YTQA - BACSU - GREMLIN Contacts

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YTQA - Putative protein YtqA

UniProt:	O35008	Sequences: MMQNNPFPYSNTEKRYHTLNYHLREHFGHKVFKVALDGGFDCPNRDGTVAHGGCTFCSAAGSGDFAGNRTDDLITQFHDIKNRMHEKWKDGKYIAYFQAFTNTHAPVEVLREKFESVLALDDVVGISIATRPDCLPDDVVDYLAELNERTYLWVELGLQTVHERTALLINRAHDFNCYVEGVNKLRKHGIRVCSHIINGLPLEDRDMMMETAKAVADLDVQGIKIHLLHLLKGTPMVKQYEKGKLEFLSQDDYVQLVCDQLEIIPPEMIVHRITGDGPIELMIGPMWSVNKWEVLGAINKELENRGSYQGKFFQRLEEESAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	322 (263)
Sequences:	3710 (2670)
Seq/√Len:	164.6

ECOLI - YHCC HEMN YGGW
BACSU - YTQA YQER HEMZ
HALSA - Q9HPR3 Q9HNU5
SULSO - Q97ZU7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
174_D	177_C	4.378	1.00
141_D	188_H	3.576	1.00
213_K	263_I	3.408	1.00
186_R	221_Q	3.288	1.00
137_D	184_K	3.198	1.00
111_R	145_E	2.954	1.00
196_I	211_T	2.770	1.00
55_T	239_Q	2.738	1.00
163_E	175_F	2.730	1.00
249_S	252_D	2.680	1.00
205_R	259_D	2.672	1.00
180_E	184_K	2.640	1.00
154_V	185_L	2.624	1.00
162_H	207_M	2.601	1.00
163_E	176_N	2.490	1.00
111_R	115_E	2.415	1.00
162_H	210_E	2.410	1.00
210_E	213_K	2.391	1.00
140_V	188_H	2.327	1.00
137_D	187_K	2.252	1.00
237_V	283_I	2.225	1.00
179_V	214_A	2.165	1.00
176_N	180_E	2.072	1.00
205_R	255_Q	2.057	1.00
186_R	219_D	2.052	1.00
183_N	187_K	2.046	1.00
178_Y	194_S	2.025	1.00
290_N	293_E	2.012	1.00
209_M	259_D	2.004	1.00
136_P	139_V	1.995	1.00
163_E	167_L	1.956	1.00
170_N	235_P	1.941	1.00
214_A	217_D	1.923	1.00
164_R	207_M	1.909	1.00
74_I	116_S	1.901	1.00
259_D	262_E	1.892	1.00
239_Q	244_K	1.873	1.00
158_L	178_Y	1.848	1.00
164_R	167_L	1.837	1.00
168_L	239_Q	1.835	1.00
196_I	215_V	1.807	1.00
142_Y	146_L	1.788	1.00
238_K	242_K	1.769	1.00
160_T	165_T	1.753	1.00
156_L	185_L	1.731	1.00
39_G	43_P	1.721	1.00
74_I	78_H	1.700	1.00
78_H	116_S	1.692	1.00
55_T	236_M	1.661	1.00
204_D	207_M	1.633	1.00
212_A	260_Q	1.613	1.00
182_V	192_V	1.578	1.00
185_L	192_V	1.567	1.00
144_A	188_H	1.562	1.00
237_V	241_E	1.554	1.00
216_A	265_P	1.546	1.00
194_S	220_V	1.541	1.00
175_F	214_A	1.522	1.00
111_R	142_Y	1.515	1.00
198_N	260_Q	1.509	1.00
107_V	142_Y	1.504	1.00
197_I	228_L	1.485	1.00
109_V	113_K	1.478	1.00
127_S	153_W	1.473	1.00
177_C	180_E	1.455	1.00
169_I	200_L	1.449	1.00
175_F	179_V	1.437	1.00
235_P	238_K	1.430	1.00
72_D	75_T	1.428	1.00
115_E	149_R	1.417	1.00
179_V	183_N	1.402	1.00
158_L	194_S	1.397	1.00
71_D	75_T	1.381	1.00
184_K	187_K	1.373	1.00
138_D	141_D	1.326	1.00
213_K	217_D	1.326	1.00
205_R	209_M	1.326	1.00
109_V	112_E	1.323	1.00
116_S	119_A	1.305	1.00
141_D	145_E	1.296	1.00
