PPIA - ECOLI - GREMLIN Contacts

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PPIA - Peptidyl-prolyl cis-trans isomerase A

UniProt:	P0AFL3	Sequences: MFKSTLAAMAAVFALSALSPAAMAAKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10757
Length:	190 (153)
Sequences:	9520 (5293)
Seq/√Len:	427.9

ECOLI - PPIA PPIB
BACSU - PPIB
HALSA - Q9HNW6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_R	160_D	3.385	1.00
34_T	39_N	3.081	1.00
41_E	154_K	2.825	1.00
110_G	156_M	2.788	1.00
131_V	163_S	2.616	1.00
66_N	185_S	2.509	1.00
108_T	151_K	2.502	1.00
107_N	113_A	2.363	1.00
32_L	39_N	2.086	1.00
113_A	128_F	2.040	1.00
68_T	81_G	2.024	1.00
33_L	40_I	1.894	1.00
33_L	42_L	1.868	1.00
40_I	159_A	1.853	1.00
42_L	112_I	1.831	1.00
33_L	186_A	1.807	1.00
54_Q	58_D	1.806	1.00
69_T	180_P	1.740	1.00
43_E	151_K	1.734	1.00
34_T	185_S	1.732	1.00
34_T	184_L	1.690	1.00
43_E	153_V	1.683	1.00
37_A	161_K	1.674	1.00
34_T	187_K	1.665	1.00
108_T	111_T	1.646	1.00
165_V	181_V	1.644	1.00
36_S	184_L	1.633	1.00
58_D	62_S	1.623	1.00
32_L	187_K	1.618	1.00
51_V	98_K	1.608	1.00
40_I	152_V	1.596	1.00
44_L	53_V	1.576	1.00
30_H	41_E	1.562	1.00
166_P	178_S	1.528	1.00
29_P	57_V	1.510	1.00
97_I	123_A	1.503	1.00
30_H	153_V	1.490	1.00
46_K	53_V	1.479	1.00
75_P	163_S	1.453	1.00
29_P	46_K	1.451	1.00
130_N	134_N	1.429	1.00
28_D	43_E	1.419	1.00
60_V	186_A	1.418	1.00
45_D	48_K	1.369	1.00
79_I	131_V	1.362	1.00
75_P	164_Q	1.350	1.00
48_K	105_L	1.348	1.00
74_I	78_M	1.331	1.00
62_S	94_N	1.316	1.00
111_T	151_K	1.307	1.00
111_T	130_N	1.306	1.00
168_H	178_S	1.300	1.00
36_S	182_V	1.285	1.00
45_D	151_K	1.283	1.00
73_V	162_I	1.279	1.00
28_D	46_K	1.270	1.00
63_G	66_N	1.270	1.00
32_L	41_E	1.239	1.00
48_K	104_G	1.224	1.00
167_T	175_N	1.210	1.00
75_P	167_T	1.210	1.00
162_I	181_V	1.209	1.00
107_N	138_D	1.197	1.00
79_I	162_I	1.189	1.00
70_F	81_G	1.182	1.00
183_I	186_A	1.168	1.00
160_D	163_S	1.164	1.00
58_D	94_N	1.134	1.00
152_V	156_M	1.127	1.00
106_R	138_D	1.126	1.00
33_L	183_I	1.118	1.00
52_S	149_F	1.109	1.00
52_S	114_M	1.090	1.00
168_H	174_Q	1.083	1.00
31_V	56_F	1.051	1.00
111_T	148_V	1.043	1.00
69_T	182_V	1.037	1.00
169_D	174_Q	1.031	1.00
98_K	121_D	1.028	1.00
42_L	129_I	1.024	1.00
110_G	160_D	1.022	1.00
74_I	175_N	1.020	1.00
51_V	54_Q	1.017	1.00
57_V	188_V	1.000	1.00
129_I	159_A	0.993	1.00
108_T	133_D	0.988	1.00
116_R	119_D	0.986	1.00
76_G	132_A	0.980	1.00
35_T	40_I	0.975	1.00
37_A	165_V	0.974	1.00
101_A	144_F	0.974	1.00
97_I	100_E	0.964	1.00
49_A	53_V	0.958	1.00
72_R	80_Q	0.957	1.00
156_M	159_A	0.941	1.00
152_V	159_A	0.932	1.00
88_M	91_K	0.930	1.00
85_T	88_M	0.929	1.00
113_A	138_D	0.920	1.00
31_V	57_V	0.914	1.00
68_T	83_G	0.908	1.00
119_D	122_S	0.902	1.00
106_R	135_A	0.898	1.00
107_N	128_F	0.897	1.00
166_P	175_N	0.889	1.00
113_A	148_V	0.884	1.00
40_I	129_I	0.878	1.00
116_R	122_S	0.875	1.00
69_T	87_Q	0.873	1.00
99_N	116_R	0.864	1.00
52_S	147_A	0.861	1.00
54_Q	57_V	0.842	1.00
41_E	153_V	0.841	1.00
168_H	176_V	0.828	1.00
69_T	176_V	0.818	1.00
59_Y	62_S	0.815	1.00
165_V	179_K	0.809	1.00
112_I	149_F	0.806	1.00
