OPENSEQ.org - 1387829518 - GREMLIN Submission

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GC_sapC_3

ID:	1387829518	Query Sequence MQYSHSIITNLLYHVTGWTDWNLALNPEGGPNWVRNFVDSPIIVDIPKDAFYKQPMFYHLGHFSKFIPEGSQRVALVASESTDLETVALLRPDGSAVVVVLNRSSEDVPLTISDPDLGFLETVSPGYSIHTYLWRRQNVILCQTCQFVMNKFSELIVNNATEELLVKGLSNACALLPDPARTKCQEVVGTFGPSLLDIFIHEVNPSSLCGVIGLCAA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	217 (216)
Sequences:	1146 (625.7)
Seq/Len:	5.306
Nf(neff/√len):	42.6

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: 5.306).

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
71_S	91_R	2.529	1.00
91_R	95_S	1.297	0.96
22_N	25_L	1.282	0.96
191_F	194_S	1.234	0.94
153_S	197_D	1.233	0.94
10_N	18_W	1.204	0.93
45_D	50_A	1.200	0.93
153_S	203_V	1.190	0.93
71_S	95_S	1.184	0.92
162_E	186_E	1.179	0.92
20_D	41_P	1.172	0.92
163_E	166_V	1.159	0.91
160_A	164_L	1.159	0.91
206_S	213_G	1.157	0.91
140_I	186_E	1.155	0.91
74_V	96_A	1.152	0.91
163_E	211_V	1.142	0.90
88_A	98_V	1.139	0.90
76_L	86_T	1.134	0.90
156_I	203_V	1.131	0.90
68_P	71_S	1.122	0.89
33_W	38_V	1.120	0.89
160_A	192_G	1.117	0.89
149_M	208_L	1.110	0.89
151_K	164_L	1.108	0.89
200_I	211_V	1.106	0.88
154_E	211_V	1.101	0.88
180_A	183_K	1.098	0.88
204_N	207_S	1.097	0.88
166_V	192_G	1.095	0.88
143_Q	151_K	1.088	0.87
155_L	166_V	1.087	0.87
186_E	197_D	1.084	0.87
174_A	185_Q	1.082	0.87
154_E	200_I	1.082	0.87
144_T	151_K	1.082	0.87
169_L	192_G	1.081	0.87
198_I	211_V	1.080	0.87
203_V	211_V	1.079	0.87
146_Q	194_S	1.078	0.87
150_N	153_S	1.078	0.87
152_F	170_S	1.077	0.87
150_N	203_V	1.073	0.86
186_E	210_G	1.072	0.86
164_L	182_T	1.072	0.86
202_E	211_V	1.067	0.86
146_Q	150_N	1.064	0.86
144_T	168_G	1.064	0.86
163_E	186_E	1.062	0.86
210_G	213_G	1.061	0.86
166_V	183_K	1.061	0.86
41_P	56_M	1.060	0.85
140_I	148_V	1.057	0.85
174_A	194_S	1.055	0.85
175_L	213_G	1.051	0.85
147_F	202_E	1.050	0.85
40_S	43_I	1.050	0.85
175_L	198_I	1.049	0.85
146_Q	206_S	1.048	0.85
153_S	198_I	1.047	0.84
151_K	160_A	1.044	0.84
153_S	183_K	1.044	0.84
175_L	189_G	1.043	0.84
155_L	198_I	1.042	0.84
61_G	65_K	1.041	0.84
140_I	147_F	1.041	0.84
187_V	198_I	1.041	0.84
198_I	203_V	1.040	0.84
153_S	170_S	1.038	0.84
153_S	179_P	1.038	0.84
144_T	171_N	1.037	0.84
198_I	206_S	1.037	0.84
193_P	197_D	1.037	0.84
150_N	204_N	1.036	0.84
164_L	186_E	1.035	0.84
151_K	171_N	1.035	0.84
146_Q	192_G	1.033	0.83
152_F	200_I	1.033	0.83
156_I	211_V	1.032	0.83
141_L	154_E	1.032	0.83
154_E	160_A	1.031	0.83
169_L	188_V	1.031	0.83
166_V	180_A	1.030	0.83
157_V	201_H	1.029	0.83
202_E	214_L	1.028	0.83
44_V	51_F	1.027	0.83
146_Q	204_N	1.027	0.83
160_A	203_V	1.027	0.83
71_S	93_D	1.027	0.83
144_T	207_S	1.027	0.83
175_L	178_D	1.027	0.83
171_N	175_L	1.025	0.83
170_S	189_G	1.025	0.83
147_F	168_G	1.024	0.83
180_A	204_N	1.022	0.82
180_A	190_T	1.022	0.82
181_R	196_L	1.021	0.82
159_N	169_L	1.021	0.82
180_A	203_V	1.021	0.82
54_Q	58_Y	1.019	0.82
186_E	198_I	1.018	0.82
17_G	23_L	1.018	0.82
183_K	207_S	1.016	0.82
11_L	67_I	1.015	0.82
192_G	211_V	1.015	0.82
157_V	197_D	1.014	0.82
194_S	200_I	1.014	0.82
147_F	151_K	1.013	0.82
153_S	207_S	1.013	0.82
39_D	43_I	1.010	0.81
43_I	54_Q	1.007	0.81
155_L	164_L	1.006	0.81
166_V	193_P	1.006	0.81
147_F	150_N	1.004	0.81
197_D	200_I	1.004	0.81
141_L	147_F	1.003	0.81
20_D	60_L	1.003	0.81
141_L	213_G	1.003	0.81
186_E	194_S	1.002	0.81
174_A	193_P	1.002	0.81
202_E	210_G	1.000	0.81
171_N	193_P	1.000	0.81

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: (08Feb14)
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
2nt0A	4	0.6313	100	0.452	Contact Map
2wnwA	2	0.6221	100	0.491	Contact Map
3clwA	6	0.5806	99.9	0.569	Contact Map
4ccdA	1	0.8664	99.9	0.598	Contact Map
4fmvA	1	0.5438	99.9	0.607	Contact Map
3kl0A	4	0.576	99.9	0.607	Contact Map
2y24A	1	0.5438	99.9	0.618	Contact Map
2qypA	2	0.3733	99.7	0.707	Contact Map
2gtgA	1	0.3594	99.7	0.711	Contact Map
3bqpA	2	0.3687	99.7	0.712	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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