OPENSEQ.org - 1509726821 - GREMLIN Submission

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E coli K12 W3110 TonB

ID:	1509726821	Query Sequence MTLDLPRRFPWPTLLSVCIHGAVVAGLLYTSVHQVIELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQALRIEGQVKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEIQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	239 (229)
Sequences:	253 (176)
Seq/Len:	1.105
Nf(neff/√len):	11.6

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: 1.105).

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
196_A	203_E	2.906	1.00
198_P	203_E	2.615	1.00
7_R	12_P	2.574	1.00
168_Q	232_I	2.487	0.99
163_Y	174_G	2.288	0.99
16_S	20_H	2.192	0.98
198_P	202_F	1.935	0.95
153_P	161_P	1.919	0.95
192_Q	223_G	1.846	0.93
197_K	203_E	1.761	0.91
158_R	226_V	1.696	0.89
182_V	218_G	1.634	0.86
153_P	213_W	1.625	0.86
174_G	230_F	1.600	0.85
19_I	193_I	1.596	0.85
163_Y	230_F	1.559	0.83
84_E	94_P	1.525	0.81
174_G	186_G	1.524	0.81
202_F	206_V	1.521	0.81
180_F	215_Y	1.487	0.78
109_Q	112_R	1.480	0.78
161_P	213_W	1.463	0.77
159_N	180_F	1.440	0.75
181_D	213_W	1.407	0.73
85_A	104_K	1.398	0.72
19_I	91_K	1.387	0.71
158_R	215_Y	1.379	0.71
63_P	67_P	1.378	0.71
74_E	193_I	1.373	0.70
163_Y	186_G	1.353	0.69
167_A	186_G	1.350	0.68
129_A	154_R	1.333	0.67
179_K	192_Q	1.333	0.67
195_S	203_E	1.325	0.66
206_V	210_M	1.324	0.66
161_P	215_Y	1.322	0.66
21_G	39_P	1.307	0.65
181_D	190_N	1.304	0.64
79_P	100_P	1.285	0.63
97_K	101_K	1.260	0.61
22_A	227_N	1.248	0.59
181_D	198_P	1.239	0.59
24_V	168_Q	1.231	0.58
26_G	211_R	1.225	0.57
155_A	206_V	1.223	0.57
94_P	214_R	1.222	0.57
177_K	227_N	1.214	0.56
40_A	56_E	1.208	0.56
153_P	216_E	1.203	0.55
10_P	30_T	1.200	0.55
66_E	86_P	1.197	0.55
197_K	206_V	1.194	0.54
161_P	173_E	1.193	0.54
198_P	206_V	1.189	0.54
197_K	202_F	1.186	0.54
202_F	205_E	1.179	0.53
116_P	121_P	1.163	0.51
167_A	174_G	1.162	0.51
163_Y	167_A	1.157	0.51
186_G	230_F	1.154	0.51
173_E	202_F	1.151	0.50
147_T	208_N	1.144	0.50
153_P	204_R	1.136	0.49
112_R	127_N	1.128	0.48
183_T	187_R	1.126	0.48
156_L	176_V	1.124	0.48
167_A	202_F	1.116	0.47
163_Y	173_E	1.116	0.47
151_S	154_R	1.108	0.46
202_F	210_M	1.101	0.46
15_L	48_T	1.100	0.45
7_R	11_W	1.099	0.45
161_P	174_G	1.091	0.45
173_E	213_W	1.087	0.44
174_G	202_F	1.084	0.44
164_P	167_A	1.082	0.44
161_P	216_E	1.082	0.44
189_D	196_A	1.081	0.44
158_R	180_F	1.081	0.44
96_P	100_P	1.080	0.44
67_P	98_P	1.079	0.43
161_P	209_A	1.073	0.43
154_R	171_R	1.073	0.43
190_N	206_V	1.068	0.42
17_V	21_G	1.066	0.42
112_R	178_V	1.062	0.42
51_T	232_I	1.061	0.42
45_I	99_K	1.061	0.42
172_I	203_E	1.060	0.42
210_M	224_I	1.059	0.42
28_L	107_Q	1.057	0.41
67_P	73_P	1.056	0.41
166_R	180_F	1.049	0.41
203_E	206_V	1.049	0.41
196_A	200_N	1.046	0.40
48_T	162_Q	1.042	0.40
151_S	233_N	1.041	0.40
155_A	215_Y	1.040	0.40
182_V	219_K	1.040	0.40
20_H	202_F	1.036	0.40
167_A	230_F	1.032	0.39
166_R	170_L	1.030	0.39
180_F	224_I	1.030	0.39
110_P	116_P	1.028	0.39
115_K	121_P	1.027	0.39
91_K	227_N	1.018	0.38
160_Q	225_V	1.018	0.38
101_K	110_P	1.017	0.38
44_P	151_S	1.017	0.38
178_V	206_V	1.017	0.38
197_K	224_I	1.013	0.37
161_P	204_R	1.012	0.37
170_L	191_V	1.011	0.37
118_E	127_N	1.007	0.37
105_K	108_E	1.007	0.37
164_P	186_G	1.005	0.37

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	0.361	Contact Map
1u07A	2	0.3766	99.9	0.623	Contact Map
2k9kA	1	0.4184	99.8	0.655	Contact Map
2m2kA	1	0.5188	99.8	0.658	Contact Map
1lr0A	1	0.477	99.6	0.702	Contact Map
4g7xB	1	0.3891	99.3	0.76	Contact Map
1tolA	1	0.4937	98.2	0.835	Contact Map
2yizA	4	0.2092	54.2	0.934	Contact Map
4l3aA	2	0.2092	46.8	0.937	Contact Map
2vxaA	12	0.2008	45.9	0.937	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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