OPENSEQ.org - 1405035023 - GREMLIN Submission

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T0808 150-329 -force run

ID:	1405035023	Query Sequence FSDYWGRRGPSVHLGYALPEGDTEWFYNEITVPKEGETMHSYYMAAGFGEGYFGMQYNSPTERRILFSVWSPFDTQNPKEIPDDQKIKLLRQGKDVHIGEFGNEGSGGQSYLKYPWKAGNTYKFLMQIRPDGNGNTTYTAYFYATDEKEWKLIASFLRPKTNTWYKRPHSFLENFSPEQG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	180 (178)
Sequences:	156 (126.1)
Seq/Len:	0.876
Nf(neff/√len):	9.5

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: 0.876).

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	2.646	0.99
71_S	106_S	2.161	0.97
66_L	109_Q	2.088	0.96
24_E	127_Q	2.049	0.95
90_L	156_F	1.979	0.94
126_M	140_A	1.766	0.88
120_N	144_A	1.747	0.87
42_Y	171_F	1.727	0.86
70_W	104_E	1.684	0.84
52_Y	173_E	1.632	0.81
70_W	101_F	1.563	0.77
3_D	179_Q	1.530	0.75
25_W	141_Y	1.504	0.73
5_W	87_I	1.462	0.70
83_D	86_K	1.434	0.68
40_H	43_Y	1.418	0.67
101_F	104_E	1.376	0.64
112_L	172_L	1.359	0.62
144_A	151_K	1.341	0.61
31_T	121_T	1.337	0.60
31_T	119_G	1.331	0.60
128_I	165_Y	1.330	0.60
79_K	85_Q	1.322	0.59
79_K	84_D	1.311	0.58
99_G	103_N	1.301	0.57
71_S	103_N	1.299	0.57
71_S	101_F	1.290	0.56
44_M	47_G	1.281	0.55
82_P	85_Q	1.271	0.54
122_Y	142_F	1.247	0.52
4_Y	134_G	1.226	0.50
44_M	156_F	1.224	0.50
3_D	43_Y	1.207	0.49
115_P	129_R	1.204	0.48
55_M	63_R	1.203	0.48
103_N	106_S	1.201	0.48
101_F	116_W	1.200	0.48
25_W	167_R	1.195	0.48
84_D	88_K	1.189	0.47
61_T	86_K	1.181	0.46
3_D	6_G	1.180	0.46
80_E	83_D	1.166	0.45
21_G	115_P	1.163	0.45
68_S	93_G	1.159	0.44
51_G	107_G	1.144	0.43
43_Y	76_Q	1.143	0.43
81_I	84_D	1.143	0.43
3_D	85_Q	1.141	0.43
41_S	96_V	1.141	0.43
40_H	51_G	1.136	0.42
79_K	83_D	1.134	0.42
82_P	103_N	1.133	0.42
70_W	102_G	1.133	0.42
23_T	83_D	1.128	0.42
6_G	81_I	1.127	0.42
70_W	103_N	1.116	0.41
37_E	40_H	1.110	0.40
112_L	153_I	1.110	0.40
131_D	134_G	1.106	0.40
24_E	179_Q	1.105	0.40
68_S	119_G	1.095	0.39
16_Y	28_N	1.083	0.38
26_F	168_P	1.081	0.38
63_R	116_W	1.078	0.37
137_T	160_K	1.072	0.37
18_L	149_E	1.071	0.37
94_K	120_N	1.068	0.37
87_I	90_L	1.064	0.36
85_Q	179_Q	1.056	0.36
36_G	154_A	1.052	0.35
46_A	66_L	1.048	0.35
15_G	167_R	1.046	0.35
62_E	174_N	1.043	0.35
49_G	131_D	1.037	0.34
135_N	157_L	1.034	0.34
66_L	111_Y	1.033	0.34
21_G	179_Q	1.030	0.34
91_R	98_I	1.030	0.34
3_D	36_G	1.027	0.33
70_W	116_W	1.026	0.33
52_Y	56_Q	1.020	0.33
49_G	132_G	1.020	0.33
4_Y	161_T	1.019	0.33
52_Y	70_W	1.019	0.33
84_D	87_I	1.017	0.32
47_G	50_E	1.015	0.32
35_E	57_Y	1.014	0.32
50_E	163_T	1.012	0.32
47_G	150_W	1.012	0.32
24_E	136_T	1.010	0.32
75_T	159_P	1.008	0.32
93_G	96_V	1.006	0.32
104_E	171_F	1.004	0.31
26_F	145_T	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
1yo8A	1	0.7778	8.6	0.959	Contact Map
3vgfA	1	0.5889	8.1	0.96	Contact Map
2bhuA	1	0.6611	4.7	0.964	Contact Map
2zwsA	1	0.3278	3	0.967	Contact Map
2eqjA	1	0.3667	2.5	0.968	Contact Map
1as4B	1	0.1833	2.5	0.968	Contact Map
2e5qA	1	0.3056	2.5	0.968	Contact Map
3uzeC	2	0.0611	2.5	0.969	Contact Map
2czvC	2	0.6278	2.3	0.969	Contact Map
1m93C	1	0.1722	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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