209_M	213_K	1.295	1.00
29_H	92_K	1.293	1.00
75_T	79_D	1.287	1.00
168_L	202_L	1.287	1.00
185_L	190_I	1.283	1.00
292_W	296_G	1.273	1.00
41_D	44_N	1.253	1.00
258_C	262_E	1.240	1.00
94_I	98_Q	1.228	1.00
191_R	221_Q	1.227	1.00
107_V	111_R	1.225	1.00
84_M	88_W	1.225	1.00
198_N	208_M	1.219	1.00
161_V	214_A	1.206	1.00
278_P	281_L	1.203	1.00
216_A	264_I	1.199	1.00
248_L	256_L	1.191	1.00
115_E	146_L	1.178	1.00
216_A	263_I	1.158	1.00
180_E	183_N	1.153	1.00
154_V	190_I	1.151	1.00
223_I	264_I	1.147	1.00
73_L	80_I	1.135	1.00
209_M	263_I	1.134	1.00
93_Y	98_Q	1.129	1.00
78_H	82_N	1.114	1.00
210_E	214_A	1.105	1.00
111_R	146_L	1.099	1.00
82_N	120_L	1.090	1.00
161_V	211_T	1.087	1.00
243_G	246_E	1.076	0.99
184_K	188_H	1.075	0.99
259_D	263_I	1.070	0.99
38_G	43_P	1.069	0.99
238_K	241_E	1.061	0.99
222_G	271_H	1.059	0.99
93_Y	124_V	1.056	0.99
182_V	218_L	1.048	0.99
29_H	91_G	1.046	0.99
37_D	43_P	1.046	0.99
78_H	120_L	1.043	0.99
182_V	194_S	1.039	0.99
79_D	83_R	1.034	0.99
208_M	260_Q	1.032	0.99
132_P	181_G	1.028	0.99
93_Y	96_Y	1.021	0.99
230_L	237_V	1.019	0.99
140_V	185_L	1.014	0.99
193_C	222_G	0.993	0.99
232_K	241_E	0.989	0.99
105_A	109_V	0.988	0.99
55_T	169_I	0.982	0.99
141_D	144_A	0.967	0.99
77_F	120_L	0.958	0.99
114_F	146_L	0.958	0.99
293_E	297_A	0.946	0.99
225_I	260_Q	0.943	0.99
160_T	166_A	0.939	0.99
107_V	139_V	0.939	0.99
112_E	116_S	0.937	0.99
178_Y	220_V	0.935	0.99
115_E	119_A	0.934	0.99
212_A	216_A	0.926	0.98
195_H	226_H	0.925	0.98
71_D	79_D	0.924	0.98
211_T	215_V	0.916	0.98
73_L	76_Q	0.915	0.98
181_G	184_K	0.911	0.98
196_I	212_A	0.911	0.98
169_I	201_P	0.906	0.98
164_R	202_L	0.905	0.98
230_L	236_M	0.905	0.98
137_D	141_D	0.903	0.98
140_V	184_K	0.896	0.98
92_K	124_V	0.890	0.98
183_N	217_D	0.889	0.98
235_P	239_Q	0.889	0.98
272_R	275_G	0.883	0.98
39_G	44_N	0.883	0.98
72_D	76_Q	0.880	0.98
78_H	112_E	0.878	0.98
273_I	276_D	0.874	0.98
37_D	69_R	0.874	0.98
81_K	122_D	0.872	0.98
194_S	215_V	0.870	0.98
36_L	43_P	0.869	0.98
132_P	171_R	0.867	0.98
81_K	120_L	0.858	0.98
167_L	174_D	0.852	0.97
97_F	117_V	0.849	0.97
135_L	181_G	0.847	0.97
80_I	84_M	0.844	0.97
73_L	77_F	0.837	0.97
254_V	297_A	0.836	0.97
79_D	82_N	0.835	0.97
94_I	99_A	0.830	0.97
254_V	258_C	0.827	0.97
161_V	215_V	0.824	0.97
104_H	134_C	0.821	0.97
205_R	252_D	0.818	0.97
112_E	115_E	0.817	0.97
75_T	112_E	0.811	0.97
53_G	170_N	0.810	0.96
99_A	102_N	0.806	0.96
236_M	245_L	0.806	0.96
206_D	210_E	0.805	0.96
142_Y	145_E	0.799	0.96
254_V	257_V	0.798	0.96
44_N	49_V	0.797	0.96
140_V	144_A	0.796	0.96
38_G	41_D	0.792	0.96
114_F	118_L	0.787	0.96
