OPENSEQ.org - 1415881667 - GREMLIN Submission

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PR

ID:	1415881667	Query Sequence MKLLLILGSVIALPTFAAGGGDLDASDYTGVSFWLVTAALLASTVFFFVERDRVSAKWKTSLTVSGLVTGIAFWHYMYMRGVWIETGDSPTVFRYIDWLLTVPLLICEFYLILAAATNVAGSLFKKLLVGSLVMLVFGYMGEAGIMAAWPAFIIGCLAWVYMIYELWAGEGKSACNTASPAVQSAYNTMMYIIIFGWAIYPVGYFTGYLMGDGGSALNLNLIYNLADFVNKILFGLIIWNVAVKESSNA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	249 (227)
Sequences:	361 (281.9)
Seq/Len:	1.590
Nf(neff/√len):	18.7

HHblits Results: (2013_03)
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: 1.590).

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
71_I	100_L	4.622	1.00
34_W	80_R	2.509	1.00
39_A	228_F	2.354	1.00
97_D	231_K	2.322	1.00
102_V	131_S	1.936	0.98
101_T	104_L	1.845	0.97
216_A	220_N	1.817	0.96
47_F	235_G	1.668	0.93
75_H	79_M	1.667	0.93
78_Y	151_A	1.660	0.93
97_D	101_T	1.638	0.92
44_T	69_T	1.616	0.92
72_A	97_D	1.530	0.89
131_S	135_L	1.529	0.89
137_F	230_N	1.502	0.87
141_G	204_Y	1.474	0.86
39_A	232_I	1.456	0.85
83_W	92_V	1.440	0.84
197_W	231_K	1.428	0.84
68_V	75_H	1.421	0.83
64_V	104_L	1.396	0.82
134_M	138_G	1.395	0.82
216_A	219_L	1.370	0.80
73_F	123_L	1.361	0.79
217_L	220_N	1.357	0.79
148_A	153_I	1.329	0.77
48_F	66_G	1.325	0.77
204_Y	211_G	1.314	0.76
72_A	166_L	1.308	0.75
75_H	142_E	1.304	0.75
65_S	162_M	1.288	0.74
138_G	231_K	1.281	0.73
36_V	73_F	1.278	0.73
65_S	235_G	1.271	0.72
104_L	141_G	1.270	0.72
204_Y	226_A	1.269	0.72
160_V	191_Y	1.264	0.72
133_V	158_A	1.260	0.71
131_S	134_M	1.257	0.71
65_S	108_E	1.256	0.71
72_A	102_V	1.254	0.71
101_T	231_K	1.247	0.70
45_V	48_F	1.246	0.70
72_A	105_L	1.241	0.70
102_V	231_K	1.237	0.69
37_T	77_M	1.220	0.68
41_L	70_G	1.220	0.68
152_F	162_M	1.218	0.68
22_D	36_V	1.205	0.67
40_L	138_G	1.202	0.66
207_G	222_I	1.200	0.66
47_F	65_S	1.198	0.66
34_W	37_T	1.195	0.66
138_G	234_F	1.180	0.64
210_M	219_L	1.172	0.63
102_V	134_M	1.167	0.63
199_I	206_T	1.161	0.62
42_A	228_F	1.161	0.62
45_V	61_S	1.160	0.62
97_D	102_V	1.159	0.62
95_Y	234_F	1.156	0.62
140_M	202_V	1.154	0.62
68_V	101_T	1.154	0.62
72_A	231_K	1.150	0.61
69_T	235_G	1.147	0.61
91_T	142_E	1.137	0.60
36_V	228_F	1.136	0.60
215_S	220_N	1.131	0.59
72_A	197_W	1.131	0.59
83_W	192_I	1.128	0.59
41_L	73_F	1.124	0.59
72_A	101_T	1.120	0.58
33_F	220_N	1.118	0.58
142_E	204_Y	1.117	0.58
205_F	212_D	1.101	0.56
101_T	131_S	1.101	0.56
159_W	162_M	1.100	0.56
22_D	25_A	1.100	0.56
104_L	127_L	1.096	0.56
68_V	104_L	1.093	0.55
72_A	134_M	1.092	0.55
215_S	218_N	1.091	0.55
40_L	72_A	1.086	0.55
101_T	138_G	1.085	0.55
135_L	231_K	1.082	0.54
106_I	143_A	1.081	0.54
154_I	206_T	1.069	0.53
45_V	70_G	1.069	0.53
97_D	104_L	1.066	0.53
231_K	235_G	1.059	0.52
80_R	224_N	1.058	0.52
43_S	232_I	1.056	0.52
26_S	217_L	1.054	0.51
43_S	236_L	1.053	0.51
209_L	247_S	1.051	0.51
100_L	122_S	1.047	0.51
44_T	156_C	1.046	0.50
68_V	189_M	1.043	0.50
77_M	81_G	1.040	0.50
101_T	230_N	1.038	0.50
99_L	132_L	1.037	0.50
182_V	194_I	1.036	0.49
106_I	115_A	1.033	0.49
134_M	137_F	1.032	0.49
36_V	132_L	1.031	0.49
189_M	233_L	1.031	0.49
36_V	39_A	1.026	0.48
206_T	222_I	1.021	0.48
105_L	156_C	1.015	0.47
72_A	104_L	1.010	0.47
196_G	229_V	1.009	0.47
36_V	40_L	1.006	0.46
154_I	210_M	1.005	0.46
97_D	230_N	1.001	0.46
241_V	245_E	1.000	0.46

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: (06Sep14)
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
4knfA	5	0.9197	100	0.157	Contact Map
4jq6A	3	0.8273	100	0.238	Contact Map
3ddlA	2	0.9157	100	0.26	Contact Map
3am6A	4	0.8715	100	0.27	Contact Map
2ei4A	1	0.9036	100	0.279	Contact Map
1m0kA	1	0.8434	100	0.279	Contact Map
1xioA	1	0.8514	100	0.283	Contact Map
3qapA	1	0.8594	100	0.284	Contact Map
4l35A	1	0.8876	100	0.294	Contact Map
4fbzA	1	0.8916	100	0.295	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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