OPENSEQ.org - 1444819041 - GREMLIN Submission

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CADH_2o72_standard

ID:	1444819041	Query Sequence DWVIPPISSPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	213 (207)
Sequences:	6818 (4681.4)
Seq/Len:	32.937
Nf(neff/√len):	325.4

HHblits Results: (2015_06)
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: 32.937).

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
115_G	128_M	4.186	1.00
68_R	72_A	3.030	1.00
181_R	185_P	3.009	1.00
7_I	22_V	2.953	1.00
105_K	201_L	2.825	1.00
146_I	193_A	2.807	1.00
151_L	192_Q	2.438	1.00
132_A	148_Y	2.314	1.00
34_V	80_A	2.307	1.00
68_R	137_D	2.177	1.00
147_A	196_L	2.151	1.00
118_M	212_T	2.039	1.00
39_T	79_H	2.034	1.00
126_S	171_V	1.992	1.00
165_I	172_I	1.990	1.00
10_P	99_T	1.986	1.00
12_N	101_Q	1.965	1.00
100_D	103_D	1.942	1.00
138_D	144_A	1.934	1.00
54_E	57_T	1.890	1.00
164_T	173_S	1.866	1.00
107_E	135_A	1.808	1.00
104_N	135_A	1.794	1.00
52_I	61_K	1.734	1.00
109_T	131_T	1.733	1.00
149_T	192_Q	1.730	1.00
166_N	169_T	1.727	1.00
37_S	79_H	1.695	1.00
8_S	99_T	1.678	1.00
69_E	103_D	1.668	1.00
116_S	210_T	1.654	1.00
79_H	91_P	1.642	1.00
50_V	74_Y	1.641	1.00
62_V	66_L	1.610	1.00
192_Q	202_S	1.602	1.00
149_T	194_A	1.580	1.00
52_I	63_T	1.579	1.00
108_F	193_A	1.550	1.00
53_I	60_L	1.548	1.00
162_M	187_Y	1.548	1.00
35_F	83_S	1.544	1.00
75_T	95_L	1.537	1.00
119_E	180_D	1.534	1.00
36_Y	80_A	1.527	1.00
71_I	74_Y	1.519	1.00
121_A	174_V	1.506	1.00
188_T	208_V	1.503	1.00
20_N	59_W	1.502	1.00
113_F	205_A	1.474	1.00
184_F	187_Y	1.467	1.00
50_V	64_E	1.458	1.00
8_S	97_T	1.456	1.00
192_Q	204_T	1.454	1.00
114_K	210_T	1.451	1.00
60_L	94_I	1.449	1.00
186_T	210_T	1.448	1.00
110_Q	113_F	1.419	1.00
164_T	175_V	1.399	0.99
116_S	212_T	1.398	0.99
81_V	89_E	1.398	0.99
145_A	196_L	1.394	0.99
73_T	97_T	1.393	0.99
129_E	171_V	1.388	0.99
174_V	179_L	1.378	0.99
172_I	207_A	1.375	0.99
112_V	208_V	1.373	0.99
139_V	145_A	1.366	0.99
121_A	125_T	1.358	0.99
36_Y	58_G	1.352	0.99
102_N	195_D	1.346	0.99
20_N	23_Q	1.338	0.99
166_N	173_S	1.335	0.99
182_E	213_D	1.308	0.99
191_V	207_A	1.306	0.99
126_S	129_E	1.305	0.99
73_T	95_L	1.286	0.99
181_R	213_D	1.273	0.99
109_T	133_T	1.272	0.99
108_F	113_F	1.271	0.99
188_T	206_T	1.267	0.99
29_D	32_G	1.255	0.99
30_K	33_K	1.235	0.98
67_D	103_D	1.225	0.98
128_M	207_A	1.219	0.98
72_A	137_D	1.218	0.98
130_V	172_I	1.209	0.98
189_L	207_A	1.208	0.98
79_H	89_E	1.189	0.98
166_N	171_V	1.182	0.98
75_T	93_E	1.180	0.98
37_S	81_V	1.173	0.98
194_A	200_G	1.170	0.97
186_T	208_V	1.163	0.97
77_F	91_P	1.162	0.97
66_L	98_V	1.149	0.97
15_G	18_P	1.146	0.97
119_E	182_E	1.142	0.97
76_L	94_I	1.141	0.97
170_G	173_S	1.138	0.97
115_G	121_A	1.132	0.97
132_A	146_I	1.105	0.96
150_I	153_Q	1.104	0.96
145_A	168_N	1.098	0.96
54_E	59_W	1.095	0.96
108_F	148_Y	1.095	0.96
147_A	167_R	1.094	0.96
126_S	173_S	1.075	0.95
119_E	181_R	1.074	0.95
66_L	74_Y	1.069	0.95
35_F	55_R	1.063	0.95
77_F	93_E	1.061	0.95
162_M	177_T	1.051	0.94
148_Y	193_A	1.044	0.94
194_A	202_S	1.039	0.94
13_E	62_V	1.035	0.94
130_V	191_V	1.021	0.93
13_E	19_K	1.020	0.93
163_F	187_Y	1.019	0.93
10_P	101_Q	1.012	0.93
68_R	100_D	1.006	0.93
23_Q	59_W	1.005	0.93
180_D	213_D	1.004	0.93

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
3qrbA	2	1	100	-0.032	Contact Map
4oy9A	1	0.9953	100	-0.009	Contact Map
4nuqA	1	0.9953	100	0.009	Contact Map
3k5rA	2	0.9812	100	0.03	Contact Map
1l3wA	1	1	100	0.039	Contact Map
3q2vA	2	1	100	0.041	Contact Map
3ppeA	2	0.9296	100	0.047	Contact Map
3q2wA	1	0.9953	100	0.053	Contact Map
1q55A	4	1	100	0.055	Contact Map
3lndA	4	0.9296	100	0.059	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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