OPENSEQ.org - 1444818979 - GREMLIN Submission

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CADH1_2o72

ID:	1444818979	Query Sequence DWVIPPISSPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	213 (207)
Sequences:	6686 (4625.4)
Seq/Len:	32.300
Nf(neff/√len):	321.5

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: 32.300).

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	4.184	1.00
146_I	193_A	3.057	1.00
181_R	185_P	2.993	1.00
68_R	72_A	2.768	1.00
105_K	201_L	2.752	1.00
7_I	22_V	2.557	1.00
34_V	80_A	2.471	1.00
132_A	148_Y	2.337	1.00
151_L	192_Q	2.294	1.00
68_R	137_D	2.281	1.00
147_A	196_L	2.067	1.00
118_M	212_T	2.061	1.00
100_D	103_D	2.034	1.00
39_T	79_H	1.961	1.00
10_P	99_T	1.949	1.00
138_D	144_A	1.939	1.00
126_S	171_V	1.919	1.00
54_E	57_T	1.854	1.00
165_I	172_I	1.846	1.00
164_T	173_S	1.844	1.00
107_E	135_A	1.824	1.00
149_T	192_Q	1.743	1.00
166_N	169_T	1.742	1.00
69_E	103_D	1.741	1.00
53_I	60_L	1.698	1.00
52_I	61_K	1.679	1.00
79_H	91_P	1.677	1.00
104_N	135_A	1.671	1.00
119_E	180_D	1.669	1.00
62_V	66_L	1.664	1.00
12_N	101_Q	1.648	1.00
71_I	74_Y	1.604	1.00
37_S	79_H	1.603	1.00
192_Q	202_S	1.582	1.00
52_I	63_T	1.558	1.00
114_K	210_T	1.550	1.00
50_V	74_Y	1.544	1.00
81_V	89_E	1.504	1.00
184_F	187_Y	1.502	1.00
108_F	113_F	1.500	1.00
129_E	171_V	1.499	1.00
50_V	64_E	1.488	1.00
36_Y	80_A	1.488	1.00
110_Q	113_F	1.486	1.00
35_F	83_S	1.482	1.00
116_S	210_T	1.473	1.00
60_L	94_I	1.468	1.00
172_I	207_A	1.468	1.00
121_A	125_T	1.456	1.00
188_T	208_V	1.454	1.00
149_T	194_A	1.442	1.00
8_S	97_T	1.417	1.00
20_N	23_Q	1.413	1.00
162_M	187_Y	1.406	0.99
109_T	131_T	1.405	0.99
174_V	179_L	1.402	0.99
166_N	173_S	1.401	0.99
75_T	95_L	1.391	0.99
8_S	99_T	1.388	0.99
121_A	174_V	1.373	0.99
188_T	206_T	1.368	0.99
164_T	175_V	1.361	0.99
116_S	212_T	1.347	0.99
108_F	193_A	1.344	0.99
73_T	97_T	1.338	0.99
126_S	129_E	1.334	0.99
102_N	195_D	1.328	0.99
181_R	213_D	1.310	0.99
67_D	103_D	1.305	0.99
109_T	133_T	1.299	0.99
182_E	213_D	1.299	0.99
113_F	205_A	1.296	0.99
186_T	210_T	1.291	0.99
112_V	208_V	1.286	0.99
29_D	32_G	1.286	0.99
119_E	182_E	1.280	0.99
79_H	89_E	1.256	0.99
145_A	196_L	1.254	0.99
20_N	59_W	1.237	0.98
15_G	18_P	1.229	0.98
191_V	207_A	1.228	0.98
166_N	171_V	1.223	0.98
150_I	153_Q	1.219	0.98
76_L	94_I	1.215	0.98
132_A	146_I	1.210	0.98
192_Q	204_T	1.207	0.98
194_A	202_S	1.204	0.98
119_E	181_R	1.196	0.98
66_L	98_V	1.192	0.98
72_A	137_D	1.185	0.98
36_Y	58_G	1.182	0.98
139_V	145_A	1.174	0.98
73_T	95_L	1.168	0.97
37_S	81_V	1.157	0.97
186_T	208_V	1.151	0.97
170_G	173_S	1.143	0.97
51_F	76_L	1.139	0.97
189_L	207_A	1.138	0.97
30_K	33_K	1.121	0.97
26_S	29_D	1.120	0.96
147_A	167_R	1.116	0.96
180_D	213_D	1.110	0.96
66_L	74_Y	1.102	0.96
179_L	211_V	1.097	0.96
130_V	172_I	1.085	0.96
54_E	61_K	1.064	0.95
180_D	183_S	1.062	0.95
163_F	187_Y	1.061	0.95
194_A	200_G	1.057	0.95
68_R	100_D	1.041	0.94
53_I	58_G	1.036	0.94
77_F	91_P	1.026	0.94
18_P	21_L	1.025	0.93
75_T	93_E	1.023	0.93
197_Q	200_G	1.022	0.93
145_A	168_N	1.022	0.93
108_F	148_Y	1.019	0.93
69_E	100_D	1.017	0.93
128_M	207_A	1.008	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	-0.015	Contact Map
4oy9A	1	0.9953	100	0.016	Contact Map
4nuqA	1	0.9953	100	0.028	Contact Map
3k5rA	2	0.9906	100	0.047	Contact Map
3q2vA	2	1	100	0.057	Contact Map
1l3wA	1	1	100	0.062	Contact Map
3q2wA	1	0.9953	100	0.067	Contact Map
3ppeA	2	0.9437	100	0.069	Contact Map
1q55A	4	1	100	0.071	Contact Map
3lndA	4	0.9437	100	0.08	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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