OPENSEQ.org - 1411761803 - GREMLIN Submission

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1EB6A

ID:	1411761803	Query Sequence TEVTDCKGDAESSLTTALSNAAKLANQAAEAAESGDESKFEEYFKTTDQQTRTTVAERLRAVAKEAGSTSGGSTTYHCNDPYGYCEPNVLAYTLPSKNEIANCDIYYSELPPLAQKCHAQDQATTTLHEFTHAPGVYQPGTEDLGYGYDAATQLSAQDALNNADSYALYANAIELKC	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	177 (175)
Sequences:	362 (314.1)
Seq/Len:	2.069
Nf(neff/√len):	23.7

HHblits Results: (2013_03)
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: 2.069).

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
21_A	66_A	2.919	1.00
128_H	132_H	2.360	1.00
143_D	146_Y	2.088	0.99
85_C	103_C	2.071	0.99
159_A	162_N	1.939	0.99
124_T	167_A	1.901	0.99
162_N	165_S	1.892	0.98
42_E	152_T	1.891	0.98
128_H	143_D	1.874	0.98
129_E	163_A	1.846	0.98
93_T	133_A	1.770	0.97
129_E	146_Y	1.744	0.97
146_Y	164_D	1.740	0.97
146_Y	163_A	1.728	0.97
128_H	146_Y	1.679	0.96
62_V	131_T	1.644	0.95
40_F	55_V	1.642	0.95
120_Q	168_L	1.606	0.95
129_E	143_D	1.598	0.94
132_H	143_D	1.597	0.94
129_E	132_H	1.573	0.94
28_A	170_A	1.563	0.94
132_H	146_Y	1.523	0.92
155_S	158_D	1.489	0.91
106_Y	122_Q	1.429	0.89
40_F	121_D	1.409	0.88
78_C	85_C	1.399	0.87
131_T	141_T	1.388	0.87
25_A	28_A	1.387	0.87
90_L	127_L	1.377	0.86
45_K	66_A	1.344	0.84
62_V	127_L	1.342	0.84
132_H	163_A	1.333	0.84
124_T	171_N	1.332	0.84
6_C	78_C	1.313	0.82
8_G	11_E	1.310	0.82
40_F	169_Y	1.308	0.82
145_G	150_A	1.295	0.81
90_L	125_T	1.289	0.81
44_F	55_V	1.284	0.80
87_P	96_S	1.284	0.80
151_A	162_N	1.280	0.80
80_D	92_Y	1.274	0.80
42_E	168_L	1.271	0.79
147_G	164_D	1.270	0.79
128_H	164_D	1.267	0.79
124_T	168_L	1.265	0.79
78_C	103_C	1.262	0.79
76_Y	130_F	1.260	0.79
102_N	126_T	1.232	0.76
91_A	125_T	1.209	0.75
107_Y	135_G	1.203	0.74
143_D	163_A	1.194	0.73
65_E	72_G	1.194	0.73
106_Y	126_T	1.181	0.72
61_A	169_Y	1.171	0.71
74_T	100_I	1.156	0.70
132_H	164_D	1.139	0.68
14_L	76_Y	1.138	0.68
40_F	52_R	1.137	0.68
11_E	15_T	1.123	0.67
51_T	160_L	1.109	0.65
59_L	170_A	1.101	0.64
114_A	123_A	1.100	0.64
40_F	44_F	1.099	0.64
59_L	139_P	1.098	0.64
145_G	162_N	1.097	0.64
40_F	162_N	1.097	0.64
118_H	121_D	1.097	0.64
80_D	83_G	1.083	0.62
55_V	83_G	1.078	0.62
20_N	123_A	1.074	0.61
55_V	160_L	1.073	0.61
125_T	129_E	1.072	0.61
123_A	171_N	1.072	0.61
31_A	37_E	1.071	0.61
9_D	49_Q	1.068	0.61
100_I	150_A	1.066	0.61
159_A	165_S	1.060	0.60
80_D	164_D	1.045	0.58
61_A	141_T	1.042	0.58
91_A	110_L	1.041	0.58
146_Y	154_L	1.039	0.58
173_I	176_K	1.036	0.57
94_L	102_N	1.036	0.57
120_Q	124_T	1.030	0.57
129_E	164_D	1.027	0.56
120_Q	171_N	1.023	0.56
55_V	89_V	1.016	0.55
35_G	147_G	1.014	0.55
113_L	123_A	1.011	0.55
45_K	121_D	1.010	0.54
128_H	163_A	1.009	0.54
136_V	139_P	1.006	0.54

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: (06Sep14)
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
1eb6A	1	1	100	0.056	Contact Map
2x3cA	1	0.8983	100	0.238	Contact Map
1g12A	1	0.904	100	0.278	Contact Map
1lmlA	1	0.8644	77.6	0.907	Contact Map
3cqbA	2	0.5537	41.9	0.926	Contact Map
4qhjA	2	0.5989	38.6	0.927	Contact Map
3dwbA	1	0.8588	27.3	0.933	Contact Map
3zukA	2	0.8362	22.2	0.936	Contact Map
1r1hA	1	0.8588	21.6	0.936	Contact Map
4jixA	2	0.6158	21	0.936	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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