OPENSEQ.org - 1453737364 - GREMLIN Submission

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2xih

ID:	1453737364	Query Sequence GKSYPTVSADYQKAVEKAKKKLRGFIAEKRCAPLMLRLAWHSAGTFDKGTKTGGPFGTIKHPAELAHSANNGLDIAVRLLEPLKAEFPILSYADFYQLAGVVAVEVTGGPEVPFHPGREDKPEPPPEGRLPDATKGSDHLRDVFGKAMGLTDQDIVALSGGHTIGAAHKERSGFEGPWTSNPLIFDNSYFTELLSGEKEGLLQLPSDKALLSDPVFRPLVDKYAADEDAFFADYAEAHQKLSELGFADA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	249 (236)
Sequences:	4621 (1759.6)
Seq/Len:	19.581
Nf(neff/√len):	114.5

HHblits Results: (2015_06)
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: 19.581).

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
223_Y	233_D	3.654	1.00
62_P	66_A	3.288	1.00
23_R	102_V	3.073	1.00
37_R	41_H	2.862	1.00
217_R	221_D	2.810	1.00
115_H	243_E	2.635	1.00
62_P	65_L	2.573	1.00
59_I	73_L	2.507	1.00
149_G	244_L	2.494	1.00
21_K	86_E	2.410	1.00
34_L	75_I	2.281	1.00
175_E	204_L	2.253	1.00
222_K	229_A	2.148	1.00
239_Q	243_E	2.119	1.00
227_E	231_F	2.105	1.00
48_K	149_G	2.033	1.00
154_D	240_K	2.024	1.00
60_K	81_E	2.020	1.00
123_E	128_G	1.984	1.00
141_R	152_D	1.982	1.00
79_L	82_P	1.887	1.00
84_K	88_P	1.821	1.00
22_L	99_A	1.787	1.00
49_G	147_A	1.784	1.00
36_L	104_V	1.769	1.00
37_R	72_G	1.767	1.00
228_D	232_A	1.742	1.00
153_Q	233_D	1.718	1.00
38_L	59_I	1.703	1.00
92_Y	96_Y	1.701	1.00
140_L	155_I	1.674	1.00
32_A	107_T	1.649	1.00
194_L	221_D	1.639	1.00
181_N	184_I	1.609	1.00
101_V	239_Q	1.594	1.00
32_A	36_L	1.594	1.00
175_E	202_L	1.587	1.00
135_K	139_H	1.574	1.00
166_A	183_L	1.556	1.00
159_S	189_Y	1.548	1.00
90_L	95_F	1.540	1.00
140_L	159_S	1.536	1.00
23_R	103_A	1.531	1.00
47_D	50_T	1.525	1.00
18_A	90_L	1.511	1.00
135_K	143_V	1.483	1.00
97_Q	242_S	1.482	1.00
34_L	72_G	1.473	1.00
166_A	182_P	1.472	1.00
75_I	79_L	1.472	1.00
150_L	154_D	1.470	1.00
32_A	106_V	1.467	1.00
37_R	71_N	1.461	1.00
71_N	170_E	1.460	1.00
73_L	77_V	1.459	1.00
215_V	218_P	1.453	1.00
81_E	85_A	1.435	1.00
22_L	26_I	1.396	0.99
31_C	34_L	1.391	0.99
154_D	237_A	1.385	0.99
153_Q	222_K	1.384	0.99
229_A	233_D	1.347	0.99
211_L	217_R	1.331	0.99
17_K	21_K	1.319	0.99
84_K	95_F	1.318	0.99
110_P	235_A	1.309	0.99
181_N	188_S	1.301	0.99
241_L	244_L	1.301	0.99
187_N	191_T	1.300	0.99
136_G	139_H	1.282	0.99
33_P	37_R	1.279	0.99
219_L	222_K	1.270	0.99
152_D	219_L	1.264	0.99
185_F	230_F	1.258	0.99
80_L	99_A	1.250	0.99
121_K	125_P	1.241	0.98
221_D	225_A	1.241	0.98
181_N	227_E	1.239	0.98
30_R	34_L	1.238	0.98
65_L	74_D	1.230	0.98
234_Y	238_H	1.221	0.98
76_A	80_L	1.212	0.98
14_A	17_K	1.209	0.98
84_K	92_Y	1.208	0.98
162_H	167_A	1.208	0.98
41_H	44_G	1.194	0.98
77_V	96_Y	1.192	0.98
42_S	45_T	1.176	0.98
157_A	237_A	1.168	0.97
13_K	17_K	1.168	0.97
17_K	20_K	1.165	0.97
42_S	55_P	1.162	0.97
113_P	235_A	1.158	0.97
20_K	24_G	1.154	0.97
37_R	167_A	1.146	0.97
137_S	206_S	1.139	0.97
110_P	231_F	1.133	0.97
16_E	20_K	1.105	0.96
71_N	169_K	1.092	0.96
156_V	210_L	1.090	0.96
151_T	154_D	1.082	0.96
138_D	142_D	1.060	0.95
192_E	201_L	1.055	0.95
190_F	220_V	1.048	0.94
162_H	165_G	1.045	0.94
13_K	20_K	1.044	0.94
65_L	77_V	1.042	0.94
141_R	155_I	1.040	0.94
194_L	220_V	1.032	0.94
154_D	244_L	1.029	0.94
157_A	233_D	1.025	0.93
157_A	230_F	1.018	0.93
150_L	244_L	1.017	0.93
39_A	100_G	1.012	0.93
35_M	99_A	1.009	0.93
153_Q	219_L	1.005	0.93
23_R	106_V	1.003	0.93
39_A	97_Q	1.002	0.92
43_A	55_P	1.000	0.92

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
2vcnA	1	0.996	100	0.065	Contact Map
1iynA	1	0.9679	100	0.153	Contact Map
5al9A	1	0	100	0.172	Contact Map
3vliA	2	0.996	100	0.173	Contact Map
3n3rA	2	0.992	100	0.173	Contact Map
3e2oA	1	0.9759	100	0.184	Contact Map
2ccaA	2	0.996	100	0.189	Contact Map
3ut2A	2	0.988	100	0.193	Contact Map
3hdlA	1	0.9317	100	0.196	Contact Map
3wxoA	1	0.992	100	0.201	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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