PPIB - ECOLI - GREMLIN Contacts

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PPIB - Peptidyl-prolyl cis-trans isomerase B

UniProt:	P23869	Sequences: MVTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQKATKEPIKNEANNGLKNTRGTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQGWGYCVFAEVVDGMDVVDKIKGVATGRSGMHQDVPKEDVIIESVTVSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10758
Length:	164 (144)
Sequences:	10365 (5523)
Seq/√Len:	460.2

ECOLI - PPIB PPIA
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
80_R	134_D	3.530	1.00
5_H	10_D	3.013	1.00
102_V	137_K	2.981	1.00
12_V	128_D	2.926	1.00
81_G	130_M	2.656	1.00
37_N	159_S	2.387	1.00
79_T	125_E	2.148	1.00
84_A	99_F	2.144	1.00
39_T	52_G	2.067	1.00
29_D	33_E	2.006	1.00
4_F	11_I	2.005	1.00
25_K	29_D	1.938	1.00
78_N	84_A	1.924	1.00
14_K	125_E	1.849	1.00
14_K	127_V	1.815	1.00
5_H	158_E	1.805	1.00
5_H	159_S	1.798	1.00
11_I	133_V	1.789	1.00
4_F	160_V	1.782	1.00
40_I	154_D	1.777	1.00
13_I	83_L	1.776	1.00
4_F	13_I	1.761	1.00
139_V	155_V	1.687	1.00
8_H	135_K	1.678	1.00
15_T	24_V	1.659	1.00
17_D	24_V	1.651	1.00
31_C	160_V	1.633	1.00
22_E	69_K	1.614	1.00
68_I	94_A	1.594	1.00
16_F	19_K	1.591	1.00
50_I	102_V	1.570	1.00
16_F	125_E	1.500	1.00
101_N	105_N	1.481	1.00
82_T	101_N	1.468	1.00
11_I	126_V	1.465	1.00
46_N	138_G	1.461	1.00
46_N	137_K	1.446	1.00
140_A	152_K	1.440	1.00
82_T	125_E	1.432	1.00
19_K	75_G	1.423	1.00
41_F	52_G	1.388	1.00
45_I	49_M	1.363	1.00
68_I	71_E	1.358	1.00
79_T	82_T	1.354	1.00
142_G	152_K	1.345	1.00
28_L	32_R	1.337	1.00
50_I	136_I	1.298	1.00
157_I	160_V	1.240	1.00
44_V	136_I	1.234	1.00
136_I	155_V	1.215	1.00
141_T	149_D	1.208	1.00
4_F	157_I	1.206	1.00
34_G	37_N	1.181	1.00
14_K	17_D	1.175	1.00
82_T	122_V	1.172	1.00
33_E	65_K	1.166	1.00
23_T	85_M	1.150	1.00
23_T	123_F	1.143	1.00
77_K	109_N	1.136	1.00
81_G	134_D	1.135	1.00
13_I	100_I	1.130	1.00
143_R	148_Q	1.125	1.00
35_F	55_F	1.125	1.00
22_E	25_K	1.106	1.00
46_N	141_T	1.097	1.00
134_D	137_K	1.089	1.00
126_V	130_M	1.083	1.00
47_G	103_V	1.069	1.00
84_A	109_N	1.049	1.00
40_I	156_I	1.049	1.00
69_K	92_H	1.036	1.00
142_G	148_Q	1.033	1.00
45_I	149_D	1.027	1.00
78_N	82_T	1.006	1.00
11_I	100_I	1.002	1.00
39_T	54_G	1.001	1.00
12_V	127_V	0.997	1.00
83_L	123_F	0.994	1.00
126_V	133_V	0.990	1.00
130_M	133_V	0.986	1.00
72_A	110_F	0.986	1.00
29_D	65_K	0.976	1.00
140_A	149_D	0.971	1.00
20_A	24_V	0.968	1.00
8_H	139_V	0.957	1.00
102_V	133_V	0.953	1.00
56_E	59_M	0.950	1.00
79_T	104_D	0.948	1.00
100_I	133_V	0.943	1.00
87_R	93_S	0.929	1.00
29_D	32_R	0.925	1.00
77_K	106_D	0.924	1.00
90_A	93_S	0.923	1.00
30_Y	33_E	0.914	1.00
43_R	51_Q	0.912	1.00
35_F	61_Q	0.909	1.00
20_A	121_C	0.901	1.00
87_R	120_Y	0.899	1.00
84_A	122_V	0.899	1.00
25_K	28_L	0.887	1.00
87_R	90_A	0.886	1.00
87_R	94_A	0.886	1.00
70_N	87_R	0.869	1.00
56_E	61_Q	0.861	1.00
70_N	94_A	0.861	1.00
7_N	158_E	0.858	1.00
130_M	134_D	0.851	1.00
