OPENSEQ.org - 1415238998 - GREMLIN Submission

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Oxa23redo

ID:	1415238998	Query Sequence MNKYFTCYVVASLFLSGCTVQHNLINETPSQIVQGHNQVIHQYFDEKNTSGVLVIQTDKKINLYGNALSRANTEYVPASTFKMLNALIGLENQKTDINEIFKWKGEKRSFTAWEKDMTLGEAMKLSAVPVYQELARRIGLDLMQKEVKRIGFGNAEIGQQVDNFWLVGPLKVTPIQEVEFVSQLAHTQLPFSEKVQANVKNMLLLEESNGYKIFGKTGWAMDIKPQVGWLTGWVEQPDGKIVAFALNMEMRSEMPASIRNELLMKSLKQLNII	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	273 (234)
Sequences:	6112 (4285.2)
Seq/Len:	26.120
Nf(neff/√len):	280.1

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: 26.120).

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
55_I	244_F	3.396	1.00
231_T	245_A	3.233	1.00
215_G	230_L	3.204	1.00
178_V	245_A	3.065	1.00
200_K	233_W	2.785	1.00
91_E	195_V	2.692	1.00
58_D	243_A	2.519	1.00
53_L	266_S	2.452	1.00
122_A	130_V	2.415	1.00
214_F	236_Q	2.365	1.00
92_N	142_L	2.315	1.00
145_K	149_R	2.289	1.00
55_I	266_S	2.252	1.00
204_L	212_K	2.214	1.00
87_L	195_V	2.189	1.00
57_T	60_K	2.151	1.00
57_T	62_N	2.142	1.00
117_M	127_A	2.096	1.00
100_I	116_D	2.062	1.00
55_I	242_V	2.027	1.00
88_I	146_E	2.023	1.00
112_A	127_A	2.015	1.00
56_Q	178_V	1.974	1.00
91_E	192_S	1.973	1.00
120_G	201_N	1.937	1.00
96_D	99_E	1.934	1.00
121_E	125_L	1.933	1.00
81_F	147_V	1.881	1.00
64_Y	242_V	1.831	1.00
192_S	195_V	1.803	1.00
84_L	180_F	1.800	1.00
99_E	137_R	1.792	1.00
264_M	268_K	1.763	1.00
118_T	121_E	1.752	1.00
103_W	127_A	1.751	1.00
263_L	267_L	1.744	1.00
246_L	263_L	1.725	1.00
182_S	243_A	1.706	1.00
57_T	241_I	1.697	1.00
174_P	245_A	1.693	1.00
232_G	267_L	1.692	1.00
95_T	119_L	1.682	1.00
117_M	121_E	1.675	1.00
121_E	124_K	1.671	1.00
59_K	239_G	1.669	1.00
53_L	246_L	1.606	1.00
122_A	131_Y	1.599	1.00
89_G	134_L	1.551	1.00
86_A	131_Y	1.550	1.00
59_K	241_I	1.547	1.00
181_V	203_L	1.538	1.00
87_L	191_F	1.535	1.00
92_N	146_E	1.534	1.00
133_E	137_R	1.531	1.00
256_A	260_N	1.500	1.00
191_F	196_Q	1.481	1.00
235_E	240_K	1.472	1.00
222_D	249_E	1.471	1.00
83_M	184_L	1.458	1.00
193_E	197_A	1.454	1.00
150_I	191_F	1.434	1.00
184_L	199_V	1.420	1.00
87_L	150_I	1.409	1.00
214_F	233_W	1.406	0.99
189_L	193_E	1.371	0.99
181_V	231_T	1.358	0.99
135_A	143_M	1.353	0.99
58_D	242_V	1.346	0.99
90_L	202_M	1.338	0.99
212_K	238_D	1.331	0.99
142_L	145_K	1.324	0.99
80_T	177_E	1.301	0.99
232_G	263_L	1.296	0.99
144_Q	148_K	1.293	0.99
114_E	127_A	1.250	0.99
141_D	145_K	1.249	0.99
97_I	202_M	1.236	0.98
53_L	244_F	1.220	0.98
83_M	123_M	1.217	0.98
139_G	142_L	1.212	0.98
201_N	204_L	1.198	0.98
152_F	172_V	1.197	0.98
50_S	250_M	1.196	0.98
177_E	231_T	1.192	0.98
123_M	202_M	1.178	0.98
45_D	48_N	1.177	0.98
234_V	267_L	1.171	0.98
54_V	175_I	1.146	0.97
257_S	261_E	1.142	0.97
123_M	203_L	1.142	0.97
185_A	233_W	1.141	0.97
54_V	178_V	1.126	0.97
57_T	64_Y	1.120	0.96
77_P	172_V	1.118	0.96
265_K	268_K	1.116	0.96
187_T	197_A	1.115	0.96
42_Q	46_E	1.114	0.96
56_Q	243_A	1.114	0.96
127_A	130_V	1.109	0.96
83_M	181_V	1.109	0.96
124_K	207_E	1.096	0.96
91_E	146_E	1.091	0.96
172_V	177_E	1.089	0.96
92_N	138_I	1.080	0.95
95_T	137_R	1.074	0.95
227_V	247_N	1.073	0.95
187_T	193_E	1.067	0.95
259_R	263_L	1.065	0.95
146_E	150_I	1.051	0.94
58_D	182_S	1.040	0.94
120_G	202_M	1.029	0.94
94_K	142_L	1.025	0.93
91_E	149_R	1.022	0.93
225_P	250_M	1.021	0.93
260_N	264_M	1.018	0.93
129_P	133_E	1.014	0.93
229_W	247_N	1.011	0.93
248_M	262_L	1.011	0.93
200_K	203_L	1.010	0.93
56_Q	182_S	1.008	0.93
117_M	125_L	1.005	0.93
102_K	116_D	1.005	0.93
87_L	196_Q	1.004	0.93
187_T	200_K	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: (06Sep14)
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
2iwbA	1	0.8901	100	0.348	Contact Map
4ovdA	1	0.9597	100	0.35	Contact Map
3hbrA	4	0.8718	100	0.36	Contact Map
4qjgA	2	0.967	100	0.362	Contact Map
3pbtA	1	0.989	100	0.364	Contact Map
3ue3A	1	0.9817	100	0.364	Contact Map
3un7A	2	0.9853	100	0.367	Contact Map
3equA	2	0.9853	100	0.367	Contact Map
4f7yA	4	0.8681	100	0.367	Contact Map
4oh0A	1	0.8718	100	0.367	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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