	1.00
30_T	37_N	0.573	1.00
245_L	248_Y	0.571	1.00
152_P	249_S	0.570	1.00
136_L	141_T	0.569	1.00
27_V	43_N	0.566	1.00
211_L	215_L	0.563	1.00
248_Y	252_K	0.563	1.00
51_G	96_K	0.560	1.00
135_L	140_L	0.559	1.00
155_N	162_L	0.557	1.00
42_V	54_T	0.555	1.00
18_K	109_D	0.555	1.00
26_G	43_N	0.555	1.00
159_A	177_T	0.552	1.00
222_L	229_P	0.552	1.00
91_Q	129_Q	0.552	1.00
126_I	129_Q	0.552	1.00
22_H	109_D	0.548	1.00
26_G	104_N	0.547	1.00
175_V	178_L	0.547	1.00
148_T	152_P	0.547	1.00
245_L	249_S	0.542	1.00
196_G	242_F	0.541	1.00
81_A	85_K	0.541	1.00
52_Y	65_L	0.540	1.00
223_I	226_G	0.539	1.00
213_H	216_K	0.538	1.00
71_D	75_V	0.538	1.00
24_R	109_D	0.538	1.00
105_E	126_I	0.538	1.00
149_P	194_L	0.536	1.00
15_V	19_A	0.536	1.00
212_S	233_M	0.536	1.00
66_Q	92_I	0.535	1.00
187_D	191_I	0.532	1.00
170_R	174_I	0.530	1.00
152_P	190_L	0.528	1.00
42_V	58_L	0.526	1.00
175_V	179_T	0.524	1.00
78_I	108_I	0.524	1.00
218_T	252_K	0.521	1.00
102_F	127_T	0.520	1.00
215_L	221_E	0.518	1.00
163_V	166_L	0.516	1.00
28_V	106_L	0.515	1.00
43_N	46_F	0.515	1.00
18_K	21_D	0.514	1.00
49_M	104_N	0.513	1.00
186_K	194_L	0.512	1.00
38_P	59_G	0.512	1.00
75_V	78_I	0.511	1.00
152_P	157_I	0.510	1.00
62_C	121_G	0.507	1.00
14_E	17_K	0.505	1.00
205_A	242_F	0.503	1.00
180_N	213_H	0.500	1.00
205_A	238_L	0.500	1.00

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
4gczA	2	0.9885	100	0.282	Contact Map
3a0rA	2	0.9004	100	0.35	Contact Map
4i5sA	2	0.9157	100	0.373	Contact Map
4r3aA	1	0.8774	100	0.417	Contact Map
3rtyA	4	0.7471	99.9	0.542	Contact Map
3mr0A	1	0.4866	99.8	0.583	Contact Map
3gdiA	2	0.6054	99.8	0.59	Contact Map
3ue6A	5	0.5096	99.8	0.595	Contact Map
4lrzE	2	0.4483	99.8	0.6	Contact Map
4gw9A	2	0.4904	99.8	0.606	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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