OPENSEQ.org - 1452699962 - GREMLIN Submission

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1b5l

ID:	1452699962	Query Sequence CYLSRKLMLDARENLKLLDRMNRLSPHSCLQDRKDFGLPQEMVEGDQLQKDQAFPVLYEMLQQSFNLFYTEHSSAAWDTTLLEQLCTGLQQQLDHLDTCRGQVMGEEDSELGNMDPIVTVKKYFQGIYDYLQEKGYSDCAWEIVRVEMMRALTVSTTLQKRLTKMGGDLNSP	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	172 (164)
Sequences:	383 (218.6)
Seq/Len:	2.335
Nf(neff/√len):	17.1

HHblits Results: (2015_06)
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: 2.335).

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
1_C	99_C	2.849	1.00
142_E	145_R	2.593	1.00
29_C	139_C	2.273	1.00
30_L	33_R	1.827	0.98
59_E	121_K	1.726	0.97
65_F	97_D	1.696	0.97
77_W	145_R	1.678	0.97
127_I	147_E	1.677	0.97
131_L	140_A	1.582	0.95
140_A	144_V	1.558	0.95
18_L	123_Y	1.548	0.94
156_T	159_Q	1.536	0.94
159_Q	163_T	1.499	0.93
131_L	141_W	1.468	0.92
13_E	86_C	1.431	0.91
2_Y	5_R	1.424	0.91
113_N	136_Y	1.405	0.90
77_W	142_E	1.372	0.88
50_K	143_I	1.367	0.88
61_L	86_C	1.337	0.86
156_T	163_T	1.321	0.86
157_T	163_T	1.293	0.84
58_Y	65_F	1.278	0.83
155_S	161_R	1.276	0.83
79_T	126_G	1.265	0.82
2_Y	7_L	1.264	0.82
156_T	161_R	1.263	0.82
36_F	123_Y	1.262	0.82
38_L	99_C	1.251	0.81
52_Q	62_Q	1.241	0.80
153_T	156_T	1.237	0.80
155_S	159_Q	1.228	0.79
141_W	145_R	1.215	0.78
58_Y	97_D	1.204	0.77
124_F	142_E	1.202	0.77
47_Q	58_Y	1.199	0.77
43_V	69_Y	1.195	0.77
13_E	94_D	1.191	0.76
136_Y	148_M	1.183	0.76
64_S	98_T	1.171	0.75
11_A	85_L	1.166	0.74
113_N	117_I	1.160	0.74
96_L	158_L	1.146	0.72
152_L	158_L	1.143	0.72
18_L	77_W	1.140	0.72
69_Y	72_H	1.133	0.71
99_C	124_F	1.124	0.70
36_F	118_V	1.115	0.69
157_T	160_K	1.111	0.69
61_L	98_T	1.103	0.68
133_E	142_E	1.099	0.68
161_R	164_K	1.091	0.67
23_R	120_V	1.088	0.67
109_S	112_G	1.088	0.67
15_L	90_Q	1.087	0.67
10_D	112_G	1.081	0.66
112_G	115_D	1.077	0.65
41_E	47_Q	1.073	0.65
158_L	161_R	1.072	0.65
154_V	159_Q	1.068	0.65
137_S	144_V	1.068	0.65
78_D	84_Q	1.064	0.64
85_L	106_E	1.060	0.64
7_L	14_N	1.057	0.63
20_R	147_E	1.055	0.63
95_H	121_K	1.055	0.63
131_L	145_R	1.054	0.63
60_M	138_D	1.047	0.62
159_Q	164_K	1.042	0.62
91_Q	127_I	1.039	0.61
107_E	111_L	1.035	0.61
159_Q	162_L	1.032	0.61
18_L	140_A	1.023	0.60
47_Q	60_M	1.019	0.59
27_H	51_D	1.019	0.59
86_C	112_G	1.018	0.59
90_Q	100_R	1.017	0.59
27_H	63_Q	1.016	0.59
79_T	118_V	1.012	0.58
147_E	150_R	1.012	0.58
70_T	128_Y	1.012	0.58
1_C	124_F	1.011	0.58
153_T	161_R	1.009	0.58
136_Y	140_A	1.007	0.58
23_R	82_L	1.004	0.57
26_P	42_M	1.002	0.57
5_R	27_H	1.000	0.57

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
3se4B	1	0.8256	100	0.016	Contact Map
1b5lA	1	0.8837	100	0.016	Contact Map
3oq3A	1	0.9651	100	0.048	Contact Map
3s9dA	2	0.7384	100	0.053	Contact Map
1au1A	2	0.9477	100	0.071	Contact Map
1wu3I	1	0.9186	100	0.093	Contact Map
3piwA	1	0.8721	100	0.14	Contact Map
3pivA	2	0.8837	100	0.17	Contact Map
2r17C	2	0.6279	16.1	0.95	Contact Map
2d48A	1	0.686	11.4	0.953	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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