OPENSEQ.org - 1485957413 - GREMLIN Submission

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B8XCH5_C2B

ID:	1485957413	Query Sequence LVEPMQYLFVRIVKARGLPPNESAYVKVRTSNHFVRSKPAVNRPGESVDSPEWNQVFALGHNRSDSAVTGATLEISAWDASSESFLGGVCFDLSEVPVRDPPDSPLAPQWYRLEGSGADQNSGRISGDIQLSVWIGTQVDEAFPEAWSSDA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	151 (142)
Sequences:	314 (122.8)
Seq/Len:	2.211
Nf(neff/√len):	10.3

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: 2.211).

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
61_H	135_I	1.706	0.97
38_K	77_A	1.653	0.96
27_K	78_W	1.651	0.96
11_R	52_E	1.599	0.95
101_P	104_S	1.589	0.95
22_E	86_L	1.526	0.93
24_A	79_D	1.513	0.93
104_S	107_A	1.478	0.92
64_S	73_L	1.470	0.91
89_V	133_V	1.470	0.91
99_R	103_D	1.413	0.89
15_A	18_L	1.405	0.89
73_L	133_V	1.391	0.88
79_D	105_P	1.374	0.87
23_S	116_S	1.363	0.87
74_E	114_E	1.357	0.86
26_V	113_L	1.353	0.86
23_S	84_S	1.307	0.84
91_F	142_A	1.296	0.83
129_I	148_S	1.286	0.82
113_L	135_I	1.278	0.82
105_P	113_L	1.269	0.81
8_L	11_R	1.265	0.81
77_A	108_P	1.264	0.81
36_R	129_I	1.259	0.80
62_N	114_E	1.239	0.79
136_G	140_D	1.232	0.78
31_S	37_S	1.229	0.78
102_P	137_T	1.217	0.77
89_V	96_V	1.213	0.77
79_D	132_S	1.210	0.76
27_K	128_D	1.206	0.76
134_W	138_Q	1.200	0.76
24_A	51_P	1.197	0.75
4_P	20_P	1.192	0.75
18_L	127_G	1.189	0.75
100_D	137_T	1.177	0.74
101_P	144_P	1.171	0.73
62_N	123_G	1.158	0.72
38_K	98_V	1.151	0.71
90_C	116_S	1.144	0.71
105_P	139_V	1.141	0.70
33_H	63_R	1.136	0.70
109_Q	129_I	1.114	0.68
65_D	80_A	1.112	0.67
25_Y	79_D	1.111	0.67
55_Q	114_E	1.100	0.66
31_S	130_Q	1.096	0.66
33_H	59_L	1.090	0.65
81_S	88_G	1.090	0.65
70_G	92_D	1.088	0.65
147_W	150_D	1.088	0.65
56_V	93_L	1.086	0.65
1_L	11_R	1.083	0.64
9_F	100_D	1.081	0.64
73_L	91_F	1.080	0.64
125_I	145_E	1.080	0.64
5_M	13_V	1.074	0.63
39_P	43_R	1.070	0.63
74_E	112_R	1.069	0.63
27_K	33_H	1.066	0.63
136_G	143_F	1.066	0.63
63_R	115_G	1.065	0.63
74_E	96_V	1.059	0.62
91_F	145_E	1.057	0.62
64_S	86_L	1.052	0.61
99_R	141_E	1.050	0.61
70_G	132_S	1.049	0.61
96_V	149_S	1.047	0.61
30_T	60_G	1.045	0.60
134_W	143_F	1.039	0.60
26_V	129_I	1.037	0.59
40_A	48_V	1.037	0.59
25_Y	71_A	1.037	0.59
114_E	147_W	1.037	0.59
91_F	131_L	1.034	0.59
61_H	73_L	1.030	0.59
79_D	85_F	1.029	0.59
81_S	124_R	1.028	0.58
4_P	95_E	1.026	0.58
28_V	72_T	1.024	0.58
65_D	148_S	1.024	0.58
134_W	140_D	1.022	0.58
39_P	132_S	1.018	0.57
140_D	143_F	1.015	0.57
8_L	15_A	1.010	0.56
101_P	130_Q	1.009	0.56
44_P	132_S	1.000	0.55

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
2cjtA	4	0.8146	99.8	0.732	Contact Map
3m7fB	1	0.7616	99.8	0.733	Contact Map
2cjsA	2	0.8675	99.7	0.748	Contact Map
3l9bA	1	0.7947	99.7	0.752	Contact Map
4p42A	2	0.8411	99.7	0.754	Contact Map
4npjA	2	0.8543	99.7	0.756	Contact Map
3qr0A	1	0.7682	99.7	0.76	Contact Map
3jzyA	1	0.7682	99.7	0.764	Contact Map
4iqhA	3	0.7947	99.7	0.764	Contact Map
3b7yA	2	0.8212	99.6	0.766	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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