OPENSEQ.org - 1485957439 - GREMLIN Submission

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B8XCH5_C2C

ID:	1485957439	Query Sequence PHVAHTRSKVYQSPKLWYLRVTVLEAQDLHIAPNLPPLTAPEIRVKAQLGFQSARTRRGSMNNHSGSFHWHEDMIFVAGEPLEDCLVLMVEDRTTKEATLLGHAMIPVSSIEQRIDERFVPSKWHTLEGEGGGGGGGGGPGGGGGGGPYCGRISLRLCLEGGYHVLEEAAHVCSDFRPTA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	180 (176)
Sequences:	234 (124.3)
Seq/Len:	1.330
Nf(neff/√len):	9.4

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: 1.330).

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
17_W	161_G	2.480	1.00
49_L	78_A	2.104	0.98
118_R	158_C	1.754	0.93
138_G	142_G	1.686	0.92
86_L	116_D	1.657	0.91
73_D	152_R	1.616	0.89
122_S	154_S	1.571	0.87
177_R	180_A	1.541	0.86
7_R	46_K	1.534	0.85
47_A	73_D	1.527	0.85
152_R	161_G	1.518	0.85
46_K	153_I	1.515	0.84
115_I	160_E	1.499	0.84
41_P	83_E	1.475	0.82
130_E	144_G	1.427	0.79
137_G	142_G	1.408	0.78
79_G	82_L	1.404	0.78
168_E	174_S	1.395	0.77
161_G	177_R	1.394	0.77
112_E	118_R	1.388	0.77
165_V	168_E	1.380	0.76
101_L	136_G	1.361	0.75
173_C	176_F	1.346	0.73
102_G	127_L	1.336	0.73
11_Y	14_P	1.325	0.72
78_A	81_P	1.301	0.70
47_A	74_M	1.296	0.69
159_L	166_L	1.295	0.69
24_L	154_S	1.285	0.68
71_H	156_R	1.269	0.67
17_W	177_R	1.252	0.65
111_I	117_E	1.247	0.65
104_A	107_P	1.241	0.64
69_H	133_G	1.234	0.64
7_R	29_L	1.233	0.64
101_L	146_G	1.230	0.63
45_V	158_C	1.228	0.63
57_R	108_V	1.216	0.62
90_V	102_G	1.215	0.62
25_E	57_R	1.214	0.62
165_V	174_S	1.198	0.60
40_A	44_R	1.197	0.60
112_E	160_E	1.193	0.60
163_Y	175_D	1.191	0.60
77_V	81_P	1.178	0.58
60_S	65_S	1.171	0.58
108_V	135_G	1.165	0.57
19_L	146_G	1.156	0.56
7_R	45_V	1.140	0.55
23_V	88_L	1.137	0.54
15_K	120_V	1.135	0.54
68_F	82_L	1.127	0.53
54_A	89_M	1.124	0.53
40_A	153_I	1.120	0.53
52_Q	116_D	1.118	0.53
160_E	173_C	1.115	0.52
6_T	79_G	1.112	0.52
106_I	155_L	1.112	0.52
136_G	143_G	1.103	0.51
23_V	74_M	1.099	0.51
10_V	27_Q	1.098	0.51
70_W	77_V	1.089	0.50
169_A	176_F	1.083	0.49
164_H	168_E	1.080	0.49
144_G	147_G	1.075	0.48
126_T	154_S	1.075	0.48
65_S	145_G	1.070	0.48
70_W	124_W	1.063	0.47
167_E	174_S	1.061	0.47
37_P	64_H	1.061	0.47
45_V	88_L	1.061	0.47
34_N	153_I	1.059	0.47
19_L	49_L	1.058	0.47
20_R	162_G	1.058	0.47
41_P	92_D	1.054	0.46
163_Y	168_E	1.053	0.46
155_L	169_A	1.053	0.46
70_W	127_L	1.052	0.46
14_P	20_R	1.049	0.46
137_G	143_G	1.049	0.46
124_W	127_L	1.049	0.46
18_Y	168_E	1.044	0.45
108_V	137_G	1.040	0.45
170_A	173_C	1.037	0.44
87_V	101_L	1.037	0.44
113_Q	161_G	1.028	0.44
17_W	113_Q	1.026	0.43
11_Y	20_R	1.021	0.43
100_L	110_S	1.017	0.43
19_L	120_V	1.014	0.42
118_R	152_R	1.013	0.42

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
2cjsA	2	0.8722	99.7	0.748	Contact Map
4npjA	2	0.8389	99.7	0.759	Contact Map
2fk9A	1	0.6944	99.7	0.759	Contact Map
3jzyA	1	0.6833	99.7	0.764	Contact Map
3kwuA	1	0.6833	99.6	0.773	Contact Map
4p42A	2	0.8389	99.6	0.774	Contact Map
4iqhA	3	0.6889	99.6	0.775	Contact Map
1cjyA	2	0.7556	99.6	0.775	Contact Map
3pycA	1	0.7	99.6	0.777	Contact Map
2cjtA	4	0.7278	99.6	0.78	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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