110_L	142_Y	0.787	0.96
71_D	109_V	0.783	0.96
215_V	220_V	0.781	0.96
158_L	161_V	0.779	0.96
75_T	78_H	0.773	0.95
216_A	268_M	0.771	0.95
36_L	41_D	0.770	0.95
82_N	116_S	0.770	0.95
39_G	42_C	0.769	0.95
49_V	177_C	0.769	0.95
163_E	174_D	0.768	0.95
91_G	122_D	0.767	0.95
246_E	252_D	0.766	0.95
135_L	184_K	0.762	0.95
262_E	266_P	0.761	0.95
137_D	188_H	0.757	0.95
95_A	98_Q	0.756	0.95
153_W	193_C	0.754	0.95
55_T	168_L	0.753	0.95
208_M	256_L	0.749	0.95
227_L	288_S	0.748	0.95
166_A	173_H	0.748	0.95
288_S	291_K	0.739	0.94
287_W	291_K	0.738	0.94
40_F	43_P	0.735	0.94
291_K	295_L	0.734	0.94
272_R	276_D	0.732	0.94
231_L	234_T	0.729	0.94
255_Q	258_C	0.727	0.94
261_L	270_V	0.727	0.94
265_P	268_M	0.724	0.94
164_R	168_L	0.723	0.93
195_H	224_K	0.722	0.93
94_I	127_S	0.721	0.93
176_N	179_V	0.721	0.93
178_Y	182_V	0.716	0.93
128_I	148_E	0.713	0.93
114_F	126_I	0.711	0.93
173_H	177_C	0.711	0.93
282_M	285_P	0.710	0.93
198_N	225_I	0.710	0.93
83_R	87_K	0.708	0.93
110_L	117_V	0.708	0.93
136_P	184_K	0.704	0.93
84_M	87_K	0.703	0.93
118_L	146_L	0.703	0.93
81_K	117_V	0.700	0.92
130_T	154_V	0.699	0.92
207_M	210_E	0.697	0.92
257_V	261_L	0.697	0.92
228_L	236_M	0.696	0.92
96_Y	99_A	0.694	0.92
165_T	200_L	0.694	0.92
159_Q	171_R	0.694	0.92
82_N	86_E	0.691	0.92
209_M	256_L	0.690	0.92
153_W	222_G	0.690	0.92
155_E	195_H	0.688	0.92
285_P	290_N	0.687	0.92
37_D	41_D	0.686	0.92
186_R	220_V	0.685	0.92
131_R	134_C	0.679	0.91
247_F	284_G	0.679	0.91
179_V	218_L	0.677	0.91
32_F	88_W	0.677	0.91
182_V	220_V	0.676	0.91
219_D	267_E	0.671	0.91
138_D	142_Y	0.671	0.91
141_D	187_K	0.670	0.91
162_H	165_T	0.667	0.90
101_T	134_C	0.664	0.90
42_C	105_A	0.664	0.90
77_F	81_K	0.663	0.90
286_M	289_V	0.657	0.90
213_K	216_A	0.653	0.89
269_I	272_R	0.652	0.89
153_W	191_R	0.651	0.89
49_V	52_G	0.649	0.89
31_V	92_K	0.647	0.89
255_Q	259_D	0.646	0.89
240_Y	283_I	0.646	0.89
106_P	109_V	0.645	0.89
58_S	231_L	0.645	0.89
279_I	289_V	0.643	0.89
85_H	91_G	0.640	0.89
98_Q	226_H	0.638	0.88
203_E	252_D	0.638	0.88
156_L	178_Y	0.636	0.88
36_L	40_F	0.634	0.88
173_H	178_Y	0.633	0.88
36_L	95_A	0.632	0.88
216_A	267_E	0.632	0.88
285_P	294_V	0.631	0.88
71_D	112_E	0.630	0.88
103_T	143_L	0.625	0.87
165_T	169_I	0.624	0.87
208_M	212_A	0.622	0.87
194_S	223_I	0.621	0.87
77_F	80_I	0.620	0.87
276_D	279_I	0.620	0.87
92_K	98_Q	0.620	0.87
236_M	239_Q	0.617	0.87
82_N	85_H	0.610	0.86
97_F	110_L	0.606	0.86
107_V	146_L	0.604	0.86
163_E	166_A	0.604	0.86
55_T	170_N	0.602	0.85
98_Q	195_H	0.601	0.85
224_K	231_L	0.601	0.85
41_D	49_V	0.599	0.85
37_D	40_F	0.599	0.85
285_P	288_S	0.598	0.85
63_G	66_A	0.597	0.85
