OPENSEQ.org - 1402364019 - GREMLIN Submission

May 4, 2021 - We are working on upgrading the webserver, some pages may not work.

Welcome: casp11@openseq.org

T0786 -force run

ID:	1402364019	Query Sequence MDTQQLYFLNDIGKQKPESIRNRSAACPFCDRENLTDILATEGSIIWLKNKFPTLKDTFQTVLIETDNCEDHIATYTEEHMRSLIRFSIKHWLNLQKNEEFTSVILYKNHGPFSGGSLHHAHMQIIGMKYVNYLDNVEQDNFQGVIVQKNEHIELNISDRPIIGFTEFNIIIEDIGCIDELANYIQQTVRYILTDFHKGCSSYNLFFYYLNEKIICKVVPRFVVSPLYVGYKIPQVSTKIEDVKIQLAAYFTKQNDAIIHKKIE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	264 (253)
Sequences:	203 (166)
Seq/Len:	0.802
Nf(neff/√len):	10.4

Jackhmmer Results: (2014_04_16)
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: 0.802).

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
204_N	207_F	2.123	0.95
197_H	204_N	1.963	0.92
27_C	69_C	1.925	0.91
186_Q	207_F	1.900	0.91
186_Q	204_N	1.873	0.90
241_E	247_L	1.848	0.89
185_I	205_L	1.836	0.89
61_T	91_H	1.798	0.87
186_Q	197_H	1.746	0.85
47_W	61_T	1.715	0.84
202_S	205_L	1.708	0.83
85_I	185_I	1.706	0.83
27_C	63_L	1.706	0.83
105_I	128_M	1.692	0.82
203_Y	206_F	1.685	0.82
196_F	202_S	1.671	0.81
190_R	202_S	1.665	0.81
57_D	129_K	1.590	0.77
199_G	205_L	1.589	0.77
197_H	205_L	1.583	0.76
73_I	81_M	1.581	0.76
28_P	53_P	1.578	0.76
184_Y	210_L	1.565	0.75
146_I	149_K	1.553	0.74
185_I	204_N	1.519	0.72
193_L	197_H	1.507	0.71
186_Q	205_L	1.497	0.70
27_C	66_T	1.496	0.70
197_H	202_S	1.496	0.70
197_H	207_F	1.483	0.69
202_S	207_F	1.463	0.68
196_F	204_N	1.458	0.67
179_D	183_N	1.448	0.67
68_N	71_D	1.444	0.66
239_K	246_Q	1.440	0.66
33_E	79_E	1.434	0.66
185_I	202_S	1.422	0.65
145_V	244_K	1.405	0.63
185_I	193_L	1.393	0.62
193_L	202_S	1.388	0.62
146_I	151_E	1.386	0.62
198_K	202_S	1.364	0.60
138_E	213_K	1.361	0.60
199_G	207_F	1.361	0.60
152_H	175_I	1.359	0.59
13_G	227_L	1.356	0.59
66_T	69_C	1.354	0.59
196_F	207_F	1.343	0.58
16_K	204_N	1.322	0.56
198_K	205_L	1.314	0.56
66_T	121_A	1.308	0.55
200_C	204_N	1.305	0.55
201_S	207_F	1.305	0.55
185_I	207_F	1.296	0.54
103_S	156_N	1.293	0.54
193_L	204_N	1.293	0.54
186_Q	202_S	1.289	0.53
128_M	133_Y	1.284	0.53
58_T	107_Y	1.281	0.53
190_R	197_H	1.279	0.53
231_Y	245_I	1.272	0.52
196_F	201_S	1.269	0.52
197_H	200_C	1.267	0.51
185_I	197_H	1.258	0.51
35_L	60_Q	1.250	0.50
194_T	200_C	1.236	0.49
17_P	144_G	1.234	0.49
186_Q	198_K	1.230	0.48
244_K	247_L	1.229	0.48
193_L	207_F	1.223	0.48
190_R	207_F	1.200	0.46
201_S	205_L	1.194	0.45
196_F	200_C	1.193	0.45
157_I	210_L	1.191	0.45
190_R	194_T	1.189	0.45
200_C	205_L	1.185	0.44
19_S	37_D	1.180	0.44
92_W	106_L	1.178	0.44
185_I	198_K	1.171	0.43
128_M	231_Y	1.169	0.43
131_V	157_I	1.169	0.43
47_W	91_H	1.166	0.43
186_Q	196_F	1.152	0.41
199_G	202_S	1.151	0.41
193_L	205_L	1.145	0.41
84_L	142_F	1.142	0.41
63_L	123_M	1.130	0.40
63_L	69_C	1.113	0.38
197_H	201_S	1.113	0.38
27_C	123_M	1.111	0.38
32_R	88_S	1.110	0.38
76_Y	174_D	1.100	0.37
190_R	201_S	1.099	0.37
176_G	250_Y	1.097	0.37
44_S	67_D	1.091	0.36
125_I	249_A	1.086	0.36
190_R	193_L	1.080	0.36
193_L	200_C	1.072	0.35
16_K	128_M	1.070	0.35
110_H	116_G	1.069	0.35
55_L	94_N	1.069	0.35
5_Q	234_P	1.068	0.35
107_Y	147_V	1.067	0.35
27_C	214_I	1.066	0.34
35_L	76_Y	1.062	0.34
241_E	244_K	1.061	0.34
196_F	199_G	1.061	0.34
35_L	48_L	1.061	0.34
102_T	231_Y	1.051	0.33
199_G	204_N	1.051	0.33
28_P	87_F	1.050	0.33
86_R	179_D	1.042	0.33
185_I	196_F	1.041	0.32
9_L	119_H	1.039	0.32
85_I	181_L	1.037	0.32
64_I	118_L	1.036	0.32
10_N	247_L	1.033	0.32
106_L	165_F	1.028	0.31
191_Y	205_L	1.026	0.31
198_K	207_F	1.021	0.31
49_K	59_F	1.020	0.31
96_Q	209_Y	1.014	0.30
150_N	177_C	1.008	0.30
37_D	140_D	1.007	0.30
138_E	142_F	1.002	0.30
107_Y	119_H	1.000	0.29

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
4qvuA	1	0.822	100	0.457	Contact Map
1gupA	4	0.9773	100	0.496	Contact Map
1z84A	2	0.9053	100	0.53	Contact Map
4i5tA	2	0.8826	100	0.729	Contact Map
3imiA	4	0.5303	98.9	0.882	Contact Map
4incA	2	0.4015	98.9	0.885	Contact Map
1y23A	5	0.5227	98.8	0.887	Contact Map
3o1cA	1	0.4129	98.8	0.888	Contact Map
3o0mA	2	0.5114	98.7	0.89	Contact Map
3r6fA	1	0.4886	98.7	0.891	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.

Page generated in 3.1253 seconds.