OPENSEQ.org - 1486044486 - GREMLIN Submission

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COW1 100-250

ID:	1486044486	Query Sequence DLPKIPIPSVPTFQPSTPVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELVLDFEAAYGRC	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	151 (147)
Sequences:	160 (122.1)
Seq/Len:	1.088
Nf(neff/√len):	10.1

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: 1.088).

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 > 50% 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_M	76_L	1.965	0.96
115_R	136_T	1.863	0.94
92_I	137_L	1.671	0.88
35_Y	122_S	1.642	0.87
92_I	107_V	1.624	0.86
46_K	71_L	1.581	0.84
33_L	58_A	1.544	0.82
81_T	96_T	1.503	0.79
138_S	143_D	1.494	0.79
36_N	72_E	1.461	0.76
30_I	106_I	1.435	0.75
38_T	69_K	1.426	0.74
23_L	110_V	1.380	0.70
120_G	124_R	1.378	0.70
77_G	93_S	1.374	0.70
122_S	127_L	1.362	0.69
41_Q	90_F	1.341	0.67
110_V	129_Y	1.333	0.67
122_S	126_D	1.329	0.66
41_Q	44_E	1.322	0.66
76_L	79_Y	1.305	0.64
54_L	75_I	1.302	0.64
108_L	123_R	1.300	0.64
67_P	72_E	1.297	0.63
132_P	144_F	1.296	0.63
122_S	146_A	1.285	0.62
67_P	73_A	1.264	0.60
49_R	75_I	1.258	0.60
34_Q	59_K	1.246	0.59
83_S	106_I	1.235	0.58
104_R	119_L	1.229	0.57
122_S	147_A	1.208	0.55
108_L	128_M	1.207	0.55
68_I	72_E	1.190	0.54
92_I	95_K	1.190	0.54
47_K	95_K	1.188	0.53
4_K	7_I	1.181	0.53
59_K	133_A	1.178	0.52
27_Q	36_N	1.178	0.52
35_Y	120_G	1.177	0.52
145_E	149_G	1.177	0.52
92_I	141_V	1.169	0.52
71_L	75_I	1.169	0.52
32_E	56_D	1.169	0.52
75_I	78_I	1.159	0.51
16_S	111_N	1.156	0.50
49_R	59_K	1.144	0.49
89_R	94_F	1.143	0.49
14_Q	17_T	1.130	0.48
35_Y	95_K	1.128	0.48
21_E	37_H	1.126	0.48
105_H	118_A	1.122	0.47
144_F	149_G	1.119	0.47
81_T	95_K	1.108	0.46
16_S	59_K	1.105	0.46
129_Y	143_D	1.097	0.45
56_D	119_L	1.097	0.45
137_L	141_V	1.092	0.44
98_F	116_Y	1.091	0.44
35_Y	137_L	1.082	0.43
37_H	40_T	1.076	0.43
99_S	136_T	1.073	0.43
31_R	103_F	1.069	0.42
120_G	147_A	1.064	0.42
5_I	24_E	1.061	0.41
31_R	80_L	1.054	0.41
12_T	15_P	1.049	0.40
118_A	147_A	1.046	0.40
37_H	110_V	1.044	0.40
95_K	107_V	1.038	0.39
79_Y	91_P	1.022	0.38
35_Y	71_L	1.021	0.38
22_R	147_A	1.019	0.38
26_V	136_T	1.018	0.38
120_G	146_A	1.016	0.37
6_P	15_P	1.015	0.37
24_E	65_A	1.013	0.37
54_L	108_L	1.010	0.37
120_G	126_D	1.007	0.37
100_G	134_F	1.002	0.36

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
4jpsB	1	0.3974	19.2	0.951	Contact Map
3j6dA	24	0.6821	17.9	0.952	Contact Map
4u65E	2	0.8344	13.4	0.954	Contact Map
3pjpA	2	0.6358	13.4	0.954	Contact Map
2shpA	2	0.5762	12.8	0.955	Contact Map
2dvjA	1	0.6887	12.7	0.955	Contact Map
3mazA	1	0.6093	11	0.956	Contact Map
2ft3A	6	0.3709	9.5	0.957	Contact Map
4g1iA	2	0.6821	9.2	0.958	Contact Map
3s9kA	1	0.6093	9.2	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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