OPENSEQ.org - 1384499927 - GREMLIN Submission

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new_trim_data

ID:	1384499927	Query Sequence MTFLKSITQEIAIVIVIFALFGLMFYLYHLPLEAYLLALGVILLLLLIFIGIKYLSFVKTISQQQQIENLENALYQLKNEQIEYKNDVESYFLTWVHQMKTPITAAQLMKLRLLWHIMRRQFITQRLVIIPFILAVSVLFMIEYTLVSIGLNSYIKQKNDFLVPFIIIANFFMALLTFIFIFYANHFMMSQRRKEFSIFMTLGMTKKSMRLIVVMETILQFIIISVVSIAGGYLLGAIFFLFIQKIMGSEVAT	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	253 (247)
Sequences:	399 (365.8)
Seq/Len:	1.615
Nf(neff/√len):	23.3

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: 1.615).

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
114_L	117_I	3.394	1.00
114_L	118_M	2.806	1.00
3_F	53_K	2.686	1.00
148_S	185_N	1.962	0.98
185_N	189_M	1.776	0.96
117_I	120_R	1.695	0.94
205_T	208_S	1.530	0.89
98_Q	136_V	1.523	0.89
132_F	217_T	1.510	0.88
136_V	177_T	1.504	0.88
132_F	240_F	1.494	0.87
202_L	206_K	1.440	0.85
135_A	180_F	1.437	0.84
77_L	80_E	1.412	0.83
41_V	49_F	1.396	0.82
117_I	135_A	1.360	0.80
135_A	188_M	1.354	0.79
201_T	205_T	1.348	0.79
152_N	180_F	1.343	0.78
37_L	41_V	1.336	0.78
7_I	53_K	1.334	0.78
140_F	227_V	1.328	0.77
180_F	237_A	1.324	0.77
3_F	6_S	1.308	0.76
134_L	175_L	1.302	0.75
109_M	116_H	1.300	0.75
187_F	199_F	1.298	0.75
63_Q	67_I	1.293	0.75
40_G	234_L	1.288	0.74
152_N	240_F	1.285	0.74
206_K	246_I	1.281	0.74
139_L	196_F	1.275	0.73
161_F	172_F	1.271	0.73
90_S	99_M	1.271	0.73
187_F	202_L	1.269	0.73
172_F	176_L	1.268	0.73
144_Y	148_S	1.267	0.73
41_V	90_S	1.266	0.72
113_L	196_F	1.260	0.72
109_M	118_M	1.257	0.72
63_Q	106_A	1.253	0.71
136_V	184_A	1.249	0.71
205_T	240_F	1.248	0.71
134_L	148_S	1.242	0.70
25_F	30_L	1.236	0.70
126_R	209_M	1.235	0.70
88_V	93_L	1.228	0.69
113_L	116_H	1.213	0.68
21_F	25_F	1.207	0.67
93_L	98_Q	1.205	0.67
98_Q	201_T	1.202	0.67
125_Q	237_A	1.197	0.66
14_V	42_I	1.195	0.66
91_Y	95_W	1.190	0.66
116_H	120_R	1.188	0.65
155_I	160_D	1.185	0.65
125_Q	180_F	1.183	0.65
54_Y	57_F	1.171	0.64
191_Q	213_V	1.170	0.64
233_Y	236_G	1.168	0.63
113_L	117_I	1.168	0.63
85_K	96_V	1.162	0.63
137_S	227_V	1.157	0.62
93_L	99_M	1.154	0.62
72_N	76_Q	1.144	0.61
40_G	48_I	1.143	0.61
35_Y	209_M	1.137	0.60
88_V	91_Y	1.135	0.60
176_L	184_A	1.132	0.60
93_L	180_F	1.132	0.60
48_I	52_I	1.120	0.59
135_A	173_M	1.119	0.59
149_I	229_I	1.116	0.58
52_I	222_I	1.108	0.57
24_M	246_I	1.107	0.57
114_L	120_R	1.105	0.57
33_E	80_E	1.104	0.57
93_L	108_L	1.103	0.57
11_I	66_Q	1.101	0.57
140_F	143_E	1.097	0.56
98_Q	131_P	1.091	0.56
75_Y	78_K	1.087	0.55
5_K	8_T	1.087	0.55
135_A	204_M	1.087	0.55
13_I	23_L	1.087	0.55
17_I	22_G	1.080	0.55
125_Q	195_E	1.080	0.55
139_L	246_I	1.079	0.54
18_F	67_I	1.073	0.54
99_M	103_I	1.071	0.54
96_V	134_L	1.068	0.53
37_L	40_G	1.057	0.52
103_I	223_I	1.056	0.52
37_L	176_L	1.050	0.51
37_L	53_K	1.047	0.51
205_T	214_V	1.045	0.51
84_Y	234_L	1.040	0.50
109_M	134_L	1.039	0.50
4_L	86_N	1.037	0.50
84_Y	197_S	1.034	0.50
80_E	226_V	1.032	0.49
145_T	239_F	1.031	0.49
188_M	239_F	1.028	0.49
192_R	195_E	1.028	0.49
73_A	76_Q	1.027	0.49
4_L	23_L	1.023	0.49
186_H	237_A	1.023	0.49
125_Q	149_I	1.020	0.48
200_M	205_T	1.017	0.48
4_L	11_I	1.016	0.48
4_L	50_I	1.016	0.48
207_K	226_V	1.014	0.48
114_L	176_L	1.013	0.47
90_S	105_A	1.012	0.47
43_L	186_H	1.012	0.47
146_L	188_M	1.012	0.47
112_R	116_H	1.010	0.47
38_A	42_I	1.002	0.46
135_A	141_M	1.001	0.46
48_I	51_G	1.000	0.46
129_I	146_L	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: (08Feb14)
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
3zccA	2	0.4348	47.1	0.951	Contact Map
2f95B	1	0.1502	23.8	0.958	Contact Map
3effK	4	0.3478	17.5	0.961	Contact Map
2c2aA	1	0.5929	13.3	0.963	Contact Map
1scfA	4	0	12.8	0.963	Contact Map
1mhsA	2	0.3676	10.4	0.965	Contact Map
3l1lA	1	0.2451	9.6	0.965	Contact Map
3giaA	1	0.2609	8.8	0.966	Contact Map
3pjsK	4	0.3478	8.8	0.966	Contact Map
4ew8A	2	0.5692	8	0.966	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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