OPENSEQ.org - 1428510289 - GREMLIN Submission

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mlkl

ID:	1428510289	Query Sequence MDKLGQIIKLGQLIYEQCEKMKYCRKQCQRLGNRVHGLLQPLQRLQAQGKKNLPDDITAALGRFDEVLKEANQQIEKFSKKSHIWKFVSVGNDKILFHEVNEKLRDVWEELLLLLQVYHWNTVSDVSQPASWQQEDRQDAEEDGNENMKVILMQLQISVEEINKTLKQCSLKPTQEIP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	178 (171)
Sequences:	224 (169.7)
Seq/Len:	1.310
Nf(neff/√len):	13.0

Jackhmmer Results: (2015_01_07)
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: 1.310).

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
164_K	167_K	2.087	0.98
146_E	151_I	1.746	0.93
61_L	71_A	1.643	0.90
150_V	153_M	1.616	0.89
162_I	166_L	1.520	0.84
64_F	94_K	1.445	0.80
78_F	104_L	1.440	0.80
148_M	152_L	1.434	0.79
160_E	163_N	1.431	0.79
146_E	150_V	1.426	0.79
146_E	152_L	1.424	0.79
111_L	115_L	1.418	0.78
34_R	111_L	1.418	0.78
25_R	125_D	1.412	0.78
148_M	151_I	1.402	0.77
155_L	158_S	1.398	0.77
70_E	103_K	1.365	0.74
18_C	61_L	1.362	0.74
154_Q	166_L	1.356	0.74
145_N	156_Q	1.344	0.73
105_R	109_E	1.327	0.71
71_A	100_V	1.321	0.71
34_R	97_F	1.311	0.70
154_Q	160_E	1.302	0.69
124_S	128_Q	1.294	0.69
135_E	139_D	1.294	0.69
163_N	166_L	1.273	0.67
165_T	168_Q	1.265	0.66
157_I	164_K	1.236	0.64
160_E	165_T	1.230	0.63
45_L	90_V	1.230	0.63
24_C	27_Q	1.229	0.63
38_L	101_N	1.226	0.63
151_I	158_S	1.220	0.62
149_K	165_T	1.216	0.62
17_Q	24_C	1.202	0.60
161_E	164_K	1.200	0.60
23_Y	35_V	1.189	0.59
158_S	161_E	1.173	0.58
24_C	67_V	1.167	0.57
154_Q	158_S	1.161	0.56
74_Q	100_V	1.158	0.56
147_N	164_K	1.151	0.55
155_L	160_E	1.149	0.55
134_Q	142_E	1.148	0.55
42_L	82_S	1.146	0.55
21_M	90_V	1.146	0.55
97_F	105_R	1.145	0.55
156_Q	159_V	1.142	0.55
40_Q	84_I	1.140	0.54
26_K	142_E	1.139	0.54
153_M	158_S	1.136	0.54
16_E	36_H	1.130	0.53
15_Y	22_K	1.124	0.53
152_L	156_Q	1.123	0.53
133_Q	140_A	1.115	0.52
65_D	72_N	1.112	0.52
158_S	163_N	1.111	0.51
146_E	149_K	1.103	0.51
70_E	80_K	1.100	0.50
158_S	165_T	1.100	0.50
151_I	157_I	1.098	0.50
108_W	112_L	1.097	0.50
168_Q	171_L	1.093	0.50
97_F	111_L	1.090	0.49
130_A	134_Q	1.088	0.49
88_V	94_K	1.088	0.49
34_R	94_K	1.076	0.48
146_E	155_L	1.075	0.48
158_S	168_Q	1.072	0.48
30_R	104_L	1.071	0.47
163_N	168_Q	1.070	0.47
150_V	162_I	1.068	0.47
38_L	112_L	1.066	0.47
143_D	152_L	1.063	0.47
163_N	170_S	1.063	0.47
159_V	164_K	1.058	0.46
14_I	28_C	1.057	0.46
161_E	168_Q	1.054	0.46
25_R	109_E	1.037	0.44
148_M	155_L	1.037	0.44
21_M	24_C	1.026	0.43
126_V	129_P	1.026	0.43
136_D	142_E	1.017	0.42
9_K	13_L	1.016	0.42
25_R	28_C	1.016	0.42
128_Q	157_I	1.016	0.42
136_D	141_E	1.015	0.42
160_E	166_L	1.008	0.41
31_L	136_D	1.006	0.41
25_R	105_R	1.005	0.41
152_L	155_L	1.004	0.41
23_Y	94_K	1.003	0.41
149_K	153_M	1.002	0.41

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: (31Jan15)
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
2msvA	1	0.8596	100	0.305	Contact Map
4btfA	1	0.809	99.9	0.375	Contact Map
4uxvA	1	0.8202	31.2	0.922	Contact Map
1n1fA	1	0.4157	26.8	0.925	Contact Map
4uy3A	1	0.573	15	0.933	Contact Map
1h6gA	2	0.6348	13.2	0.935	Contact Map
4fzsA	2	0.9045	11.7	0.936	Contact Map
3mq9A	8	0.4438	11.5	0.936	Contact Map
3ojaB	1	0.7528	11.1	0.937	Contact Map
2ilkA	1	0.4157	8.7	0.939	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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