OPENSEQ.org - 1405445853 - GREMLIN Submission

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T0836 30-204 -force run

ID:	1405445853	Query Sequence PHGHDATYFQAIFRWLHVLFGILWIGLLYYFNFVQIRVMPQIPAELKPAVSKYIAPEALFWFRWAALATWVMGVLLAYNRGYLVEAFTLGLAGGYTPGVDMGFTFIGTGMWLATVMFFNVWVFIWPNQKIALGIVEADADAKAKAAKTAMLVSRTNTLLSIPMLATMAMHQTLFG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	175 (167)
Sequences:	115 (75.8)
Seq/Len:	0.689
Nf(neff/√len):	5.9

Jackhmmer Results: (2014_04_16)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 0.689).

Sequences per length for each position, AFTER the coverage/gap filter was applied

Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

i	j	Scaled score	Prob
147_K	151_L	2.411	0.98
31_F	58_A	2.279	0.96
70_W	114_T	2.276	0.96
138_D	141_A	2.035	0.92
64_W	67_L	1.991	0.91
117_F	122_V	1.908	0.88
20_F	72_M	1.828	0.85
107_G	111_W	1.814	0.85
118_F	122_V	1.718	0.80
130_I	137_A	1.608	0.74
118_F	123_F	1.593	0.73
18_V	168_A	1.580	0.72
18_V	166_T	1.577	0.72
30_Y	33_F	1.510	0.67
129_K	135_V	1.494	0.66
55_A	132_L	1.486	0.65
31_F	59_L	1.474	0.64
31_F	127_N	1.468	0.64
158_L	165_A	1.455	0.63
52_K	133_G	1.444	0.62
52_K	55_A	1.373	0.56
83_L	88_T	1.363	0.55
147_K	158_L	1.362	0.55
30_Y	35_Q	1.343	0.53
75_L	79_N	1.340	0.53
77_A	110_M	1.332	0.52
42_I	49_A	1.330	0.52
31_F	148_T	1.314	0.51
130_I	145_A	1.302	0.50
74_V	79_N	1.301	0.50
16_L	72_M	1.274	0.48
115_V	159_L	1.272	0.47
66_A	69_T	1.248	0.45
58_A	127_N	1.247	0.45
28_L	163_M	1.237	0.45
108_T	166_T	1.230	0.44
18_V	76_L	1.220	0.43
36_I	131_A	1.215	0.43
76_L	148_T	1.213	0.43
60_F	70_W	1.192	0.41
21_G	120_V	1.185	0.40
12_I	161_I	1.184	0.40
82_Y	110_M	1.176	0.40
86_A	111_W	1.172	0.39
32_N	35_Q	1.168	0.39
113_A	140_D	1.168	0.39
124_I	149_A	1.161	0.38
64_W	157_T	1.160	0.38
13_F	75_L	1.158	0.38
28_L	149_A	1.141	0.37
113_A	155_T	1.140	0.37
40_P	46_L	1.140	0.37
86_A	107_G	1.138	0.37
43_P	146_A	1.133	0.36
144_K	148_T	1.132	0.36
133_G	142_K	1.120	0.35
149_A	163_M	1.120	0.35
38_V	54_I	1.114	0.35
120_V	124_I	1.105	0.34
31_F	149_A	1.099	0.34
40_P	110_M	1.097	0.33
59_L	149_A	1.086	0.33
81_G	157_T	1.078	0.32
48_P	52_K	1.074	0.32
39_M	54_I	1.071	0.31
33_F	106_I	1.065	0.31
147_K	150_M	1.064	0.31
28_L	124_I	1.063	0.31
165_A	168_A	1.060	0.31
58_A	124_I	1.058	0.31
33_F	157_T	1.056	0.30
32_N	163_M	1.052	0.30
70_W	117_F	1.051	0.30
131_A	152_V	1.050	0.30
123_F	152_V	1.049	0.30
58_A	145_A	1.046	0.30
36_I	150_M	1.044	0.30
34_V	163_M	1.044	0.30
31_F	56_P	1.042	0.29
124_I	163_M	1.041	0.29
57_E	169_M	1.031	0.29
30_Y	55_A	1.021	0.28
67_L	130_I	1.019	0.28
22_I	108_T	1.015	0.28
42_I	48_P	1.013	0.27
14_R	142_K	1.003	0.27

Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).

Text file of contact predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

NEW Features

Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.

HHsearch Results: (12Jul14)
GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.

PDB	M	Cov	P(%)	HHΔ
1hx2A	1	0.1143	1.5	0.977	Contact Map
2kluA	1	0.3657	1.4	0.977	Contact Map
2k1kA	2	0.2114	1.3	0.978	Contact Map
2fhoA	1	0.0914	1.2	0.978	Contact Map
1eaiC	2	0.12	1.1	0.979	Contact Map
2jv4A	1	0.2629	1.1	0.979	Contact Map
1e0lA	1	0.1886	1.1	0.979	Contact Map
4gd3A	2	0.6629	1	0.979	Contact Map
3kw2A	2	0.2914	1	0.979	Contact Map
2r5vA	2	0.28	1	0.979	Contact Map

M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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