OPENSEQ.org - 1429126423 - GREMLIN Submission

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ID:	1429126423	Query Sequence MRGSHHHHHHGSITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	207 (192)
Sequences:	314 (217.4)
Seq/Len:	1.635
Nf(neff/√len):	15.7

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: 1.635).

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
34_L	40_Y	2.001	0.98
33_I	37_R	1.942	0.98
130_I	136_Q	1.770	0.96
152_S	155_L	1.688	0.94
166_P	190_T	1.657	0.93
39_I	90_I	1.547	0.90
104_F	144_L	1.546	0.90
34_L	37_R	1.464	0.86
78_L	202_K	1.452	0.85
30_I	83_V	1.419	0.84
58_T	63_L	1.411	0.83
73_Q	77_W	1.397	0.82
26_F	86_L	1.371	0.81
151_C	185_L	1.331	0.78
100_E	104_F	1.329	0.78
39_I	93_I	1.321	0.77
92_N	149_V	1.313	0.77
62_E	66_Y	1.301	0.76
27_S	155_L	1.299	0.75
70_V	83_V	1.298	0.75
19_A	28_F	1.294	0.75
121_K	129_E	1.291	0.75
119_R	162_D	1.284	0.74
31_N	63_L	1.272	0.73
74_L	196_N	1.259	0.72
23_A	75_K	1.254	0.72
37_R	166_P	1.250	0.71
136_Q	145_P	1.241	0.71
90_I	149_V	1.231	0.70
29_G	152_S	1.214	0.68
39_I	134_I	1.210	0.68
19_A	63_L	1.203	0.67
70_V	155_L	1.195	0.66
31_N	153_F	1.194	0.66
155_L	170_E	1.183	0.65
37_R	100_E	1.179	0.65
32_S	53_L	1.175	0.65
38_G	134_I	1.174	0.64
132_S	138_T	1.171	0.64
112_A	117_A	1.169	0.64
90_I	104_F	1.160	0.63
55_L	82_S	1.158	0.63
101_R	158_Y	1.154	0.62
83_V	108_C	1.153	0.62
86_L	139_A	1.151	0.62
99_L	174_P	1.146	0.62
96_G	106_I	1.145	0.62
29_G	133_V	1.138	0.61
108_C	163_L	1.136	0.61
88_V	178_T	1.136	0.61
132_S	157_I	1.136	0.61
71_V	197_S	1.135	0.61
50_K	90_I	1.133	0.60
58_T	157_I	1.128	0.60
25_F	197_S	1.126	0.60
34_L	45_F	1.121	0.59
87_V	172_S	1.119	0.59
61_L	173_G	1.119	0.59
63_L	66_Y	1.116	0.59
102_W	140_T	1.110	0.58
18_S	193_H	1.110	0.58
81_C	117_A	1.107	0.58
39_I	84_Q	1.106	0.58
26_F	58_T	1.093	0.56
61_L	69_N	1.093	0.56
74_L	83_V	1.090	0.56
101_R	169_W	1.090	0.56
27_S	67_L	1.089	0.56
104_F	190_T	1.079	0.55
44_T	171_E	1.078	0.55
69_N	134_I	1.077	0.55
13_I	78_L	1.076	0.54
129_E	145_P	1.072	0.54
14_T	154_D	1.070	0.54
48_V	132_S	1.068	0.54
37_R	40_Y	1.063	0.53
33_I	53_L	1.060	0.53
38_G	135_R	1.060	0.53
72_E	106_I	1.060	0.53
35_Y	42_S	1.054	0.52
67_L	149_V	1.048	0.52
24_E	51_Y	1.043	0.51
13_I	54_T	1.043	0.51
107_E	114_D	1.042	0.51
67_L	194_K	1.038	0.50
127_Q	155_L	1.037	0.50
26_F	134_I	1.036	0.50
194_K	202_K	1.034	0.50
72_E	203_I	1.034	0.50
67_L	97_E	1.032	0.50
89_V	95_S	1.029	0.50
145_P	201_Y	1.026	0.49
129_E	188_F	1.022	0.49
81_C	157_I	1.022	0.49
77_W	193_H	1.021	0.49
74_L	86_L	1.021	0.49
33_I	40_Y	1.019	0.48
102_W	141_V	1.019	0.48
71_V	203_I	1.016	0.48
81_C	179_N	1.015	0.48
193_H	199_V	1.014	0.48
80_K	178_T	1.014	0.48
137_I	159_T	1.011	0.48
137_I	183_V	1.010	0.48
35_Y	146_L	1.008	0.47
37_R	144_L	1.007	0.47
81_C	110_K	1.007	0.47
47_R	89_V	1.006	0.47
16_R	96_G	1.004	0.47
113_K	179_N	1.002	0.47

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
2vfxA	12	0.9952	100	0.092	Contact Map
4aezB	3	0.913	100	0.111	Contact Map
3abdA	2	0.8937	100	0.195	Contact Map
4trkA	1	0.9903	100	0.243	Contact Map
4tzmA	2	0.9662	100	0.296	Contact Map
4j2gA	2	0.7246	95.6	0.891	Contact Map
2qyfB	2	0.8116	59.7	0.933	Contact Map
2iojA	2	0.3865	9.7	0.956	Contact Map
3eh2A	3	0.5894	8.1	0.957	Contact Map
1yrkA	1	0.5362	7	0.958	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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