YACD - BACSU - GREMLIN Contacts

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YACD - Putative peptidyl-prolyl cis-trans isomerase YacD

UniProt:	P37566	Sequences: MKSRTIWTIILGALLVCCIAVAYTLTKSQAGASSSGESIATIGGKSVTREEWLKEMEDQYGKSTLEDMINVRVVEQLAKKNKLKISKSEVDREFLLIKAVNNSFYEDEHTTEKEWKDQIRYNILLEDLLTRDIDISNKELESFYNKNKELYQFDDSYRIRHIVVKDEEEAREVLKELKGGSSFEAVAAERSTDRYTSPYGGDLGFVTEASDNIPSAYIEEAKTLKEDEWSQEPIKVSNGYAIIQLKEKLKARTFSFDEVKDQIRRQIAMDQLGDKATVKTLWKEADVSWFYGEKSTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	297 (260)
Sequences:	5841 (4958)
Seq/√Len:	307.5

ECOLI - PPID SURA
BACSU - YACD PRSA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
167_E	171_R	4.033	1.00
174_L	178_K	3.617	1.00
176_E	181_S	3.248	1.00
160_R	246_K	3.092	1.00
209_A	218_I	2.973	1.00
166_D	169_E	2.866	1.00
139_E	271_Q	2.866	1.00
158_R	202_D	2.627	1.00
226_E	247_E	2.599	1.00
77_L	80_K	2.548	1.00
140_L	256_F	2.513	1.00
225_K	228_E	2.504	1.00
215_S	219_E	2.477	1.00
143_F	147_N	2.469	1.00
141_E	145_N	2.423	1.00
224_L	230_S	2.360	1.00
156_S	249_L	2.331	1.00
45_K	72_R	2.307	1.00
172_E	176_E	2.292	1.00
43_G	76_Q	2.277	1.00
142_S	146_K	2.205	1.00
182_S	185_A	2.117	1.00
175_K	179_G	2.106	1.00
174_L	242_I	2.006	1.00
205_F	247_E	1.995	1.00
77_L	81_N	1.992	1.00
173_V	190_R	1.975	1.00
160_R	244_Q	1.966	1.00
49_R	53_L	1.951	1.00
174_L	232_E	1.894	1.00
205_F	249_L	1.872	1.00
173_V	186_V	1.831	1.00
177_L	186_V	1.818	1.00
158_R	247_E	1.809	1.00
161_H	241_A	1.779	1.00
264_R	268_A	1.774	1.00
91_D	116_K	1.768	1.00
157_Y	222_K	1.761	1.00
141_E	256_F	1.759	1.00
165_K	192_T	1.756	1.00
93_E	96_L	1.744	1.00
70_N	282_W	1.742	1.00
208_E	222_K	1.732	1.00
145_N	148_K	1.722	1.00
155_D	248_K	1.706	1.00
89_E	127_D	1.704	1.00
40_A	65_L	1.696	1.00
55_E	71_V	1.684	1.00
206_V	213_I	1.605	1.00
236_V	241_A	1.596	1.00
174_L	233_P	1.585	1.00
147_N	150_L	1.582	1.00
47_V	68_M	1.575	1.00
255_S	258_E	1.569	1.00
158_R	246_K	1.558	1.00
271_Q	274_D	1.553	1.00
263_I	267_I	1.549	1.00
224_L	228_E	1.545	1.00
185_A	189_E	1.534	1.00
140_L	264_R	1.524	1.00
255_S	259_V	1.501	1.00
171_R	175_K	1.500	1.00
169_E	172_E	1.497	1.00
224_L	245_L	1.486	1.00
235_K	240_Y	1.474	1.00
136_S	139_E	1.457	1.00
176_E	190_R	1.452	1.00
168_E	172_E	1.451	1.00
169_E	190_R	1.440	1.00
236_V	239_G	1.394	1.00
261_D	264_R	1.393	1.00
86_S	89_E	1.379	1.00
143_F	263_I	1.338	1.00
229_W	244_Q	1.338	1.00
137_N	260_K	1.325	1.00
91_D	95_L	1.325	1.00
39_I	52_W	1.315	1.00
53_L	61_G	1.308	1.00
175_K	178_K	1.305	1.00
157_Y	248_K	1.305	1.00
138_K	142_S	1.289	1.00