54_C	57_C	0.595	0.85
186_R	192_V	0.594	0.85
132_P	173_H	0.593	0.85
76_Q	80_I	0.592	0.84
53_G	61_G	0.588	0.84
125_G	153_W	0.584	0.84
131_R	224_K	0.583	0.84
212_A	263_I	0.581	0.83
145_E	183_N	0.579	0.83
144_A	190_I	0.579	0.83
105_A	110_L	0.578	0.83
289_V	293_E	0.578	0.83
205_R	256_L	0.578	0.83
110_L	114_F	0.576	0.83
272_R	277_G	0.576	0.83
74_I	85_H	0.576	0.83
212_A	215_V	0.573	0.82
182_V	186_R	0.572	0.82
78_H	81_K	0.571	0.82
74_I	119_A	0.571	0.82
232_K	237_V	0.571	0.82
198_N	257_V	0.568	0.82
74_I	113_K	0.567	0.82
50_A	170_N	0.567	0.82
40_F	105_A	0.566	0.82
236_M	240_Y	0.566	0.82
49_V	172_A	0.565	0.82
29_H	33_K	0.564	0.81
135_L	139_V	0.564	0.81
192_V	221_Q	0.564	0.81
110_L	143_L	0.562	0.81
50_A	172_A	0.562	0.81
128_I	234_T	0.562	0.81
81_K	121_D	0.561	0.81
248_L	253_Y	0.560	0.81
55_T	235_P	0.558	0.81
40_F	109_V	0.557	0.81
206_D	209_M	0.556	0.81
101_T	201_P	0.556	0.81
118_L	126_I	0.555	0.80
246_E	249_S	0.555	0.80
80_I	83_R	0.554	0.80
192_V	220_V	0.554	0.80
169_I	236_M	0.552	0.80
220_V	268_M	0.552	0.80
115_E	142_Y	0.551	0.80
193_C	271_H	0.551	0.80
125_G	193_C	0.545	0.79
179_V	217_D	0.544	0.79
239_Q	242_K	0.541	0.79
116_S	120_L	0.540	0.79
135_L	140_V	0.539	0.78
156_L	192_V	0.539	0.78
72_D	80_I	0.538	0.78
108_E	112_E	0.538	0.78
65_F	68_N	0.537	0.78
56_F	271_H	0.533	0.78
41_D	104_H	0.530	0.77
95_A	123_V	0.528	0.77
95_A	99_A	0.527	0.77
224_K	275_G	0.526	0.77
56_F	194_S	0.526	0.77
231_L	277_G	0.525	0.77
85_H	89_K	0.524	0.77
283_I	294_V	0.520	0.76
123_V	126_I	0.520	0.76
59_A	231_L	0.518	0.76
133_D	173_H	0.517	0.76
31_V	36_L	0.516	0.75
155_E	224_K	0.516	0.75
230_L	239_Q	0.514	0.75
37_D	99_A	0.514	0.75
133_D	172_A	0.513	0.75
225_I	257_V	0.512	0.75
52_G	235_P	0.512	0.75
105_A	113_K	0.512	0.75
212_A	264_I	0.511	0.75
281_L	285_P	0.510	0.75
52_G	170_N	0.509	0.74
165_T	207_M	0.507	0.74
271_H	275_G	0.507	0.74
94_I	125_G	0.506	0.74
34_V	80_I	0.506	0.74
115_E	118_L	0.506	0.74
72_D	116_S	0.503	0.74
275_G	278_P	0.503	0.74
30_K	33_K	0.502	0.73
79_D	112_E	0.501	0.73
215_V	223_I	0.500	0.73

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
1oltA	1	0.9441	100	0.481	Contact Map
4jc0A	1	0.9379	100	0.604	Contact Map
2qgqA	1	0.7578	100	0.61	Contact Map
1r30A	2	0.8758	100	0.662	Contact Map
4u0oB	1	0.7795	99.9	0.666	Contact Map
3iixA	1	0.9068	99.9	0.675	Contact Map
4wcxA	1	0.913	99.9	0.679	Contact Map
3t7vA	1	0.8882	99.9	0.682	Contact Map
4r33A	2	0.913	99.9	0.688	Contact Map
4rtbA	2	0.9068	99.9	0.693	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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