OPENSEQ.org - 1516190191 - GREMLIN Submission

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1JM7

ID:	1516190191	Query Sequence MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	200 (185)
Sequences:	273 (185.4)
Seq/Len:	1.476
Nf(neff/√len):	13.6

HHblits Results: (2016_02)
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: 1.476).

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
149_C	152_C	2.286	0.99
27_C	44_C	2.013	0.98
128_C	131_C	1.970	0.98
39_C	44_C	1.853	0.96
34_P	39_C	1.804	0.95
27_C	39_C	1.788	0.95
24_C	27_C	1.787	0.95
41_H	61_C	1.715	0.94
187_S	192_L	1.701	0.93
128_C	144_C	1.683	0.93
188_K	195_D	1.680	0.93
138_P	146_H	1.585	0.90
44_C	47_C	1.551	0.88
34_P	44_C	1.532	0.87
24_C	39_C	1.517	0.87
146_H	162_P	1.490	0.85
27_C	34_P	1.482	0.85
34_P	41_H	1.480	0.85
128_C	152_C	1.474	0.84
27_C	47_C	1.461	0.84
40_D	145_E	1.447	0.83
138_P	162_P	1.429	0.82
192_L	195_D	1.428	0.82
48_M	143_G	1.417	0.81
128_C	149_C	1.413	0.81
187_S	190_R	1.378	0.79
40_D	146_H	1.376	0.78
189_L	192_L	1.373	0.78
109_R	117_A	1.371	0.78
39_C	47_C	1.339	0.76
41_H	64_C	1.331	0.75
144_C	149_C	1.328	0.75
42_I	79_F	1.295	0.72
142_G	146_H	1.289	0.72
16_N	28_L	1.286	0.72
188_K	191_N	1.285	0.71
22_L	119_L	1.282	0.71
24_C	44_C	1.275	0.71
190_R	193_L	1.273	0.70
144_C	152_C	1.267	0.70
47_C	145_E	1.257	0.69
38_K	47_C	1.252	0.69
138_P	183_I	1.250	0.68
38_K	141_L	1.245	0.68
141_L	148_F	1.239	0.67
24_C	34_P	1.238	0.67
47_C	129_S	1.226	0.66
33_E	75_E	1.220	0.66
131_C	144_C	1.206	0.64
38_K	129_S	1.199	0.64
191_N	194_H	1.199	0.64
75_E	83_V	1.168	0.61
164_C	176_N	1.168	0.61
109_R	112_W	1.163	0.60
36_S	86_L	1.158	0.60
43_F	148_F	1.155	0.59
113_A	116_R	1.154	0.59
107_D	111_A	1.140	0.58
187_S	195_D	1.138	0.58
34_P	161_C	1.137	0.58
190_R	194_H	1.133	0.57
164_C	171_Q	1.130	0.57
187_S	194_H	1.128	0.57
140_C	147_I	1.122	0.56
18_M	115_S	1.117	0.56
12_Q	190_R	1.115	0.55
12_Q	187_S	1.112	0.55
16_N	19_Q	1.090	0.53
190_R	195_D	1.087	0.53
131_C	152_C	1.076	0.51
80_S	84_E	1.056	0.49
161_C	164_C	1.051	0.49
135_L	179_L	1.051	0.49
27_C	152_C	1.049	0.49
33_E	46_F	1.045	0.48
41_H	44_C	1.042	0.48
12_Q	193_L	1.037	0.47
31_I	34_P	1.036	0.47
62_P	72_S	1.035	0.47
109_R	113_A	1.035	0.47
127_R	153_V	1.032	0.47
137_E	150_S	1.029	0.47
44_C	152_C	1.028	0.46
12_Q	195_D	1.026	0.46
40_D	164_C	1.023	0.46
188_K	192_L	1.022	0.46
135_L	146_H	1.020	0.46
127_R	137_E	1.016	0.45
189_L	195_D	1.013	0.45
61_C	64_C	1.011	0.45
131_C	149_C	1.007	0.44
42_I	76_S	1.007	0.44
114_H	118_A	1.006	0.44
39_C	164_C	1.002	0.44

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: (06Aug15)
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
4wz3B	1	0.845	100	0.504	Contact Map
4cfgA	2	0.075	99.8	0.62	Contact Map
4ap4A	1	0.565	99.8	0.653	Contact Map
1jm7A	1	0.515	99.6	0.691	Contact Map
4kblA	2	0.73	99.5	0.709	Contact Map
2c2lA	4	0.465	99.5	0.71	Contact Map
2kreA	1	0.46	99.5	0.717	Contact Map
2kr4A	1	0.425	99.5	0.717	Contact Map
1z6uA	2	0.46	99.5	0.718	Contact Map
2f42A	1	0.46	99.5	0.72	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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