CotJB - PFAM28P - GREMLIN Contacts

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CotJB - CotJB protein

PFAM:	PF12652	Sequences: EELLKEIQALDFALVELNLYLDTHPDDQEALALYNEYAKERKELKKEYEKKYGPLTNFGVSSSDPWQWIDDPWPWE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (75)
Sequences:	2997 (2340)
Seq/√Len:	270.1
META:	0.803

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_D	41_R	2.850	1.00
41_R	45_K	2.553	1.00
18_N	57_N	2.200	1.00
13_A	37_Y	2.183	1.00
5_K	9_A	2.100	1.00
15_V	18_N	2.063	1.00
47_E	51_K	2.009	1.00
49_E	59_G	1.935	1.00
17_L	33_L	1.844	1.00
71_D	76_E	1.819	1.00
5_K	8_Q	1.804	1.00
7_I	44_L	1.777	1.00
40_E	43_E	1.677	1.00
46_K	50_K	1.657	1.00
10_L	37_Y	1.526	1.00
38_A	42_K	1.525	1.00
48_Y	53_G	1.457	1.00
20_Y	27_D	1.449	1.00
42_K	46_K	1.428	1.00
14_L	41_R	1.426	1.00
33_L	36_E	1.425	1.00
31_L	35_N	1.406	1.00
14_L	37_Y	1.356	1.00
10_L	44_L	1.352	1.00
2_E	6_E	1.275	1.00
67_Q	70_D	1.271	1.00
7_I	45_K	1.266	1.00
27_D	30_A	1.262	1.00
39_K	43_E	1.249	1.00
6_E	40_E	1.248	1.00
14_L	38_A	1.232	1.00
40_E	44_L	1.215	1.00
45_K	49_E	1.203	1.00
7_I	41_R	1.194	1.00
29_E	32_A	1.158	1.00
56_T	60_V	1.140	1.00
36_E	40_E	1.126	1.00
28_Q	32_A	1.123	1.00
6_E	9_A	1.118	1.00
15_V	19_L	1.078	1.00
65_P	70_D	1.049	1.00
31_L	66_W	1.033	1.00
43_E	47_E	1.024	1.00
4_L	8_Q	1.019	1.00
11_D	45_K	1.005	1.00
34_Y	38_A	0.966	1.00
6_E	44_L	0.931	1.00
69_I	73_W	0.916	1.00
47_E	50_K	0.911	1.00
66_W	69_I	0.879	1.00
54_P	67_Q	0.864	1.00
18_N	34_Y	0.857	1.00
33_L	37_Y	0.848	1.00
28_Q	64_D	0.828	0.99
11_D	15_V	0.822	0.99
12_F	16_E	0.815	0.99
62_S	65_P	0.804	0.99
8_Q	11_D	0.789	0.99
37_Y	40_E	0.783	0.99
6_E	47_E	0.758	0.99
13_A	16_E	0.756	0.99
36_E	39_K	0.745	0.99
6_E	10_L	0.740	0.99
7_I	10_L	0.739	0.99
10_L	40_E	0.736	0.99
10_L	41_R	0.724	0.99
13_A	33_L	0.705	0.98
35_N	38_A	0.703	0.98
18_N	22_D	0.703	0.98
14_L	57_N	0.695	0.98
3_L	47_E	0.680	0.98
4_L	55_L	0.678	0.98
13_A	17_L	0.674	0.98
53_G	73_W	0.672	0.98
20_Y	24_H	0.666	0.98
3_L	44_L	0.662	0.97
3_L	7_I	0.660	0.97
34_Y	57_N	0.659	0.97
38_A	60_V	0.658	0.97
18_N	68_W	0.658	0.97
7_I	55_L	0.653	0.97
21_L	66_W	0.653	0.97
15_V	58_F	0.652	0.97
22_D	68_W	0.650	0.97
45_K	56_T	0.618	0.96
25_P	69_I	0.618	0.96
44_L	47_E	0.603	0.96
20_Y	30_A	0.600	0.95
35_N	61_S	0.598	0.95
23_T	27_D	0.591	0.95
35_N	59_G	0.580	0.95
3_L	48_Y	0.576	0.94
4_L	48_Y	0.568	0.94
48_Y	52_Y	0.566	0.94
49_E	53_G	0.566	0.94
11_D	14_L	0.566	0.94
20_Y	33_L	0.563	0.94
60_V	63_S	0.563	0.94
65_P	69_I	0.560	0.93
32_A	36_E	0.557	0.93
10_L	17_L	0.552	0.93
33_L	76_E	0.550	0.93
46_K	49_E	0.541	0.92
7_I	48_Y	0.540	0.92
21_L	34_Y	0.528	0.91
59_G	62_S	0.527	0.91
73_W	76_E	0.526	0.91
18_N	58_F	0.521	0.91
8_Q	16_E	0.519	0.91
12_F	20_Y	0.502	0.89
7_I	11_D	0.501	0.89
19_L	76_E	0.500	0.89

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
3rczB	1	0.6316	27.4	0.885	Contact Map
2mnuB	1	0.25	27.3	0.885	Contact Map
1wwzA	2	0.7368	16.5	0.897	Contact Map
2ayvA	1	0.5789	16.1	0.897	Contact Map
2wpxA	1	0.7237	16	0.897	Contact Map
2gjdA	4	0.6316	14.4	0.899	Contact Map
1zdnA	2	0.5789	14.2	0.899	Contact Map
2fbnA	2	0.5921	14.1	0.899	Contact Map
3bzhA	2	0.5921	13.9	0.9	Contact Map
2j8mA	2	0.8158	13.6	0.9	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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