132_V	135_K	0.850	1.00
24_V	28_L	0.847	1.00
23_T	121_C	0.846	1.00
78_N	109_N	0.834	1.00
40_I	150_V	0.814	1.00
8_H	153_E	0.813	1.00
67_P	95_T	0.813	1.00
49_M	102_V	0.813	1.00
67_P	88_T	0.808	1.00
80_R	103_V	0.795	1.00
77_K	84_A	0.795	1.00
139_V	153_E	0.793	1.00
73_N	110_F	0.790	1.00
142_G	150_V	0.785	1.00
12_V	129_G	0.784	1.00
44_V	50_I	0.764	1.00
55_F	61_Q	0.757	1.00
13_I	126_V	0.754	1.00
80_R	130_M	0.750	1.00
64_T	95_T	0.750	1.00
29_D	34_G	0.746	1.00
44_V	155_V	0.744	1.00
131_D	135_K	0.743	1.00
27_F	123_F	0.733	1.00
44_V	102_V	0.726	1.00
56_E	60_K	0.723	1.00
51_Q	97_Q	0.721	1.00
7_N	156_I	0.719	1.00
42_H	97_Q	0.719	1.00
22_E	68_I	0.718	1.00
9_G	132_V	0.718	1.00
6_T	11_I	0.714	1.00
19_K	76_L	0.713	1.00
6_T	132_V	0.704	1.00
100_I	126_V	0.686	1.00
49_M	107_F	0.686	1.00
35_F	96_A	0.679	1.00
20_A	72_A	0.678	1.00
85_M	94_A	0.675	1.00
38_N	156_I	0.673	1.00
80_R	102_V	0.671	1.00
63_A	66_E	0.669	1.00
78_N	101_N	0.665	1.00
46_N	102_V	0.663	1.00
103_V	107_F	0.658	1.00
6_T	9_G	0.657	1.00
26_N	66_E	0.655	1.00
20_A	73_N	0.655	1.00
48_F	51_Q	0.645	1.00
51_Q	86_A	0.641	1.00
78_N	99_F	0.634	0.99
141_T	152_K	0.631	0.99
128_D	131_D	0.625	0.99
70_N	92_H	0.624	0.99
129_G	132_V	0.620	0.99
88_T	93_S	0.619	0.99
54_G	58_G	0.615	0.99
80_R	104_D	0.612	0.99
17_D	25_K	0.612	0.99
127_V	131_D	0.609	0.99
106_D	109_N	0.601	0.99
38_N	158_E	0.599	0.99
66_E	95_T	0.595	0.99
79_T	109_N	0.595	0.99
35_F	39_T	0.593	0.99
43_R	86_A	0.592	0.99
149_D	152_K	0.589	0.99
79_T	101_N	0.588	0.99
10_D	132_V	0.586	0.99
8_H	155_V	0.582	0.99
75_G	78_N	0.579	0.99
73_N	121_C	0.576	0.99
8_H	132_V	0.575	0.99
141_T	151_P	0.574	0.99
39_T	55_F	0.573	0.99
62_K	66_E	0.563	0.99
47_G	137_K	0.560	0.99
26_N	29_D	0.560	0.99
135_K	138_G	0.559	0.99
17_D	28_L	0.558	0.99
86_A	97_Q	0.556	0.99
19_K	73_N	0.553	0.99
16_F	82_T	0.550	0.99
55_F	95_T	0.548	0.98
37_N	160_V	0.548	0.98
126_V	129_G	0.547	0.98
44_V	151_P	0.546	0.98
45_I	48_F	0.540	0.98
23_T	68_I	0.538	0.98
50_I	100_I	0.535	0.98
150_V	154_D	0.535	0.98
131_D	134_D	0.529	0.98
140_A	143_R	0.522	0.98
26_N	68_I	0.521	0.98
15_T	124_A	0.520	0.98
102_V	134_D	0.518	0.98
76_L	79_T	0.518	0.98
20_A	23_T	0.517	0.98
25_K	64_T	0.515	0.98
48_F	108_L	0.514	0.98
64_T	68_I	0.513	0.98
151_P	155_V	0.512	0.98
15_T	123_F	0.511	0.98
19_K	74_N	0.509	0.98
55_F	60_K	0.508	0.98
83_L	124_A	0.507	0.98
8_H	136_I	0.503	0.97
70_N	120_Y	0.502	0.97
27_F	85_M	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
1lopA	1	1	100	0.116	Contact Map
1w74A	1	0.9085	100	0.119	Contact Map
3s6mA	1	0.9756	100	0.123	Contact Map
2k7nA	1	0.9146	100	0.126	Contact Map
1v9tA	1	0.9817	100	0.128	Contact Map
2poeA	1	0.9207	100	0.128	Contact Map
2fu0A	1	0.9085	100	0.129	Contact Map
2b71A	1	0.9024	100	0.129	Contact Map
3bo7A	3	0.9024	100	0.13	Contact Map
1zkcA	1	0.9207	100	0.133	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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