OPENSEQ.org - 1481829375 - GREMLIN Submission

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BupsM_18956_a

ID:	1481829375	Query Sequence MVPPTIPELVARAGKLPFLCDHLALADGAQGAYARLRDFRLESVYEPIYDVSMPGAPQSTSLSDAIERYGDELGFQAVTHAGGAPFDPIGAVADDQELVALDRLARSLHAINFFGAQRHGLLFLRVHERLLKSVKYDHGKHFSTVLKGFGLPPERIVIELPAAAVAHKTFLGYLTKSYQHYGFKVADKLPDPGRILAVESDMARPDYIKMDAAIALREGMVKALVGYAQRVRIPLIFDHVVDETQFELLRQYDVRLVQGPVFSQPAAV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	268 (221)
Sequences:	23515 (17592.7)
Seq/Len:	106.403
Nf(neff/√len):	1183.4

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: 106.403).

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
51_V	257_V	3.870	1.00
157_V	207_Y	2.952	1.00
102_D	130_L	2.859	1.00
143_S	181_Y	2.775	1.00
248_L	252_Y	2.691	1.00
179_Q	206_D	2.686	1.00
42_E	82_G	2.640	1.00
263_S	266_A	2.574	1.00
103_R	141_H	2.562	1.00
45_Y	112_N	2.389	1.00
50_D	53_M	2.370	1.00
104_L	108_L	2.277	1.00
186_A	207_Y	2.223	1.00
107_S	148_G	2.197	1.00
229_Q	255_R	2.179	1.00
246_F	262_F	2.169	1.00
243_E	247_E	2.121	1.00
48_I	256_L	2.098	1.00
222_K	230_R	2.071	1.00
242_D	245_Q	2.069	1.00
44_V	267_A	1.893	1.00
246_F	257_V	1.890	1.00
218_E	248_L	1.882	1.00
157_V	186_A	1.874	1.00
31_G	83_G	1.862	1.00
222_K	252_Y	1.836	1.00
212_A	239_H	1.832	1.00
201_D	217_R	1.814	1.00
48_I	207_Y	1.799	1.00
108_L	112_N	1.757	1.00
207_Y	236_I	1.700	1.00
240_V	257_V	1.698	1.00
92_V	101_L	1.697	1.00
184_K	206_D	1.686	1.00
108_L	111_I	1.685	1.00
121_L	184_K	1.673	1.00
175_T	185_V	1.665	1.00
152_P	155_R	1.652	1.00
121_L	157_V	1.651	1.00
246_F	250_R	1.627	1.00
53_M	71_D	1.609	1.00
222_K	226_G	1.603	1.00
246_F	261_V	1.601	1.00
112_N	116_A	1.570	1.00
208_I	228_A	1.562	1.00
49_Y	262_F	1.554	1.00
79_T	105_A	1.554	1.00
48_I	157_V	1.549	1.00
40_R	83_G	1.545	1.00
34_A	38_D	1.525	1.00
234_P	256_L	1.503	1.00
39_F	108_L	1.500	1.00
73_L	256_L	1.499	1.00
243_E	261_V	1.498	1.00
234_P	255_R	1.471	1.00
145_V	149_F	1.470	1.00
43_S	105_A	1.464	1.00
237_F	254_V	1.448	1.00
41_L	79_T	1.446	1.00
225_V	254_V	1.436	1.00
113_F	116_A	1.416	1.00
110_A	145_V	1.410	1.00
225_V	252_Y	1.405	0.99
107_S	145_V	1.396	0.99
207_Y	234_P	1.371	0.99
260_P	265_P	1.364	0.99
146_L	183_F	1.317	0.99
113_F	151_L	1.315	0.99
157_V	184_K	1.310	0.99
126_V	136_Y	1.307	0.99
99_V	133_S	1.295	0.99
257_V	262_F	1.290	0.99
226_G	230_R	1.270	0.99
126_V	158_I	1.259	0.99
123_F	157_V	1.248	0.99
48_I	74_G	1.243	0.98
172_G	176_K	1.225	0.98
146_L	153_P	1.216	0.98
228_A	235_L	1.214	0.98
144_T	148_G	1.210	0.98
111_I	149_F	1.203	0.98
172_G	202_M	1.186	0.98
119_H	155_R	1.177	0.98
40_R	81_A	1.173	0.98
187_D	205_P	1.163	0.97
48_I	123_F	1.162	0.97
107_S	149_F	1.154	0.97
143_S	147_K	1.154	0.97
132_K	166_A	1.150	0.97
79_T	101_L	1.142	0.97
247_E	250_R	1.141	0.97
74_G	121_L	1.136	0.97
75_F	120_G	1.132	0.97
219_G	230_R	1.122	0.97
214_I	217_R	1.106	0.96
143_S	177_S	1.102	0.96
43_S	104_L	1.101	0.96
170_F	174_L	1.088	0.96
54_P	250_R	1.087	0.96
158_I	183_F	1.086	0.96
117_Q	155_R	1.086	0.96
45_Y	77_A	1.080	0.95
225_V	235_L	1.079	0.95
50_D	73_L	1.078	0.95
176_K	180_H	1.075	0.95
109_H	122_L	1.072	0.95
51_V	246_F	1.060	0.95
50_D	71_D	1.048	0.94
207_Y	256_L	1.044	0.94
76_Q	125_R	1.043	0.94
243_E	246_F	1.037	0.94
45_Y	75_F	1.031	0.94
107_S	111_I	1.031	0.94
141_H	145_V	1.027	0.94
205_P	233_I	1.026	0.94
223_A	230_R	1.019	0.93
113_F	122_L	1.004	0.93
99_V	130_L	1.003	0.93
77_A	122_L	1.003	0.93
43_S	77_A	1.001	0.92
42_E	267_A	1.001	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: (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
4kieA	1	0.8731	100	0.283	Contact Map
4hjfA	1	0.8545	100	0.286	Contact Map
4rnhA	1	0.9328	100	0.298	Contact Map
4q6jA	2	0.8358	100	0.304	Contact Map
2r6oA	2	0.8433	100	0.306	Contact Map
3pjxA	1	0.9216	100	0.306	Contact Map
3sy8A	4	0.9328	100	0.307	Contact Map
3s83A	1	0.8284	100	0.31	Contact Map
4fojA	1	0.8545	100	0.311	Contact Map
4j40A	2	0.8507	100	0.311	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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