OPENSEQ.org - 1492603654 - GREMLIN Submission

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2yq9 -force run

ID:	1492603654	Query Sequence GGLEKDFLPLYFGWFLTKKSSETLRKAGQVFLEELGNHKAFKKELRHFISGDEPKEKLELVSYFGKRPPGVLHCTTKFCDYGKAAGAEEYAQQEVVKRSYGKAFKLSISALFVTPKTAGAQVVLTDQELQLWPSDLDKPSASEGLPPGSRAHVTLGCAADVQPAQTGLDLLDILQQVKGGSQGEAVGELPRGKLYSLGKGRWMLSLTKKMEVKAIFTGYYG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	221 (220)
Sequences:	57 (37.9)
Seq/Len:	0.259
Nf(neff/√len):	2.6

HHblits Results: (2016_02)
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: 0.259).

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
21_S	177_V	1.803	0.57
150_R	164_A	1.757	0.54
84_A	87_A	1.727	0.52
208_K	218_G	1.709	0.51
106_L	117_T	1.606	0.45
114_T	151_A	1.569	0.42
98_R	160_D	1.567	0.42
96_V	101_G	1.566	0.42
48_F	89_E	1.554	0.41
114_T	117_T	1.516	0.39
98_R	101_G	1.514	0.39
164_A	167_G	1.476	0.36
60_L	86_G	1.476	0.36
150_R	167_G	1.464	0.36
113_V	173_I	1.431	0.34
119_G	166_T	1.429	0.34
173_I	201_R	1.411	0.33
116_K	197_L	1.391	0.32
127_Q	137_D	1.375	0.31
85_A	113_V	1.362	0.30
80_D	84_A	1.356	0.30
18_K	69_P	1.355	0.30
122_V	131_L	1.334	0.28
4_E	112_F	1.326	0.28
5_K	219_Y	1.311	0.27
31_F	111_L	1.292	0.26
50_S	125_T	1.287	0.26
106_L	120_A	1.286	0.26
174_L	182_Q	1.282	0.26
114_T	124_L	1.269	0.25
124_L	132_W	1.268	0.25
117_T	132_W	1.255	0.24
153_V	214_A	1.254	0.24
138_K	145_L	1.246	0.24
106_L	124_L	1.239	0.24
122_V	153_V	1.234	0.23
38_H	196_S	1.230	0.23
12_F	206_L	1.228	0.23
72_L	106_L	1.223	0.23
142_S	160_D	1.218	0.23
95_V	99_S	1.216	0.23
148_G	152_H	1.206	0.22
125_T	128_E	1.198	0.22
132_W	167_G	1.190	0.21
91_A	214_A	1.187	0.21
76_T	204_L	1.185	0.21
64_F	69_P	1.179	0.21
21_S	54_P	1.170	0.21
118_A	125_T	1.165	0.20
75_T	90_Y	1.163	0.20
159_A	213_K	1.154	0.20
114_T	132_W	1.152	0.20
40_A	45_L	1.152	0.20
38_H	136_L	1.149	0.20
82_G	155_L	1.145	0.20
29_Q	54_P	1.145	0.20
79_C	122_V	1.141	0.19
84_A	97_K	1.135	0.19
135_D	150_R	1.128	0.19
41_F	202_W	1.126	0.19
2_G	197_L	1.124	0.19
42_K	156_G	1.122	0.19
70_G	186_V	1.120	0.19
117_T	154_T	1.110	0.18
44_E	208_K	1.107	0.18
106_L	132_W	1.101	0.18
16_L	32_L	1.100	0.18
115_P	132_W	1.096	0.18
126_D	131_L	1.092	0.18
36_G	174_L	1.088	0.17
116_K	132_W	1.088	0.17
60_L	192_G	1.084	0.17
213_K	219_Y	1.082	0.17
122_V	146_P	1.076	0.17
117_T	124_L	1.076	0.17
117_T	151_A	1.071	0.17
54_P	178_K	1.070	0.17
129_L	149_S	1.064	0.16
157_C	194_L	1.063	0.16
141_A	168_L	1.062	0.16
197_L	201_R	1.060	0.16
75_T	148_G	1.060	0.16
75_T	152_H	1.060	0.16
106_L	149_S	1.057	0.16
18_K	187_G	1.057	0.16
10_L	115_P	1.057	0.16
133_P	165_Q	1.057	0.16
104_F	121_Q	1.054	0.16
57_K	69_P	1.053	0.16
121_Q	135_D	1.050	0.16
60_L	82_G	1.045	0.16
72_L	149_S	1.045	0.16
166_T	169_D	1.044	0.16
157_C	198_G	1.043	0.16
153_V	212_V	1.042	0.16
85_A	88_E	1.039	0.16
164_A	200_G	1.037	0.16
150_R	166_T	1.034	0.15
157_C	166_T	1.032	0.15
127_Q	139_P	1.030	0.15
157_C	162_Q	1.027	0.15
117_T	158_A	1.026	0.15
6_D	199_K	1.025	0.15
138_K	156_G	1.024	0.15
102_K	108_I	1.023	0.15
129_L	154_T	1.021	0.15
96_V	160_D	1.019	0.15
64_F	82_G	1.017	0.15
116_K	167_G	1.015	0.15
172_D	200_G	1.014	0.15
21_S	195_Y	1.011	0.15
148_G	169_D	1.010	0.15
152_H	169_D	1.010	0.15
193_K	209_K	1.009	0.15
8_L	87_A	1.009	0.15
39_K	218_G	1.008	0.15
114_T	149_S	1.004	0.14
104_F	135_D	1.002	0.14

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: (06Aug15)
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
2xmiA	1	0.9774	100	0.01	Contact Map
2i3eA	1	0.9683	100	0.054	Contact Map
4jjaA	1	0.2489	54	0.961	Contact Map
4h7wA	1	0.7511	26.4	0.967	Contact Map
2pnwA	1	0.4027	24.8	0.967	Contact Map
4k05A	2	0.267	19.7	0.969	Contact Map
1vgjA	1	0.7692	9.3	0.973	Contact Map
3w8kA	1	0.267	9	0.973	Contact Map
4ohnA	1	0.2489	5.8	0.975	Contact Map
4lxcA	4	0.3484	5.6	0.976	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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