64_F	125_S	0.805	1.00
99_N	123_A	0.802	1.00
30_H	43_E	0.800	1.00
109_R	132_A	0.795	1.00
39_N	187_K	0.795	1.00
156_M	160_D	0.793	1.00
64_F	84_F	0.784	1.00
37_A	179_K	0.782	1.00
31_V	186_A	0.782	1.00
107_N	130_N	0.778	1.00
31_V	60_V	0.777	1.00
80_Q	126_Q	0.772	1.00
131_V	159_A	0.769	1.00
53_V	57_V	0.764	1.00
49_A	147_A	0.757	1.00
135_A	138_D	0.757	1.00
109_R	156_M	0.752	1.00
84_F	87_Q	0.752	1.00
78_M	131_V	0.747	1.00
84_F	90_Q	0.747	1.00
35_T	70_F	0.745	1.00
73_V	79_I	0.740	1.00
121_D	144_F	0.739	1.00
116_R	123_A	0.738	1.00
35_T	158_V	0.729	1.00
96_P	118_A	0.729	1.00
56_F	149_F	0.719	1.00
71_H	126_Q	0.713	1.00
51_V	97_I	0.704	1.00
129_I	152_V	0.703	1.00
116_R	146_Y	0.702	1.00
57_V	61_N	0.700	1.00
42_L	152_V	0.693	1.00
73_V	181_V	0.689	1.00
158_V	161_K	0.687	1.00
96_P	124_T	0.682	1.00
69_T	86_E	0.681	1.00
85_T	89_Q	0.680	1.00
88_M	92_K	0.668	1.00
75_P	131_V	0.666	1.00
73_V	131_V	0.665	1.00
37_A	158_V	0.663	1.00
67_N	182_V	0.655	0.99
167_T	177_P	0.654	0.99
101_A	104_G	0.652	0.99
66_N	186_A	0.641	0.99
63_G	90_Q	0.641	0.99
28_D	45_D	0.639	0.99
114_M	123_A	0.633	0.99
78_M	136_F	0.630	0.99
67_N	184_L	0.628	0.99
49_A	101_A	0.624	0.99
85_T	90_Q	0.624	0.99
52_S	97_I	0.621	0.99
61_N	188_V	0.615	0.99
89_Q	125_S	0.612	0.99
155_G	158_V	0.612	0.99
41_E	155_G	0.611	0.99
43_E	46_K	0.607	0.99
76_G	163_S	0.598	0.99
109_R	131_V	0.596	0.99
28_D	47_Q	0.594	0.99
38_G	158_V	0.593	0.99
84_F	124_T	0.593	0.99
105_L	148_V	0.592	0.99
72_R	115_A	0.591	0.99
99_N	121_D	0.587	0.99
59_Y	64_F	0.586	0.99
175_N	178_S	0.576	0.99
79_I	129_I	0.567	0.98
167_T	178_S	0.566	0.98
154_K	157_D	0.565	0.98
157_D	161_K	0.561	0.98
80_Q	115_A	0.559	0.98
102_D	144_F	0.558	0.98
58_D	61_N	0.558	0.98
35_T	38_G	0.557	0.98
63_G	185_S	0.552	0.98
49_A	102_D	0.551	0.98
106_R	144_F	0.549	0.98
64_F	90_Q	0.549	0.98
109_R	133_D	0.549	0.98
48_K	102_D	0.547	0.98
153_V	157_D	0.546	0.98
108_T	138_D	0.540	0.98
115_A	126_Q	0.533	0.98
29_P	188_V	0.532	0.98
161_K	164_Q	0.531	0.98
169_D	175_N	0.531	0.98
88_M	93_P	0.529	0.98
132_A	136_F	0.529	0.98
37_A	181_V	0.526	0.98
45_D	111_T	0.523	0.97
95_P	124_T	0.523	0.97
73_V	177_P	0.520	0.97
68_T	84_F	0.518	0.97
55_N	95_P	0.518	0.97
27_G	43_E	0.518	0.97
93_P	124_T	0.518	0.97
176_V	180_P	0.517	0.97
118_A	122_S	0.516	0.97
27_G	46_K	0.516	0.97
81_G	112_I	0.515	0.97
77_F	80_Q	0.513	0.97
68_T	85_T	0.509	0.97
112_I	150_G	0.508	0.97
39_N	158_V	0.506	0.97
157_D	160_D	0.505	0.97
40_I	156_M	0.505	0.97
35_T	184_L	0.504	0.97
66_N	187_K	0.503	0.97
108_T	130_N	0.500	0.97

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
1v9tA	1	0.8474	100	0.169	Contact Map
2x7kA	1	0.8474	100	0.173	Contact Map
2k7nA	1	0.8579	100	0.177	Contact Map
2oseA	3	0.8684	100	0.179	Contact Map
3s6mA	1	0.8158	100	0.181	Contact Map
2b71A	1	0.8737	100	0.187	Contact Map
1mzwA	1	0.8211	100	0.187	Contact Map
1lopA	1	0.8211	100	0.189	Contact Map
3bo7A	3	0.8053	100	0.192	Contact Map
2poeA	1	0.8105	100	0.192	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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