CFEM - PFAM28P - GREMLIN Contacts

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CFEM - CFEM domain

PFAM:	PF05730	Sequences: QLSDLPACALTCLTSALAASSGCSLTDVACLCTNAAFQSAVTDCVASACTAADALAALNAAQALCA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (64)
Sequences:	2318 (2022)
Seq/√Len:	252.8
META:	0.138

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_C	44_C	4.922	1.00
23_C	30_C	3.744	1.00
50_T	53_D	2.662	1.00
59_N	63_A	2.130	1.00
51_A	55_L	2.086	1.00
7_A	10_L	2.051	1.00
9_A	57_A	1.961	1.00
34_N	37_F	1.914	1.00
31_L	37_F	1.785	1.00
8_C	49_C	1.775	1.00
55_L	59_N	1.675	1.00
5_L	9_A	1.650	1.00
17_L	20_S	1.525	1.00
35_A	39_S	1.431	1.00
53_D	56_A	1.431	1.00
11_T	15_S	1.424	1.00
16_A	40_A	1.353	1.00
36_A	40_A	1.336	1.00
10_L	14_T	1.296	1.00
42_T	46_A	1.245	1.00
58_L	62_Q	1.232	1.00
63_A	66_A	1.199	1.00
36_A	39_S	1.163	1.00
59_N	62_Q	1.133	1.00
6_P	9_A	1.105	1.00
9_A	61_A	1.080	1.00
17_L	31_L	1.075	1.00
19_A	40_A	1.061	1.00
28_V	64_L	1.058	1.00
4_D	64_L	1.024	1.00
50_T	55_L	0.964	1.00
29_A	33_T	0.962	1.00
32_C	65_C	0.943	1.00
13_L	37_F	0.935	1.00
5_L	60_A	0.928	1.00
16_A	43_D	0.922	1.00
62_Q	66_A	0.902	1.00
26_T	31_L	0.868	1.00
39_S	42_T	0.858	0.99
13_L	41_V	0.850	0.99
22_G	34_N	0.826	0.99
38_Q	42_T	0.820	0.99
13_L	31_L	0.818	0.99
55_L	58_L	0.808	0.99
55_L	61_A	0.783	0.99
7_A	11_T	0.774	0.99
31_L	41_V	0.765	0.99
9_A	60_A	0.763	0.99
43_D	47_S	0.755	0.99
6_P	11_T	0.742	0.98
11_T	14_T	0.739	0.98
50_T	57_A	0.734	0.98
17_L	28_V	0.726	0.98
11_T	48_A	0.723	0.98
45_V	57_A	0.717	0.98
6_P	53_D	0.706	0.98
56_A	59_N	0.692	0.98
58_L	66_A	0.690	0.98
9_A	48_A	0.689	0.98
51_A	54_A	0.682	0.97
54_A	61_A	0.679	0.97
14_T	25_L	0.670	0.97
19_A	22_G	0.669	0.97
21_S	34_N	0.649	0.96
14_T	18_A	0.645	0.96
38_Q	62_Q	0.641	0.96
5_L	42_T	0.640	0.96
16_A	41_V	0.635	0.96
4_D	28_V	0.635	0.96
13_L	45_V	0.633	0.96
15_S	48_A	0.625	0.96
39_S	43_D	0.625	0.96
33_T	36_A	0.624	0.96
3_S	10_L	0.621	0.95
13_L	16_A	0.620	0.95
4_D	60_A	0.620	0.95
14_T	43_D	0.608	0.95
52_A	55_L	0.605	0.95
34_N	38_Q	0.601	0.95
52_A	56_A	0.590	0.94
35_A	51_A	0.590	0.94
4_D	63_A	0.589	0.94
37_F	41_V	0.589	0.94
17_L	37_F	0.574	0.93
9_A	49_C	0.574	0.93
24_S	52_A	0.571	0.93
55_L	66_A	0.568	0.93
59_N	64_L	0.547	0.91
60_A	64_L	0.545	0.91
18_A	21_S	0.539	0.91
45_V	58_L	0.520	0.89
54_A	58_L	0.519	0.89
26_T	62_Q	0.515	0.89
35_A	42_T	0.509	0.88
28_V	41_V	0.503	0.88
3_S	35_A	0.500	0.87

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
2ln4A	1	0.4697	3.3	0.84	Contact Map
2fqaA	1	0.4091	1.6	0.864	Contact Map
4ttnB	1	0.3939	1.5	0.866	Contact Map
2lamA	1	0.4394	1.5	0.867	Contact Map
2e3eA	1	0.5	1.2	0.873	Contact Map
2lr5A	1	0.5	1.2	0.875	Contact Map
1i2uA	1	0.5	1.1	0.877	Contact Map
2kozA	1	0.5	1.1	0.878	Contact Map
1kalA	1	0.3636	1	0.879	Contact Map
2e3gA	1	0.4848	1	0.88	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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