OPENSEQ.org - 1405035249 - GREMLIN Submission

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T0808 150-330 -force run

ID:	1405035249	Query Sequence FSDYWGRRGPSVHLGYALPEGDTEWFYNEITVPKEGETMHSYYMAAGFGEGYFGMQYNSPTERRILFSVWSPFDTQNPKEIPDDQKIKLLRQGKDVHIGEFGNEGSGGQSYLKYPWKAGNTYKFLMQIRPDGNGNTTYTAYFYATDEKEWKLIASFLRPKTNTWYKRPHSFLENFSPEQGY	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	181 (178)
Sequences:	155 (124.7)
Seq/Len:	0.871
Nf(neff/√len):	9.3

Jackhmmer Results: (2014_04_16)
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: 0.871).

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
77_N	80_E	2.637	0.99
71_S	106_S	2.241	0.97
66_L	109_Q	2.109	0.96
24_E	127_Q	2.028	0.95
90_L	156_F	1.914	0.92
126_M	140_A	1.847	0.90
120_N	144_A	1.776	0.88
70_W	104_E	1.735	0.86
42_Y	171_F	1.576	0.78
40_H	43_Y	1.570	0.78
70_W	101_F	1.566	0.77
52_Y	173_E	1.537	0.75
31_T	121_T	1.464	0.70
5_W	87_I	1.440	0.68
101_F	104_E	1.433	0.68
31_T	119_G	1.418	0.67
25_W	141_Y	1.359	0.62
79_K	85_Q	1.345	0.61
83_D	86_K	1.337	0.60
128_I	165_Y	1.329	0.59
84_D	88_K	1.319	0.58
122_Y	142_F	1.301	0.57
82_P	85_Q	1.301	0.57
3_D	179_Q	1.299	0.57
44_M	47_G	1.291	0.56
112_L	153_I	1.278	0.55
144_A	151_K	1.259	0.53
80_E	83_D	1.255	0.53
99_G	103_N	1.253	0.53
71_S	101_F	1.252	0.53
3_D	43_Y	1.246	0.52
71_S	103_N	1.245	0.52
21_G	115_P	1.241	0.52
115_P	129_R	1.238	0.51
70_W	102_G	1.236	0.51
103_N	106_S	1.220	0.50
46_A	66_L	1.218	0.50
62_E	174_N	1.215	0.49
44_M	156_F	1.212	0.49
79_K	84_D	1.206	0.48
112_L	172_L	1.192	0.47
4_Y	134_G	1.188	0.47
23_T	83_D	1.183	0.46
70_W	103_N	1.182	0.46
104_E	171_F	1.160	0.44
84_D	87_I	1.159	0.44
82_P	103_N	1.157	0.44
79_K	83_D	1.154	0.44
68_S	93_G	1.151	0.44
25_W	167_R	1.144	0.43
94_K	120_N	1.137	0.42
45_A	65_I	1.137	0.42
51_G	107_G	1.136	0.42
3_D	85_Q	1.127	0.41
101_F	116_W	1.121	0.41
63_R	116_W	1.114	0.40
66_L	111_Y	1.111	0.40
20_E	146_D	1.106	0.40
41_S	96_V	1.097	0.39
32_V	43_Y	1.096	0.39
135_N	157_L	1.091	0.38
18_L	149_E	1.090	0.38
47_G	150_W	1.084	0.38
137_T	160_K	1.083	0.38
87_I	90_L	1.078	0.37
36_G	154_A	1.072	0.37
16_Y	28_N	1.071	0.37
55_M	63_R	1.071	0.37
131_D	134_G	1.057	0.36
24_E	179_Q	1.055	0.35
88_K	133_N	1.052	0.35
15_G	18_L	1.052	0.35
68_S	119_G	1.050	0.35
26_F	168_P	1.049	0.35
3_D	6_G	1.046	0.35
4_Y	126_M	1.037	0.34
50_E	163_T	1.031	0.33
6_G	10_P	1.027	0.33
37_E	40_H	1.026	0.33
4_Y	161_T	1.024	0.33
52_Y	70_W	1.024	0.33
20_E	30_I	1.023	0.33
120_N	133_N	1.020	0.33
26_F	145_T	1.019	0.33
61_T	86_K	1.019	0.33
52_Y	56_Q	1.018	0.32
32_V	48_F	1.017	0.32
93_G	96_V	1.017	0.32
102_G	110_S	1.015	0.32
15_G	178_E	1.014	0.32
83_D	132_G	1.013	0.32
60_P	80_E	1.007	0.32
108_G	170_S	1.006	0.32
144_A	176_S	1.006	0.32
75_T	159_P	1.005	0.31
73_F	177_P	1.000	0.31

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: (05Jul14)
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
2bhuA	1	0.6464	5.9	0.962	Contact Map
1yo8A	1	0.7735	5.5	0.963	Contact Map
3vgfA	1	0.5856	3.7	0.966	Contact Map
2zwsA	1	0.326	3.2	0.967	Contact Map
3uzeC	2	0.0608	2.9	0.968	Contact Map
2eqjA	1	0.3646	2.8	0.968	Contact Map
2e5qA	1	0.3039	2.8	0.968	Contact Map
2czvC	2	0.6243	2.7	0.968	Contact Map
1as4B	1	0.1823	2.6	0.968	Contact Map
1m93C	1	0.1713	2	0.97	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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