OPENSEQ.org - 1453737259 - GREMLIN Submission

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1vkb

ID:	1453737259	Query Sequence MAHIFVYGTLKRGQPNHKVMLDHSHGLAAFRGRGCTVESFPLVIAGEHNIPWLLYLPGKGHCVTGEIYEVDEQMLRFLDDFEDCPSMYQRTALQVQVLEWEGDGDPGDSVQCFVYTTATYAPEWLFLPYHESYDSEGPHGLRYNPRENR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	149 (149)
Sequences:	505 (349.5)
Seq/Len:	3.389
Nf(neff/√len):	28.6

HHblits Results: (2015_06)
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: 3.389).

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
53_L	114_V	2.591	1.00
146_R	149_R	2.574	1.00
79_D	115_Y	1.833	0.99
10_L	51_P	1.816	0.99
41_P	58_G	1.811	0.99
34_G	95_V	1.790	0.99
75_L	90_R	1.786	0.99
40_F	116_T	1.721	0.99
19_V	81_F	1.700	0.99
145_P	148_N	1.654	0.98
12_R	30_F	1.544	0.97
53_L	63_V	1.528	0.97
5_F	65_G	1.511	0.97
136_E	142_R	1.455	0.96
137_G	140_G	1.450	0.96
67_I	112_C	1.441	0.95
135_S	139_H	1.428	0.95
5_F	8_G	1.414	0.95
136_E	148_N	1.396	0.94
144_N	148_N	1.370	0.94
96_Q	109_S	1.365	0.93
79_D	90_R	1.342	0.93
95_V	112_C	1.328	0.92
6_V	10_L	1.324	0.92
82_E	115_Y	1.324	0.92
39_S	56_L	1.318	0.92
34_G	67_I	1.308	0.91
94_Q	109_S	1.303	0.91
11_K	66_E	1.300	0.91
142_R	146_R	1.280	0.90
82_E	90_R	1.268	0.90
1_M	72_E	1.264	0.89
42_L	53_L	1.249	0.89
102_G	105_D	1.244	0.88
141_L	147_E	1.230	0.88
13_G	70_V	1.227	0.87
84_C	113_F	1.221	0.87
94_Q	111_Q	1.218	0.87
12_R	17_H	1.211	0.86
25_H	74_M	1.208	0.86
52_W	117_T	1.198	0.86
90_R	113_F	1.197	0.86
142_R	145_P	1.192	0.85
138_P	145_P	1.191	0.85
92_A	111_Q	1.175	0.84
51_P	82_E	1.166	0.84
112_C	127_L	1.163	0.83
44_I	68_Y	1.143	0.82
9_T	51_P	1.139	0.82
50_I	117_T	1.117	0.80
86_S	145_P	1.110	0.79
11_K	43_V	1.103	0.79
67_I	110_V	1.098	0.78
42_L	70_V	1.098	0.78
19_V	145_P	1.097	0.78
2_A	72_E	1.086	0.77
5_F	10_L	1.074	0.76
92_A	113_F	1.072	0.76
42_L	45_A	1.064	0.75
52_W	66_E	1.061	0.75
141_L	145_P	1.055	0.74
34_G	112_C	1.053	0.74
138_P	148_N	1.053	0.74
137_G	147_E	1.049	0.73
95_V	98_L	1.048	0.73
6_V	16_N	1.046	0.73
79_D	82_E	1.046	0.73
42_L	50_I	1.039	0.72
44_I	70_V	1.034	0.72
32_G	36_T	1.032	0.72
67_I	128_P	1.030	0.72
137_G	141_L	1.029	0.71
10_L	82_E	1.024	0.71
131_E	147_E	1.022	0.71
48_H	81_F	1.016	0.70
11_K	68_Y	1.010	0.69
15_P	49_N	1.008	0.69
139_H	142_R	1.003	0.69
72_E	96_Q	1.002	0.69
132_S	136_E	1.002	0.69

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
1vkbA	1	0.9732	100	0.17	Contact Map
3judA	1	0.953	100	0.267	Contact Map
2g0qA	1	0.8792	99.9	0.423	Contact Map
2jqvA	1	0.8792	99.9	0.447	Contact Map
1xhsA	1	0.745	99.8	0.454	Contact Map
1v30A	1	0.7852	99.8	0.462	Contact Map
2qikA	1	0.8322	99.8	0.474	Contact Map
3cryA	2	0.8993	99.8	0.476	Contact Map
4issA	2	0.8322	99.8	0.51	Contact Map
4gysA	2	0	99.7	0.537	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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