OPENSEQ.org - 1402885931 - GREMLIN Submission

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T0793_middle_domain

ID:	1402885931	Query Sequence YDLTPKGTFDNWFNMYIDEVKGHLLLELAVIFGISALVTSFLKHKHEIEFAGILFSFTGQSSTGKSTAAALAVSVAGNPTKGNETLFRSWNATRNALEGYLSNNYGIPIVFDELSSTTLRDTTGLLYSIAEGQGRQRSNVHGEVKTPKNWGTSVISTSEYSIFNDSAQNDGLRVRTIEINEQFTTNATNADNIKKAVALNYGHVLPLVAKYLINREDEVIQWFYKEVDWFEAKLKDETNNTGIRMFKRYAVITTSAKILGRVLSTDIDIANIRDYFIDYHTHTVSERSLADKAIDVIIQFVA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	302 (291)
Sequences:	407 (330.1)
Seq/Len:	1.399
Nf(neff/√len):	19.4

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: 1.399).

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
76_A	205_L	3.284	1.00
29_A	57_F	3.044	1.00
90_W	156_S	2.937	1.00
17_I	204_V	2.889	1.00
11_N	200_N	2.880	1.00
62_S	244_R	2.868	1.00
55_F	252_I	2.746	1.00
20_V	30_V	2.675	1.00
28_L	252_I	2.532	1.00
9_F	203_H	2.422	1.00
56_S	158_S	2.378	0.99
61_S	170_D	2.374	0.99
31_I	256_A	2.326	0.99
211_Y	262_V	2.317	0.99
200_N	203_H	2.313	0.99
96_A	136_Q	2.303	0.99
204_V	264_S	2.262	0.99
177_I	245_M	2.215	0.99
95_N	138_S	2.176	0.99
69_A	155_I	2.157	0.99
53_I	248_R	2.141	0.99
34_I	204_V	2.100	0.98
66_S	157_T	2.082	0.98
260_G	265_T	2.082	0.98
33_G	75_V	2.077	0.98
138_S	142_G	2.065	0.98
260_G	266_D	2.058	0.98
71_L	193_I	2.025	0.98
26_L	68_A	1.925	0.97
73_V	110_V	1.898	0.97
159_E	171_G	1.886	0.96
9_F	207_L	1.865	0.96
257_K	270_A	1.813	0.95
95_N	137_R	1.802	0.95
91_N	135_R	1.780	0.95
25_L	279_Y	1.755	0.94
106_G	151_G	1.731	0.93
69_A	157_T	1.729	0.93
11_N	203_H	1.692	0.92
70_A	194_K	1.683	0.92
98_E	134_G	1.678	0.92
9_F	204_V	1.667	0.92
207_L	210_K	1.612	0.90
110_V	157_T	1.607	0.90
115_S	169_N	1.607	0.90
30_V	34_I	1.578	0.88
127_Y	159_E	1.560	0.88
101_L	109_I	1.548	0.87
209_A	213_I	1.532	0.86
183_F	192_N	1.515	0.86
57_F	155_I	1.512	0.85
15_M	200_N	1.471	0.83
56_S	156_S	1.452	0.82
56_S	113_E	1.447	0.82
10_D	13_F	1.444	0.82
52_G	116_S	1.392	0.78
95_N	99_G	1.386	0.78
98_E	137_R	1.380	0.77
170_D	241_T	1.309	0.72
195_K	224_Y	1.243	0.66
34_I	208_V	1.241	0.66
215_R	262_V	1.236	0.66
206_P	213_I	1.235	0.65
94_R	121_D	1.229	0.65
12_W	204_V	1.226	0.65
206_P	209_A	1.224	0.64
53_I	153_S	1.218	0.64
30_V	204_V	1.215	0.64
55_F	177_I	1.214	0.63
61_S	190_A	1.213	0.63
230_F	254_T	1.206	0.63
127_Y	171_G	1.193	0.62
66_S	70_A	1.184	0.61
92_A	97_L	1.182	0.60
69_A	110_V	1.169	0.59
52_G	152_T	1.158	0.58
69_A	92_A	1.151	0.57
111_F	209_A	1.150	0.57
208_V	211_Y	1.130	0.55
51_A	244_R	1.128	0.55
170_D	289_L	1.128	0.55
19_E	183_F	1.122	0.54
36_A	108_P	1.122	0.54
19_E	192_N	1.117	0.54
25_L	53_I	1.110	0.53
241_T	289_L	1.100	0.52
251_V	257_K	1.091	0.51
117_T	122_T	1.087	0.51
42_L	251_V	1.086	0.51
28_L	128_S	1.078	0.50
25_L	181_E	1.074	0.50
203_H	206_P	1.069	0.49
23_H	131_E	1.067	0.49
138_S	143_E	1.065	0.49
223_F	254_T	1.064	0.49
138_S	144_V	1.060	0.48
98_E	256_A	1.058	0.48
128_S	157_T	1.058	0.48
116_S	280_H	1.055	0.48
140_V	144_V	1.055	0.48
62_S	190_A	1.055	0.48
79_P	265_T	1.053	0.48
129_I	154_V	1.052	0.47
203_H	207_L	1.049	0.47
99_G	138_S	1.049	0.47
169_N	190_A	1.041	0.46
77_G	158_S	1.032	0.45
61_S	241_T	1.026	0.45
9_F	13_F	1.023	0.44
186_N	190_A	1.021	0.44
191_D	212_L	1.018	0.44
271_N	285_S	1.016	0.44
51_A	62_S	1.015	0.44
69_A	137_R	1.010	0.43
191_D	194_K	1.008	0.43
14_N	18_D	1.008	0.43
36_A	152_T	1.006	0.43
114_L	122_T	1.003	0.42

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: (07Jun14)
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
1ofhA	3	0.9139	97.4	0.907	Contact Map
3vfdA	1	0.755	97.3	0.909	Contact Map
4b4tJ	1	0.8046	97.3	0.909	Contact Map
1r6bX	1	0.8311	97.3	0.91	Contact Map
2r44A	1	0.9205	97.3	0.91	Contact Map
3sylA	2	0.8444	97.2	0.91	Contact Map
3pvsA	4	0.7815	97.2	0.911	Contact Map
3hwsA	6	0.8874	97.1	0.911	Contact Map
3nbxX	1	0.8742	97.1	0.912	Contact Map
3bosA	2	0.7185	97	0.912	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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