OPENSEQ.org - 1428411019 - GREMLIN Submission

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HET-S1-227 -force run

ID:	1428411019	Query Sequence MSEPFEIVAGALGVAGLFNNCVACFEYVQLGRHFGRDYERCQLRLDIAKVRLSRWGEAVQINDDPRFHSSAPIDKSVQLAKSIVEEILLLFESAQKTSKRYELVADQQDLVVFEDKDMKPIGRALHRRLKDLVSRRQKQTSLAKKTAWALYDGKSLEKIVDQVAGFVDELEKAFPIEAVCHKLAENEIEEVEDEASLTILKDAAGGIDAAMSDAAAQKIDAIVGRNSAKDIRTEK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	235 (228)
Sequences:	107 (97.3)
Seq/Len:	0.469
Nf(neff/√len):	6.4

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: 0.469).

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
3_E	10_G	2.360	0.94
13_G	16_G	2.173	0.90
101_Y	152_D	2.133	0.89
54_R	208_D	1.687	0.68
10_G	21_C	1.623	0.63
4_P	44_R	1.599	0.62
80_A	174_F	1.598	0.62
45_L	163_V	1.558	0.59
3_E	6_E	1.533	0.57
54_R	151_Y	1.516	0.56
148_W	152_D	1.472	0.52
52_L	91_F	1.446	0.50
33_H	169_E	1.427	0.49
87_I	169_E	1.414	0.48
44_R	173_A	1.405	0.47
31_G	213_D	1.384	0.46
27_Y	80_A	1.377	0.45
51_R	171_E	1.366	0.44
58_A	91_F	1.361	0.44
225_R	228_A	1.351	0.43
169_E	215_A	1.347	0.43
92_E	160_V	1.320	0.41
13_G	52_L	1.310	0.40
87_I	118_M	1.307	0.40
48_A	54_R	1.294	0.39
21_C	101_Y	1.292	0.39
47_I	83_I	1.291	0.39
34_F	54_R	1.290	0.39
25_F	32_R	1.284	0.38
16_G	187_E	1.284	0.38
22_V	25_F	1.282	0.38
36_R	39_E	1.272	0.37
110_L	123_R	1.270	0.37
24_C	31_G	1.255	0.36
18_F	27_Y	1.239	0.35
111_V	206_G	1.235	0.35
100_R	215_A	1.234	0.35
41_C	48_A	1.219	0.34
24_C	142_L	1.215	0.33
48_A	149_A	1.213	0.33
34_F	43_L	1.213	0.33
16_G	28_V	1.211	0.33
51_R	168_D	1.208	0.33
93_S	150_L	1.205	0.33
152_D	193_D	1.197	0.32
95_Q	214_A	1.190	0.32
80_A	163_V	1.188	0.32
152_D	197_L	1.187	0.32
25_F	35_G	1.187	0.32
69_S	156_L	1.185	0.31
27_Y	98_S	1.181	0.31
151_Y	208_D	1.178	0.31
64_D	191_V	1.168	0.30
124_A	141_S	1.168	0.30
89_L	160_V	1.165	0.30
24_C	48_A	1.163	0.30
56_G	91_F	1.163	0.30
48_A	167_V	1.157	0.30
173_A	188_I	1.153	0.29
87_I	200_L	1.144	0.29
66_R	72_P	1.140	0.29
29_Q	32_R	1.140	0.29
90_L	159_I	1.131	0.28
61_I	150_L	1.124	0.28
3_E	21_C	1.120	0.27
101_Y	148_W	1.119	0.27
44_R	84_V	1.115	0.27
17_L	122_G	1.112	0.27
31_G	176_I	1.110	0.27
188_I	196_S	1.110	0.27
25_F	58_A	1.104	0.26
18_F	37_D	1.104	0.26
220_D	223_V	1.104	0.26
21_C	193_D	1.103	0.26
153_G	182_K	1.103	0.26
4_P	78_Q	1.098	0.26
73_I	111_V	1.096	0.26
25_F	163_V	1.095	0.26
91_F	129_L	1.091	0.26
80_A	176_I	1.090	0.26
149_A	186_N	1.089	0.25
17_L	89_L	1.089	0.25
39_E	200_L	1.082	0.25
221_A	227_S	1.081	0.25
163_V	190_E	1.078	0.25
9_A	194_E	1.074	0.25
27_Y	48_A	1.071	0.24
54_R	187_E	1.068	0.24
127_R	156_L	1.068	0.24
92_E	181_H	1.067	0.24
183_L	191_V	1.066	0.24
51_R	91_F	1.066	0.24
156_L	212_S	1.065	0.24
158_K	162_Q	1.065	0.24
60_Q	204_A	1.064	0.24
48_A	98_S	1.060	0.24
13_G	140_T	1.046	0.23
32_R	42_Q	1.043	0.23
52_L	56_G	1.042	0.23
12_L	133_V	1.040	0.23
100_R	206_G	1.039	0.23
41_C	150_L	1.038	0.23
5_F	8_V	1.036	0.23
37_D	148_W	1.036	0.23
12_L	195_A	1.034	0.22
144_K	162_Q	1.033	0.22
26_E	165_G	1.032	0.22
2_S	185_E	1.028	0.22
82_S	92_E	1.027	0.22
23_A	185_E	1.024	0.22
47_I	59_V	1.024	0.22
21_C	74_D	1.019	0.22
48_A	80_A	1.015	0.21
103_L	155_S	1.014	0.21
156_L	166_F	1.014	0.21
215_A	222_I	1.014	0.21
1_M	6_E	1.012	0.21
118_M	154_K	1.007	0.21
1_M	214_A	1.006	0.21
25_F	104_V	1.006	0.21
32_R	35_G	1.004	0.21
151_Y	163_V	1.003	0.21
32_R	38_Y	1.003	0.21
6_E	159_I	1.001	0.21
12_L	146_T	1.001	0.21
59_V	94_A	1.000	0.21

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
2wvqA	2	0.9064	100	0.32	Contact Map
4btfA	1	0.6383	27.5	0.953	Contact Map
2msvA	1	0.583	22.5	0.955	Contact Map
4ogqG	1	0.1404	15.6	0.958	Contact Map
1q90G	1	0.1106	15	0.958	Contact Map
4lnjA	2	0.6638	13.7	0.959	Contact Map
4kk2A	2	0.4809	10.1	0.961	Contact Map
3oyrA	2	0.5064	9.8	0.962	Contact Map
3lfjA	2	0.4936	9.7	0.962	Contact Map
3aqbB	2	0.5234	7.9	0.963	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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