102_N	106_E	1.262	1.00
41_T	46_S	1.257	1.00
37_E	49_R	1.257	1.00
38_S	46_S	1.240	1.00
168_E	171_R	1.238	1.00
140_L	263_I	1.235	1.00
158_R	205_F	1.231	1.00
51_E	72_R	1.223	1.00
36_G	50_E	1.198	1.00
111_T	114_E	1.188	1.00
66_E	70_N	1.177	1.00
214_P	238_N	1.169	1.00
177_L	229_W	1.162	1.00
268_A	272_L	1.161	1.00
147_N	151_Y	1.160	1.00
164_V	173_V	1.153	1.00
88_S	92_R	1.144	1.00
120_R	124_L	1.128	1.00
87_K	120_R	1.126	1.00
260_K	264_R	1.125	1.00
72_R	75_E	1.125	1.00
156_S	205_F	1.124	1.00
226_E	245_L	1.119	1.00
112_E	116_K	1.119	1.00
166_D	192_T	1.119	1.00
140_L	267_I	1.116	1.00
270_D	274_D	1.088	1.00
144_Y	255_S	1.086	1.00
238_N	241_A	1.079	1.00
117_D	121_Y	1.072	1.00
104_F	107_D	1.050	1.00
256_F	260_K	1.047	1.00
55_E	68_M	1.046	1.00
117_D	120_R	1.043	1.00
167_E	240_Y	1.042	1.00
95_L	98_K	1.040	1.00
45_K	76_Q	1.036	1.00
219_E	223_T	1.035	1.00
48_T	51_E	1.034	1.00
95_L	99_A	1.033	1.00
277_T	280_T	1.031	1.00
62_K	66_E	1.031	1.00
186_V	190_R	1.027	1.00
159_I	206_V	1.027	1.00
163_V	239_G	1.019	1.00
21_V	24_T	1.019	1.00
193_D	196_T	1.016	1.00
172_E	190_R	1.015	1.00
245_L	248_K	1.013	1.00
56_M	61_G	0.982	1.00
96_L	99_A	0.980	1.00
155_D	250_K	0.979	1.00
202_D	246_K	0.976	1.00
52_W	65_L	0.973	1.00
157_Y	221_A	0.973	1.00
142_S	145_N	0.967	1.00
143_F	146_K	0.967	1.00
103_S	106_E	0.966	1.00
172_E	175_K	0.966	1.00
75_E	79_K	0.964	1.00
176_E	189_E	0.962	1.00
169_E	192_T	0.960	1.00
217_Y	241_A	0.955	1.00
263_I	266_Q	0.938	1.00
182_S	186_V	0.936	1.00
181_S	186_V	0.933	1.00
202_D	205_F	0.932	1.00
42_I	45_K	0.929	1.00
194_R	197_S	0.921	1.00
167_E	235_K	0.921	1.00
138_K	141_E	0.920	1.00
207_T	212_N	0.916	1.00
73_V	281_L	0.914	1.00
161_H	217_Y	0.913	1.00
78_A	124_L	0.912	1.00
94_F	116_K	0.909	1.00
52_W	64_T	0.905	1.00
72_R	76_Q	0.899	1.00
103_S	107_D	0.899	1.00
171_R	174_L	0.894	1.00
174_L	177_L	0.890	1.00
234_I	243_I	0.887	1.00
160_R	184_E	0.885	1.00
266_Q	270_D	0.885	1.00
121_Y	124_L	0.883	1.00
185_A	188_A	0.869	1.00
104_F	108_E	0.866	1.00
23_Y	26_T	0.853	1.00
173_V	176_E	0.853	1.00
181_S	185_A	0.853	1.00
92_R	95_L	0.849	1.00
49_R	61_G	0.848	1.00
279_K	282_W	0.848	1.00
161_H	236_V	0.841	1.00
221_A	243_I	0.839	1.00
160_R	202_D	0.839	1.00
191_S	201_G	0.838	1.00
45_K	79_K	0.835	1.00
27_K	30_A	0.833	1.00
137_N	141_E	0.831	1.00
148_K	151_Y	0.825	1.00
252_R	258_E	0.820	1.00
220_E	234_I	0.820	1.00
52_W	68_M	0.816	1.00
157_Y	245_L	0.810	1.00
233_P	240_Y	0.805	1.00
102_N	112_E	0.802	1.00
259_V	262_Q	0.801	1.00
141_E	144_Y	0.799	1.00
143_F	151_Y	0.797	1.00
