OPENSEQ.org - 1418188633 - GREMLIN Submission

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

107610861084_10901074108610771081_1084107210841099

ID:	1418188633	Query Sequence ELQLRWQEYRELVLLLLQWMRHHTAAFEERFPSSFEEVRILREQLSKFAAVELPAKEADKNRSKGIYQSLEGAVQAGQLKVPPGYHPLDVEKEWKKLLDAYVEMLMRAYPWTRRLNALQRIVTKLQMEAGLAEEQLNQADALLQSDVRLLAAGKVPQRAGEVERDLDKADSMIRLLFNDVQTLKDGRHPQGEQMYRRVYRLHKRLVAIRTEYNLRLK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	217 (216)
Sequences:	991 (600.1)
Seq/Len:	4.588
Nf(neff/√len):	40.8

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: 4.588).

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
64_K	91_E	2.422	1.00
45_L	101_Y	2.320	1.00
180_V	194_M	2.199	1.00
24_T	93_E	2.167	1.00
19_W	56_K	2.107	1.00
48_F	53_L	2.040	1.00
23_H	52_E	1.912	1.00
41_L	104_M	1.876	1.00
13_V	63_S	1.849	1.00
45_L	48_F	1.691	0.99
175_L	178_N	1.642	0.99
128_E	132_A	1.631	0.99
149_L	152_A	1.600	0.99
53_L	101_Y	1.593	0.99
32_P	41_L	1.551	0.99
170_D	174_R	1.522	0.98
34_S	37_E	1.489	0.98
19_W	52_E	1.484	0.98
16_L	56_K	1.477	0.98
48_F	94_W	1.474	0.98
128_E	169_A	1.474	0.98
97_L	156_P	1.469	0.98
37_E	41_L	1.463	0.98
155_V	159_A	1.431	0.97
15_L	194_M	1.393	0.97
56_K	59_D	1.374	0.96
34_S	123_T	1.373	0.96
31_F	41_L	1.369	0.96
133_E	204_R	1.367	0.96
151_A	176_L	1.356	0.96
39_R	116_N	1.355	0.96
177_F	202_H	1.354	0.96
9_Y	104_M	1.348	0.96
42_R	108_A	1.341	0.96
120_R	123_T	1.338	0.96
27_F	52_E	1.333	0.96
20_M	93_E	1.324	0.95
67_Y	129_A	1.312	0.95
102_V	105_L	1.308	0.95
78_Q	81_V	1.305	0.95
57_E	61_N	1.299	0.95
148_R	154_K	1.289	0.94
94_W	105_L	1.284	0.94
12_L	66_I	1.268	0.94
43_E	46_S	1.260	0.93
146_D	156_P	1.254	0.93
40_I	151_A	1.251	0.93
38_V	112_T	1.247	0.93
34_S	38_V	1.242	0.93
48_F	105_L	1.241	0.93
94_W	111_W	1.212	0.92
129_A	135_Q	1.212	0.92
136_L	162_V	1.201	0.91
75_Q	78_Q	1.190	0.91
9_Y	139_A	1.189	0.91
103_E	110_P	1.188	0.90
111_W	114_R	1.181	0.90
23_H	94_W	1.181	0.90
92_K	95_K	1.179	0.90
77_G	81_V	1.175	0.90
131_L	143_L	1.173	0.90
118_L	180_V	1.159	0.89
105_L	108_A	1.155	0.89
171_S	174_R	1.155	0.89
36_E	205_L	1.142	0.88
36_E	43_E	1.122	0.87
145_S	149_L	1.121	0.87
45_L	53_L	1.117	0.86
53_L	125_L	1.115	0.86
56_K	60_K	1.114	0.86
144_Q	147_V	1.112	0.86
161_E	168_K	1.110	0.86
67_Y	87_P	1.109	0.86
6_W	57_E	1.108	0.86
140_D	155_V	1.101	0.85
9_Y	118_L	1.100	0.85
91_E	213_N	1.099	0.85
9_Y	26_A	1.096	0.85
32_P	38_V	1.095	0.85
146_D	191_G	1.080	0.84
31_F	104_M	1.067	0.83
115_L	118_L	1.065	0.83
48_F	125_L	1.065	0.83
150_L	154_K	1.056	0.82
109_Y	179_D	1.055	0.82
34_S	212_Y	1.055	0.82
68_Q	164_R	1.054	0.82
28_E	195_Y	1.051	0.82
41_L	90_V	1.048	0.81
9_Y	121_I	1.045	0.81
68_Q	107_R	1.038	0.80
20_M	24_T	1.035	0.80
136_L	194_M	1.032	0.80
190_Q	193_Q	1.029	0.80
38_V	43_E	1.022	0.79
65_G	68_Q	1.022	0.79
92_K	96_K	1.018	0.79
84_G	89_D	1.017	0.79
75_Q	89_D	1.014	0.78
115_L	182_T	1.012	0.78
153_G	156_P	1.009	0.78
24_T	96_K	1.009	0.78
104_M	115_L	1.008	0.78
16_L	90_V	1.006	0.77
166_L	212_Y	1.003	0.77

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

See coupling matrix (for protein design or mutagenesis)
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
2odvA	1	0.9447	99.9	0.3	Contact Map
1s35A	1	0.9447	99.9	0.302	Contact Map
3fb2A	2	0.9171	99.9	0.305	Contact Map
1u5pA	1	0.9539	99.9	0.307	Contact Map
3eduA	1	0.8664	99.8	0.314	Contact Map
3edvA	2	0.9677	99.8	0.319	Contact Map
1u4qA	2	0.9631	99.8	0.319	Contact Map
1cunA	3	0.9447	99.8	0.321	Contact Map
1quuA	1	0.9677	99.8	0.328	Contact Map
3kbtA	2	0.8802	99.8	0.33	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 1.4416 seconds.