Col_cuticle_N - PFAM28P - GREMLIN Contacts

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Col_cuticle_N - Nematode cuticle collagen N-terminal domain

PFAM:	PF01484	Sequences: YVAVAFSTVAILACLITLPMLYNYIQSVQSEVQDEMDFFKVRADDAWKEM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	50 (49)
Sequences:	1992 (1420)
Seq/√Len:	202.9
META:	0.325

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_Y	39_F	2.890	1.00
24_Y	28_V	2.164	1.00
29_Q	33_Q	2.074	1.00
26_Q	29_Q	1.933	1.00
34_D	37_D	1.932	1.00
38_F	42_R	1.925	1.00
47_W	50_M	1.815	1.00
42_R	46_A	1.653	1.00
7_S	11_I	1.613	1.00
16_I	19_P	1.575	1.00
5_A	9_V	1.557	1.00
30_S	33_Q	1.443	1.00
2_V	38_F	1.434	1.00
37_D	41_V	1.330	1.00
4_V	35_E	1.304	1.00
23_N	27_S	1.199	1.00
19_P	28_V	1.185	1.00
41_V	45_D	1.133	1.00
10_A	14_C	1.121	1.00
21_L	24_Y	1.109	1.00
32_V	36_M	1.107	1.00
42_R	45_D	1.096	1.00
32_V	37_D	1.079	1.00
9_V	45_D	1.045	1.00
30_S	37_D	1.037	1.00
17_T	25_I	1.036	1.00
25_I	35_E	1.031	1.00
8_T	15_L	1.016	1.00
40_K	44_D	1.014	1.00
5_A	8_T	1.002	1.00
14_C	31_E	0.984	1.00
28_V	32_V	0.981	1.00
11_I	31_E	0.950	0.99
41_V	44_D	0.944	0.99
28_V	33_Q	0.929	0.99
22_Y	25_I	0.892	0.99
17_T	21_L	0.858	0.99
14_C	45_D	0.856	0.99
33_Q	37_D	0.848	0.99
27_S	31_E	0.827	0.98
13_A	17_T	0.821	0.98
2_V	6_F	0.808	0.98
46_A	49_E	0.788	0.98
8_T	22_Y	0.780	0.98
28_V	36_M	0.768	0.97
15_L	38_F	0.762	0.97
20_M	23_N	0.762	0.97
25_I	40_K	0.747	0.97
26_Q	30_S	0.740	0.97
26_Q	33_Q	0.729	0.97
10_A	40_K	0.713	0.96
2_V	21_L	0.712	0.96
27_S	30_S	0.692	0.95
28_V	31_E	0.679	0.95
45_D	50_M	0.678	0.95
14_C	26_Q	0.670	0.94
12_L	16_I	0.658	0.94
34_D	47_W	0.648	0.93
17_T	24_Y	0.632	0.93
27_S	41_V	0.631	0.93
22_Y	29_Q	0.627	0.92
18_L	21_L	0.612	0.91
18_L	44_D	0.595	0.90
20_M	32_V	0.564	0.88
14_C	42_R	0.553	0.87
39_F	46_A	0.552	0.87
10_A	19_P	0.551	0.86
32_V	46_A	0.533	0.85
40_K	43_A	0.525	0.84
39_F	47_W	0.523	0.83
6_F	21_L	0.510	0.82
32_V	47_W	0.508	0.82
24_Y	35_E	0.505	0.81
35_E	48_K	0.500	0.81

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
3mhsE	1	0.52	9	0.802	Contact Map
2clyA	1	0.58	7.4	0.81	Contact Map
4mt1A	3	0.56	6.5	0.814	Contact Map
3ne5A	3	0.6	4.7	0.826	Contact Map
4k0jA	3	0.56	4	0.832	Contact Map
3qprA	8	0.02	3.9	0.832	Contact Map
1bf5A	2	0.5	3.5	0.836	Contact Map
2ygkA	2	0.6	2.7	0.846	Contact Map
3rvyA	3	0.5	2.7	0.846	Contact Map
4k5yA	1	0.98	2.6	0.847	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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