191_S	200_G	0.797	1.00
171_R	232_E	0.795	1.00
144_Y	256_F	0.795	1.00
174_L	229_W	0.794	1.00
226_E	248_K	0.793	1.00
159_I	213_I	0.792	1.00
64_T	68_M	0.790	1.00
28_S	31_G	0.790	1.00
162_I	187_A	0.787	1.00
217_Y	238_N	0.787	1.00
218_I	222_K	0.781	0.99
139_E	142_S	0.779	0.99
29_Q	32_A	0.778	0.99
177_L	242_I	0.777	0.99
89_E	92_R	0.775	0.99
277_T	281_L	0.773	0.99
85_I	90_V	0.771	0.99
208_E	218_I	0.770	0.99
135_I	267_I	0.770	0.99
16_V	19_I	0.765	0.99
18_C	21_V	0.764	0.99
213_I	217_Y	0.764	0.99
173_V	177_L	0.763	0.99
116_K	120_R	0.762	0.99
209_A	212_N	0.761	0.99
187_A	201_G	0.754	0.99
20_A	23_Y	0.752	0.99
191_S	194_R	0.752	0.99
71_V	121_Y	0.751	0.99
122_N	126_E	0.750	0.99
180_G	186_V	0.745	0.99
124_L	128_L	0.744	0.99
163_V	241_A	0.743	0.99
259_V	263_I	0.740	0.99
227_D	246_K	0.739	0.99
257_D	260_K	0.738	0.99
170_A	177_L	0.737	0.99
225_K	245_L	0.729	0.99
66_E	282_W	0.728	0.99
187_A	197_S	0.722	0.99
38_S	48_T	0.722	0.99
115_W	119_I	0.722	0.99
40_A	69_I	0.719	0.99
85_I	123_I	0.719	0.99
41_T	44_G	0.718	0.99
159_I	221_A	0.717	0.99
254_F	258_E	0.711	0.99
81_N	128_L	0.710	0.99
229_W	233_P	0.708	0.99
50_E	54_K	0.705	0.99
93_E	126_E	0.704	0.99
213_I	218_I	0.704	0.99
184_E	244_Q	0.704	0.99
214_P	237_S	0.703	0.99
92_R	96_L	0.702	0.99
147_N	263_I	0.702	0.99
220_E	223_T	0.701	0.99
225_K	248_K	0.700	0.99
67_D	71_V	0.700	0.99
216_A	219_E	0.697	0.99
135_I	139_E	0.696	0.99
191_S	196_T	0.696	0.99
270_D	273_G	0.695	0.99
230_S	233_P	0.693	0.99
170_A	174_L	0.693	0.99
59_Q	62_K	0.692	0.99
39_I	48_T	0.692	0.99
59_Q	63_S	0.691	0.99
40_A	47_V	0.690	0.99
65_L	69_I	0.689	0.99
52_W	56_M	0.687	0.99
166_D	170_A	0.686	0.99
87_K	91_D	0.685	0.99
219_E	222_K	0.684	0.99
30_A	33_S	0.683	0.99
217_Y	243_I	0.680	0.99
71_V	75_E	0.680	0.99
262_Q	265_R	0.673	0.98
155_D	251_A	0.670	0.98
68_M	72_R	0.668	0.98
137_N	264_R	0.667	0.98
193_D	197_S	0.664	0.98
22_A	25_L	0.661	0.98
155_D	208_E	0.660	0.98
174_L	230_S	0.652	0.98
98_K	101_N	0.652	0.98
55_E	64_T	0.648	0.98
184_E	200_G	0.648	0.98
88_S	91_D	0.647	0.98
169_E	173_V	0.646	0.98
72_R	121_Y	0.642	0.98
176_E	179_G	0.641	0.98
63_S	66_E	0.641	0.98
39_I	49_R	0.641	0.98
144_Y	259_V	0.641	0.98
75_E	78_A	0.640	0.98
17_C	20_A	0.640	0.98
21_V	25_L	0.639	0.98
97_I	101_N	0.638	0.98
79_K	84_K	0.630	0.98
149_E	152_Q	0.630	0.98
85_I	127_D	0.626	0.98
137_N	256_F	0.625	0.98
170_A	242_I	0.625	0.98
156_S	207_T	0.624	0.98
93_E	97_I	0.622	0.97
113_K	116_K	0.616	0.97
269_M	273_G	0.614	0.97
118_Q	121_Y	0.613	0.97
22_A	26_T	0.613	0.97
261_D	265_R	0.613	0.97
50_E	53_L	0.613	0.97
