OPENSEQ.org - 1437218747 - GREMLIN Submission

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

noc

ID:	1437218747	Query Sequence MKHSFSRFFGLGEKEQEPEIAEHDTNKEEILEIPVNAIVPNRFQPRTIFSDEKIKELAMTIHTHGIIQPIVVRHTEEEGQYELIAGERRWRAVQSLEWEKIPAIIKDFSDTETASVALIENLQREELSSIEEAHAYARLLELHDLTQEALAQRLGKGQSTIANKLRLLKLPQPVQEAIMEKKITERHARALIPLKQPELQVTLLTEIIEKSLNVKQTEDRVVKMLEQGQRKPKPRRKAFSRDTRIAMNTIRQSLSMVEDSGVKLNTEEEEFEEYIQLTIRIPK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	283 (264)
Sequences:	5575 (4321)
Seq/Len:	21.117
Nf(neff/√len):	265.9

Jackhmmer Results: (2015_01_07)
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: 21.117).

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
32_E	100_K	4.517	1.00
39_V	80_Q	3.940	1.00
137_A	141_E	3.483	1.00
58_A	95_S	3.207	1.00
83_L	90_W	3.172	1.00
206_E	210_K	3.099	1.00
207_I	217_T	3.067	1.00
109_S	112_E	2.988	1.00
173_P	201_V	2.964	1.00
38_I	83_L	2.737	1.00
34_P	37_A	2.582	1.00
70_I	101_I	2.570	1.00
134_H	175_Q	2.482	1.00
66_I	93_V	2.451	1.00
177_A	204_L	2.426	1.00
37_A	80_Q	2.391	1.00
33_I	103_A	2.279	1.00
147_Q	162_A	2.254	1.00
55_K	95_S	2.240	1.00
53_K	125_E	2.202	1.00
33_I	72_V	2.182	1.00
72_V	103_A	2.169	1.00
55_K	59_M	2.161	1.00
157_G	160_T	2.141	1.00
176_E	180_E	2.090	1.00
54_I	95_S	2.065	1.00
51_D	95_S	2.027	1.00
73_R	82_E	2.027	1.00
212_L	220_R	2.025	1.00
54_I	58_A	1.969	1.00
66_I	102_P	1.940	1.00
216_Q	219_D	1.915	1.00
138_R	142_L	1.886	1.00
35_V	90_W	1.872	1.00
108_F	116_V	1.858	1.00
90_W	94_Q	1.833	1.00
70_I	83_L	1.783	1.00
149_A	152_Q	1.781	1.00
51_D	55_K	1.773	1.00
140_L	150_L	1.751	1.00
93_V	98_W	1.742	1.00
34_P	100_K	1.728	1.00
39_V	82_E	1.718	1.00
38_I	72_V	1.713	1.00
130_I	175_Q	1.710	1.00
59_M	62_H	1.652	1.00
148_E	152_Q	1.640	1.00
73_R	110_D	1.632	1.00
85_A	120_E	1.558	1.00
136_Y	154_L	1.528	1.00
205_T	209_E	1.513	1.00
199_L	202_T	1.513	1.00
41_N	113_T	1.503	1.00
75_T	82_E	1.503	1.00
50_S	53_K	1.497	1.00
187_H	214_V	1.496	1.00
70_I	103_A	1.488	1.00
67_I	71_V	1.485	1.00
39_V	75_T	1.481	1.00
159_S	162_A	1.477	1.00
132_E	164_K	1.475	1.00
171_P	200_Q	1.468	1.00
37_A	79_G	1.463	1.00
206_E	220_R	1.461	1.00
87_E	91_R	1.433	1.00
73_R	113_T	1.430	1.00
177_A	208_I	1.415	1.00
203_L	220_R	1.392	0.99
178_I	188_A	1.390	0.99
164_K	185_E	1.388	0.99
93_V	96_L	1.386	0.99
172_Q	175_Q	1.377	0.99
45_P	117_A	1.363	0.99
134_H	179_M	1.349	0.99
171_P	201_V	1.335	0.99
128_S	179_M	1.330	0.99
61_I	66_I	1.326	0.99
55_K	58_A	1.318	0.99
243_T	251_R	1.293	0.99
32_E	102_P	1.291	0.99
58_A	96_L	1.283	0.99
53_K	56_E	1.278	0.99
196_Q	199_L	1.274	0.99
74_H	107_D	1.262	0.99
132_E	156_K	1.260	0.99
42_R	82_E	1.259	0.99
201_V	205_T	1.253	0.99
41_N	117_A	1.248	0.99
273_E	277_L	1.235	0.98
190_A	217_T	1.220	0.98
61_I	93_V	1.218	0.98
136_Y	150_L	1.208	0.98
174_V	204_L	1.206	0.98
58_A	62_H	1.202	0.98
163_N	189_R	1.198	0.98
249_T	253_S	1.196	0.98
248_N	251_R	1.190	0.98
35_V	93_V	1.169	0.97
75_T	78_E	1.162	0.97
137_A	169_K	1.152	0.97
66_I	101_I	1.150	0.97
84_I	108_F	1.148	0.97
74_H	79_G	1.143	0.97
150_L	161_I	1.135	0.97
204_L	208_I	1.132	0.97
176_E	179_M	1.127	0.97
120_E	124_R	1.122	0.97
31_L	105_I	1.121	0.97
187_H	190_A	1.115	0.96
160_T	164_K	1.107	0.96
171_P	174_V	1.087	0.96
75_T	80_Q	1.084	0.96
57_L	88_R	1.072	0.95
115_S	153_R	1.072	0.95
59_M	63_T	1.066	0.95
40_P	90_W	1.062	0.95
64_H	112_E	1.058	0.95
93_V	101_I	1.058	0.95
36_N	94_Q	1.057	0.95
70_I	90_W	1.037	0.94
212_L	217_T	1.030	0.94
219_D	223_K	1.029	0.94
207_I	212_L	1.024	0.93
35_V	94_Q	1.022	0.93
194_L	203_L	1.007	0.93
66_I	70_I	1.004	0.93
173_P	205_T	1.003	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: (31Jan15)
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
1vz0A	8	0.6784	100	0.27	Contact Map
1r71A	4	0.3922	99.9	0.6	Contact Map
1vk1A	1	0.6466	99.8	0.632	Contact Map
1xw3A	1	0.3675	99.8	0.636	Contact Map
1yzsA	1	0.371	99.8	0.641	Contact Map
3mkyB	2	0.3852	99.5	0.709	Contact Map
1zx4A	2	0.5618	98.2	0.824	Contact Map
2hwjA	6	0.6042	96.8	0.866	Contact Map
3vwbA	1	0.4064	92.2	0.898	Contact Map
1lmb3	2	0.3039	86	0.909	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 1.2291 seconds.