OPENSEQ.org - 1400180885 - GREMLIN Submission

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T0780

ID:	1400180885	Query Sequence MKKNSLYIISSLFFACVLFVYATATNFQNSTSARQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASEMQESTRKFKVTADLTDAGVGTIEVPLSIEDLPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENVMVSDKEVSITSDQETLDRIDKIIAVLPTSERITGNYSGSVPLQAIDRNGVVLPAVITPFDTIMKVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	259 (229)
Sequences:	538 (466.2)
Seq/Len:	2.349
Nf(neff/√len):	30.8

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: 2.349).

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
132_G	174_E	2.715	1.00
184_A	200_V	2.678	1.00
93_V	109_L	2.512	1.00
167_V	218_P	2.275	1.00
95_A	109_L	2.133	1.00
164_D	221_T	2.073	0.99
192_I	196_Y	2.014	0.99
206_D	210_V	1.980	0.99
184_A	202_L	1.979	0.99
139_K	166_E	1.956	0.99
137_K	140_V	1.892	0.99
203_Q	211_V	1.817	0.98
204_A	216_I	1.805	0.98
136_Q	170_T	1.694	0.97
42_T	73_T	1.608	0.96
100_A	131_I	1.598	0.96
162_V	221_T	1.583	0.95
136_Q	168_S	1.581	0.95
141_K	144_P	1.571	0.95
157_I	160_V	1.563	0.95
171_S	214_A	1.548	0.95
199_S	220_D	1.536	0.94
204_A	214_A	1.528	0.94
105_I	131_I	1.487	0.93
100_A	105_I	1.459	0.92
167_V	216_I	1.453	0.92
140_V	182_I	1.444	0.91
22_A	171_S	1.438	0.91
108_P	111_I	1.431	0.91
101_G	105_I	1.425	0.91
49_P	203_Q	1.401	0.90
195_N	226_T	1.400	0.90
145_E	183_I	1.393	0.89
196_Y	225_V	1.383	0.89
176_L	179_I	1.370	0.88
119_T	195_N	1.357	0.88
11_S	15_A	1.353	0.87
10_S	86_E	1.348	0.87
51_D	92_K	1.344	0.87
74_G	79_S	1.329	0.86
132_G	172_D	1.308	0.85
100_A	107_V	1.301	0.84
50_I	127_I	1.295	0.84
21_Y	103_G	1.295	0.84
182_I	204_A	1.271	0.83
202_L	221_T	1.245	0.81
158_E	226_T	1.242	0.80
144_P	162_V	1.234	0.80
95_A	218_P	1.232	0.80
142_I	164_D	1.231	0.80
179_I	214_A	1.227	0.79
103_G	115_P	1.218	0.79
49_P	52_I	1.215	0.78
182_I	202_L	1.210	0.78
184_A	204_A	1.208	0.78
68_V	93_V	1.204	0.78
140_V	179_I	1.193	0.77
133_K	173_Q	1.176	0.75
47_N	50_I	1.175	0.75
50_I	64_F	1.174	0.75
157_I	225_V	1.170	0.75
171_S	176_L	1.169	0.75
179_I	216_I	1.167	0.74
96_D	108_P	1.163	0.74
175_T	213_P	1.161	0.74
149_S	191_R	1.160	0.74
169_I	179_I	1.157	0.74
196_Y	224_K	1.150	0.73
43_N	71_V	1.149	0.73
99_D	102_V	1.140	0.72
54_Y	184_A	1.138	0.72
42_T	151_I	1.135	0.71
178_R	206_D	1.133	0.71
102_V	133_K	1.129	0.71
107_V	151_I	1.128	0.71
200_V	211_V	1.128	0.71
11_S	18_L	1.124	0.70
104_T	130_K	1.123	0.70
202_L	220_D	1.122	0.70
142_I	162_V	1.119	0.70
139_K	168_S	1.117	0.70
192_I	227_T	1.114	0.69
137_K	165_K	1.099	0.68
70_V	91_F	1.096	0.68
99_D	165_K	1.094	0.67
182_I	200_V	1.091	0.67
142_I	202_L	1.086	0.67
18_L	22_A	1.081	0.66
68_V	142_I	1.080	0.66
119_T	169_I	1.080	0.66
19_F	151_I	1.076	0.66
14_F	18_L	1.069	0.65
152_D	193_T	1.068	0.65
116_N	133_K	1.066	0.64
202_L	208_N	1.066	0.64
13_F	68_V	1.065	0.64
149_S	192_I	1.058	0.64
163_S	222_I	1.056	0.63
55_N	91_F	1.051	0.63
48_V	73_T	1.048	0.63
52_I	98_T	1.044	0.62
106_E	202_L	1.038	0.61
59_Y	102_V	1.033	0.61
114_L	120_A	1.032	0.61
72_L	185_V	1.031	0.61
19_F	86_E	1.028	0.60
47_N	62_S	1.028	0.60
12_L	69_S	1.026	0.60
11_S	124_P	1.025	0.60
223_M	226_T	1.018	0.59
9_I	52_I	1.017	0.59
33_A	36_V	1.017	0.59
56_S	210_V	1.016	0.59
58_K	72_L	1.010	0.58
13_F	148_P	1.008	0.58
97_L	107_V	1.003	0.58

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: (10May14)
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
2kq1A	1	0.4479	99.8	0.691	Contact Map
2kpsA	1	0.3784	99.6	0.737	Contact Map
3lywA	1	0.3243	99.3	0.769	Contact Map
2kxyA	1	0.3861	99.3	0.773	Contact Map
2xwxA	2	0.4788	9.3	0.958	Contact Map
2zjrS	1	0.4633	8.5	0.958	Contact Map
3j1rA	21	0.0888	6.1	0.961	Contact Map
1feuA	2	0.4981	3.4	0.965	Contact Map
1qleD	1	0.0888	3.2	0.966	Contact Map
2dibA	1	0.4595	3.2	0.966	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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