25_L	28_S	0.612	0.97
222_K	245_L	0.609	0.97
144_Y	148_K	0.606	0.97
116_K	119_I	0.605	0.97
220_E	224_L	0.603	0.97
184_E	188_A	0.602	0.97
193_D	201_G	0.601	0.97
18_C	22_A	0.601	0.97
256_F	259_V	0.600	0.97
20_A	25_L	0.600	0.97
164_V	170_A	0.597	0.97
75_E	121_Y	0.596	0.97
183_F	187_A	0.595	0.97
73_V	282_W	0.593	0.97
40_A	52_W	0.592	0.97
262_Q	266_Q	0.591	0.97
164_V	192_T	0.591	0.97
21_V	26_T	0.589	0.97
63_S	67_D	0.588	0.96
120_R	123_I	0.587	0.96
267_I	270_D	0.585	0.96
78_A	128_L	0.584	0.96
85_I	124_L	0.584	0.96
178_K	229_W	0.583	0.96
110_T	118_Q	0.583	0.96
75_E	125_L	0.582	0.96
137_N	140_L	0.581	0.96
176_E	186_V	0.579	0.96
122_N	125_L	0.572	0.96
187_A	191_S	0.571	0.96
228_E	244_Q	0.569	0.96
144_Y	263_I	0.568	0.96
52_W	61_G	0.568	0.96
77_L	281_L	0.568	0.96
159_I	217_Y	0.565	0.96
19_I	23_Y	0.561	0.95
110_T	114_E	0.559	0.95
105_Y	110_T	0.556	0.95
119_I	123_I	0.554	0.95
184_E	187_A	0.552	0.95
206_V	221_A	0.551	0.95
123_I	128_L	0.550	0.95
192_T	197_S	0.547	0.95
265_R	269_M	0.545	0.95
187_A	200_G	0.544	0.95
254_F	259_V	0.543	0.95
183_F	201_G	0.543	0.95
39_I	65_L	0.541	0.94
196_T	200_G	0.539	0.94
113_K	117_D	0.538	0.94
40_A	68_M	0.536	0.94
57_E	61_G	0.534	0.94
227_D	244_Q	0.534	0.94
214_P	236_V	0.529	0.94
177_L	180_G	0.529	0.94
19_I	22_A	0.528	0.94
267_I	271_Q	0.526	0.94
207_T	218_I	0.526	0.94
55_E	67_D	0.525	0.94
214_P	217_Y	0.524	0.93
171_R	233_P	0.523	0.93
167_E	233_P	0.522	0.93
150_L	266_Q	0.522	0.93
216_A	237_S	0.521	0.93
183_F	191_S	0.520	0.93
135_I	140_L	0.520	0.93
269_M	272_L	0.520	0.93
42_I	69_I	0.519	0.93
129_L	132_D	0.518	0.93
177_L	182_S	0.517	0.93
16_V	23_Y	0.516	0.93
76_Q	80_K	0.515	0.93
140_L	260_K	0.515	0.93
182_S	244_Q	0.513	0.93
196_T	214_P	0.512	0.93
216_A	235_K	0.511	0.93
268_A	271_Q	0.511	0.93
170_A	233_P	0.510	0.93
228_E	245_L	0.507	0.92
235_K	238_N	0.507	0.92
161_H	203_L	0.503	0.92
105_Y	108_E	0.503	0.92
106_E	109_H	0.502	0.92
143_F	270_D	0.501	0.92
133_I	268_A	0.500	0.92
165_K	169_E	0.500	0.92
31_G	34_S	0.500	0.92

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
3nrkA	3	0.8586	100	0.261	Contact Map
4wo7A	2	0.8215	100	0.298	Contact Map
1m5yA	1	0.8013	100	0.315	Contact Map
3rgcA	2	0.7946	100	0.336	Contact Map
3rfwA	2	0.7778	100	0.34	Contact Map
1yw5A	1	0.5017	99.9	0.611	Contact Map
3tc5A	1	0.404	99.8	0.654	Contact Map
1jnsA	1	0.3098	99.8	0.659	Contact Map
2m08A	1	0.3131	99.8	0.662	Contact Map
3i6cA	1	0.3064	99.7	0.667	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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