OPENSEQ.org - 1509993080 - GREMLIN Submission

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E coli K12 W3110 TonB e-04 50 gaps

ID:	1509993080	Query Sequence MTLDLPRRFPWPTLLSVCIHGAVVAGLLYTSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEIQ	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	239 (229)
Sequences:	297 (211.4)
Seq/Len:	1.297
Nf(neff/√len):	14.0

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: 1.297).

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 > 50% 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
196_A	203_E	3.225	1.00
198_P	203_E	2.783	1.00
7_R	12_P	2.421	0.99
16_S	20_H	2.310	0.99
163_Y	174_G	2.220	0.99
168_Q	232_I	2.031	0.98
197_K	203_E	1.964	0.97
153_P	161_P	1.838	0.95
163_Y	230_F	1.836	0.95
198_P	202_F	1.763	0.93
163_Y	167_A	1.760	0.93
192_Q	223_G	1.721	0.92
129_A	154_R	1.653	0.90
84_E	94_P	1.647	0.90
74_E	193_I	1.638	0.89
155_A	215_Y	1.638	0.89
26_G	211_R	1.587	0.87
180_F	215_Y	1.579	0.87
181_D	190_N	1.564	0.86
202_F	206_V	1.534	0.85
82_P	100_P	1.521	0.84
206_V	210_M	1.516	0.84
19_I	193_I	1.481	0.82
161_P	173_E	1.480	0.82
167_A	230_F	1.477	0.82
182_V	218_G	1.448	0.80
161_P	213_W	1.446	0.80
179_K	192_Q	1.423	0.78
159_N	180_F	1.412	0.78
158_R	226_V	1.409	0.77
165_A	232_I	1.381	0.75
19_I	91_K	1.379	0.75
153_P	213_W	1.377	0.75
174_G	186_G	1.349	0.73
197_K	202_F	1.324	0.71
164_P	167_A	1.324	0.71
173_E	202_F	1.313	0.70
198_P	206_V	1.308	0.70
21_G	39_P	1.304	0.69
15_L	48_T	1.303	0.69
195_S	203_E	1.298	0.69
63_P	67_P	1.283	0.67
163_Y	173_E	1.282	0.67
152_G	203_E	1.237	0.63
158_R	215_Y	1.237	0.63
167_A	202_F	1.217	0.61
197_K	206_V	1.209	0.61
21_G	36_I	1.205	0.60
158_R	180_F	1.183	0.58
115_K	121_P	1.182	0.58
181_D	202_F	1.181	0.58
191_V	207_K	1.172	0.57
161_P	215_Y	1.171	0.57
177_K	227_N	1.157	0.56
202_F	205_E	1.153	0.55
156_L	173_E	1.149	0.55
161_P	216_E	1.143	0.54
67_P	98_P	1.136	0.54
28_L	104_K	1.132	0.53
156_L	176_V	1.131	0.53
97_K	101_K	1.129	0.53
44_P	151_S	1.124	0.52
87_V	93_K	1.108	0.51
151_S	165_A	1.103	0.50
109_Q	112_R	1.103	0.50
66_E	86_P	1.102	0.50
116_P	121_P	1.102	0.50
33_H	221_G	1.096	0.50
203_E	206_V	1.095	0.50
167_A	174_G	1.089	0.49
161_P	204_R	1.088	0.49
170_L	191_V	1.086	0.49
201_M	215_Y	1.085	0.49
10_P	30_T	1.082	0.48
40_A	56_E	1.082	0.48
17_V	21_G	1.080	0.48
85_A	104_K	1.077	0.48
17_V	27_L	1.077	0.48
153_P	204_R	1.068	0.47
210_M	224_I	1.068	0.47
157_S	161_P	1.067	0.47
153_P	216_E	1.064	0.46
8_R	221_G	1.063	0.46
151_S	154_R	1.058	0.46
151_S	232_I	1.056	0.46
14_L	97_K	1.052	0.45
173_E	213_W	1.049	0.45
176_V	214_R	1.049	0.45
42_A	54_D	1.045	0.45
13_T	138_A	1.043	0.44
18_C	217_P	1.034	0.44
155_A	181_D	1.032	0.43
197_K	233_N	1.026	0.43
77_P	96_P	1.025	0.43
157_S	173_E	1.025	0.43
189_D	195_S	1.024	0.43
14_L	21_G	1.021	0.42
216_E	219_K	1.020	0.42
45_I	99_K	1.017	0.42
81_P	98_P	1.017	0.42
39_P	56_E	1.011	0.41
39_P	182_V	1.009	0.41
118_E	127_N	1.009	0.41
170_L	180_F	1.005	0.41
134_T	141_A	1.004	0.41
182_V	219_K	1.003	0.41
178_V	217_P	1.000	0.40
160_Q	225_V	1.000	0.40
24_V	27_L	1.000	0.40

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
2grxC	2	0.3264	100	0.335	Contact Map
1u07A	2	0.3766	99.8	0.604	Contact Map
2m2kA	1	0.5188	99.8	0.636	Contact Map
2k9kA	1	0.4184	99.8	0.638	Contact Map
1lr0A	1	0.4812	99.6	0.683	Contact Map
4g7xB	1	0.3891	99.2	0.748	Contact Map
1tolA	1	0.5314	98.5	0.811	Contact Map
2yizA	4	0.2092	37.9	0.936	Contact Map
2vxaA	12	0.2008	37.7	0.936	Contact Map
3onrA	12	0.2218	29.6	0.939	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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