OPENSEQ.org - 1403811297 - GREMLIN Submission

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T0833 -force run

ID:	1403811297	Query Sequence MKTSVWGKSILALVFTFMCSLAISAASPKDYLYDTKEENGKIISKVVFLQENGLLNKQVRYEFQYNENGKVSEKKAFRWDRTNDEWVPFYQITYQYDDQSGEIKTNYGMWDKKKKNFSLNVQNMIIPSTNYEEIFS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	136 (130)
Sequences:	88 (71.2)
Seq/Len:	0.677
Nf(neff/√len):	6.2

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: 0.677).

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
75_K	117_F	2.031	0.92
77_F	88_P	1.885	0.87
75_K	116_N	1.691	0.78
10_I	83_N	1.666	0.77
77_F	117_F	1.651	0.76
23_I	39_N	1.630	0.75
80_D	87_V	1.629	0.75
66_N	70_K	1.547	0.69
76_A	88_P	1.532	0.68
9_S	60_R	1.435	0.60
22_A	103_I	1.420	0.59
30_D	60_R	1.414	0.59
22_A	70_K	1.406	0.58
59_V	92_I	1.392	0.57
22_A	66_N	1.388	0.57
36_K	46_V	1.368	0.55
49_L	57_K	1.364	0.55
63_F	94_Y	1.343	0.53
39_N	53_G	1.317	0.51
11_L	106_N	1.291	0.49
31_Y	124_M	1.291	0.49
54_L	113_K	1.246	0.45
44_S	63_F	1.226	0.43
60_R	92_I	1.209	0.42
36_K	78_R	1.208	0.42
39_N	117_F	1.205	0.41
5_V	106_N	1.205	0.41
20_S	115_K	1.201	0.41
63_F	112_K	1.193	0.40
111_D	118_S	1.171	0.39
32_L	86_W	1.169	0.39
58_Q	108_G	1.162	0.38
64_Q	118_S	1.160	0.38
70_K	111_D	1.157	0.38
63_F	76_A	1.156	0.38
44_S	60_R	1.147	0.37
79_W	107_Y	1.132	0.36
74_K	126_I	1.129	0.35
105_T	124_M	1.123	0.35
108_G	124_M	1.116	0.34
14_V	20_S	1.114	0.34
63_F	89_F	1.107	0.34
58_Q	105_T	1.105	0.34
59_V	71_V	1.105	0.34
22_A	67_E	1.104	0.34
48_F	98_D	1.104	0.34
108_G	126_I	1.102	0.33
15_F	20_S	1.099	0.33
76_A	90_Y	1.098	0.33
43_I	86_W	1.096	0.33
58_Q	126_I	1.095	0.33
3_T	14_V	1.095	0.33
70_K	96_Y	1.086	0.32
11_L	93_T	1.081	0.32
49_L	58_Q	1.078	0.32
21_L	87_V	1.074	0.31
29_K	67_E	1.069	0.31
70_K	129_T	1.059	0.30
16_T	83_N	1.049	0.30
70_K	75_K	1.044	0.29
78_R	89_F	1.030	0.28
80_D	101_G	1.029	0.28
17_F	92_I	1.027	0.28
62_E	120_N	1.021	0.28
57_K	91_Q	1.018	0.27
104_K	117_F	1.012	0.27
62_E	88_P	1.003	0.26
53_G	85_E	1.000	0.26
46_V	78_R	1.000	0.26

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: (17Jul14)
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
3mswA	1	0.8088	100	0.281	Contact Map
4ghbA	2	0.5956	87.6	0.898	Contact Map
4iglB	2	0.7868	30.8	0.933	Contact Map
4o9xA	1	0.9338	19.5	0.939	Contact Map
4iglA	2	0.7279	8.8	0.948	Contact Map
4iwtA	2	0.375	3.8	0.956	Contact Map
1hcxA	2	0.375	2.9	0.958	Contact Map
2y69D	2	0.5588	2.7	0.959	Contact Map
1qleD	1	0.1691	2.7	0.959	Contact Map
1v54D	2	0.5588	2.6	0.959	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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