OPENSEQ.org - 1429766051 - GREMLIN Submission

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TASK1 CTD deletion

ID:	1429766051	Query Sequence MKRQNVRTLALIVCTFTYLLVGAAVFDALESEPEMIERQRLELRQLELRARYNLSEGGYEELERVVLRLKPHKAGVQWRFAGSFYFAITVITTIGYGHAAPSTDGGKVFCMFYALLGIPLTLVMFQSLGERINTFVRYLLHRAKRGLGMRHAEVSMANMVLIGFVSCISTLCIGAAAFSYYERWTFFQAYYYCFITLTTIGFGDYVALQKDQALQTQPQYVAFSFVYILTGLTVIGAFLNLVVL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	244 (241)
Sequences:	551 (363.3)
Seq/Len:	2.286
Nf(neff/√len):	23.4

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: 2.286).

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
86_F	110_C	3.049	1.00
107_K	188_Q	2.918	1.00
174_G	227_Y	2.164	1.00
90_V	202_F	2.158	1.00
191_Y	204_D	2.097	1.00
201_G	204_D	1.912	0.99
25_V	109_F	1.864	0.99
196_T	202_F	1.821	0.98
188_Q	205_Y	1.764	0.98
18_Y	22_G	1.646	0.96
184_W	199_T	1.598	0.95
29_L	109_F	1.589	0.95
187_F	197_L	1.583	0.95
227_Y	234_V	1.568	0.95
103_T	106_G	1.563	0.95
105_G	109_F	1.560	0.95
18_Y	23_A	1.504	0.93
22_G	26_F	1.500	0.93
191_Y	203_G	1.489	0.93
86_F	101_P	1.473	0.92
170_T	174_G	1.472	0.92
235_I	239_L	1.466	0.92
97_G	204_D	1.453	0.91
164_F	172_C	1.447	0.91
90_V	200_I	1.418	0.90
19_L	91_I	1.395	0.89
87_A	178_F	1.388	0.89
86_F	115_L	1.374	0.88
196_T	228_I	1.374	0.88
185_T	188_Q	1.371	0.88
199_T	203_G	1.365	0.87
225_F	239_L	1.352	0.87
227_Y	235_I	1.309	0.84
199_T	204_D	1.307	0.84
195_I	199_T	1.303	0.84
112_F	196_T	1.296	0.84
178_F	197_L	1.294	0.83
123_V	228_I	1.274	0.82
61_E	200_I	1.270	0.82
191_Y	195_I	1.259	0.81
89_T	94_I	1.255	0.81
182_E	201_G	1.251	0.80
23_A	84_F	1.248	0.80
30_E	78_W	1.243	0.80
18_Y	26_F	1.240	0.80
107_K	193_C	1.237	0.79
174_G	234_V	1.229	0.79
227_Y	236_G	1.228	0.79
184_W	201_G	1.214	0.78
119_P	232_L	1.208	0.77
91_I	167_C	1.183	0.75
234_V	237_A	1.180	0.75
71_P	143_A	1.179	0.75
124_M	236_G	1.173	0.74
23_A	113_Y	1.173	0.74
100_A	113_Y	1.169	0.74
90_V	128_L	1.167	0.74
125_F	197_L	1.164	0.73
98_H	197_L	1.162	0.73
2_K	6_V	1.153	0.72
123_V	133_N	1.152	0.72
124_M	239_L	1.152	0.72
174_G	224_S	1.149	0.72
100_A	188_Q	1.148	0.72
34_E	89_T	1.147	0.72
108_V	128_L	1.140	0.71
121_T	186_F	1.137	0.71
18_Y	78_W	1.132	0.70
45_Q	49_R	1.130	0.70
196_T	201_G	1.128	0.70
114_A	119_P	1.126	0.70
49_R	52_Y	1.123	0.70
99_A	191_Y	1.119	0.69
236_G	239_L	1.118	0.69
34_E	90_V	1.113	0.69
4_Q	8_T	1.110	0.68
111_M	187_F	1.109	0.68
207_A	227_Y	1.104	0.68
79_R	174_G	1.098	0.67
5_N	8_T	1.097	0.67
83_S	190_Y	1.096	0.67
184_W	202_F	1.088	0.66
77_Q	174_G	1.081	0.65
121_T	194_F	1.079	0.65
9_L	223_F	1.074	0.65
23_A	131_R	1.072	0.64
84_F	236_G	1.071	0.64
96_Y	129_G	1.068	0.64
124_M	127_S	1.067	0.64
221_V	234_V	1.066	0.64
92_T	114_A	1.065	0.64
33_P	46_L	1.063	0.63
100_A	175_A	1.060	0.63
151_H	165_V	1.060	0.63
175_A	193_C	1.058	0.63
83_S	193_C	1.057	0.63
127_S	197_L	1.054	0.62
96_Y	119_P	1.054	0.62
94_I	202_F	1.052	0.62
196_T	207_A	1.052	0.62
88_I	227_Y	1.050	0.62
103_T	129_G	1.047	0.62
149_M	164_F	1.038	0.61
22_G	30_E	1.037	0.60
26_F	30_E	1.036	0.60
89_T	126_Q	1.033	0.60
59_Y	63_E	1.031	0.60
85_Y	125_F	1.028	0.59
168_I	173_I	1.027	0.59
108_V	228_I	1.026	0.59
124_M	187_F	1.025	0.59
11_L	202_F	1.023	0.59
77_Q	87_A	1.021	0.59
119_P	197_L	1.020	0.59
121_T	187_F	1.019	0.58
26_F	113_Y	1.018	0.58
65_V	68_R	1.015	0.58
236_G	240_N	1.015	0.58
25_V	28_A	1.013	0.58
25_V	172_C	1.010	0.57
113_Y	200_I	1.010	0.57
110_C	195_I	1.008	0.57
80_F	200_I	1.006	0.57
191_Y	201_G	1.005	0.57

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: (31Jan15)
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
4bw5A	4	0.9713	100	0.337	Contact Map
4twkA	2	0.959	100	0.341	Contact Map
3ukmA	4	0.9467	100	0.349	Contact Map
4wfeA	2	0.9713	100	0.35	Contact Map
3pjsK	4	0.5615	99.6	0.777	Contact Map
2k1eA	4	0.4139	99.6	0.779	Contact Map
2a9hA	4	0.3934	99.6	0.78	Contact Map
3effK	4	0.4877	99.6	0.781	Contact Map
2ih3C	1	0.3975	99.6	0.785	Contact Map
3vouA	2	0.4303	99.5	0.793	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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