OPENSEQ.org - 1400509785 - GREMLIN Submission

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

tram

ID:	1400509785	Query Sequence KWNNRVVSFVHAIVSSIWGLYILLNDPELWSDWPDDPWYYSSWLVKFYYAFSLGYFLYDLIVMLLYYRKRGDFWEMLLHHVVTLVLFYFSYFYNFGRFGIVVFLLHEISTPFLNLRWFLKYLGGYSKKSSLYRFNGVLFAVTFFVFRIVLFPYLIYWVYWDVWPLPLWKVPWPVPWIFLVLLLVLFVLNIYWFYLILR	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	198 (197)
Sequences:	669 (480.1)
Seq/Len:	3.396
Nf(neff/√len):	34.2

HHblits Results: (2013_03)
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: 3.396).

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
109_S	143_F	2.338	1.00
136_G	139_F	2.099	1.00
113_L	139_F	1.908	1.00
12_A	110_T	1.893	1.00
117_W	196_I	1.868	0.99
110_T	114_N	1.867	0.99
107_E	110_T	1.810	0.99
140_A	196_I	1.631	0.98
52_S	56_F	1.617	0.98
135_N	193_F	1.580	0.98
191_Y	195_L	1.540	0.97
9_F	12_A	1.527	0.97
8_S	55_Y	1.515	0.97
106_H	110_T	1.485	0.96
59_D	107_E	1.474	0.96
130_S	134_F	1.443	0.95
144_F	193_F	1.442	0.95
1_K	5_R	1.436	0.95
56_F	107_E	1.427	0.95
5_R	12_A	1.400	0.94
11_H	52_S	1.393	0.94
54_G	189_N	1.391	0.94
56_F	59_D	1.362	0.93
112_F	135_N	1.342	0.93
109_S	192_W	1.331	0.92
143_F	148_I	1.327	0.92
19_G	22_I	1.307	0.91
21_Y	26_D	1.301	0.91
80_H	106_H	1.296	0.91
58_Y	80_H	1.295	0.91
143_F	151_F	1.284	0.90
152_P	189_N	1.284	0.90
60_L	80_H	1.284	0.90
144_F	148_I	1.271	0.90
85_V	113_L	1.266	0.89
88_Y	141_V	1.246	0.88
116_R	132_Y	1.240	0.88
135_N	139_F	1.236	0.88
152_P	155_I	1.231	0.88
56_F	151_F	1.229	0.88
148_I	184_V	1.226	0.87
103_F	151_F	1.223	0.87
109_S	114_N	1.220	0.87
114_N	118_F	1.215	0.87
13_I	16_S	1.209	0.86
52_S	104_L	1.196	0.86
4_N	80_H	1.193	0.85
7_V	58_Y	1.175	0.84
63_M	80_H	1.175	0.84
83_T	91_Y	1.171	0.84
111_P	143_F	1.171	0.84
106_H	151_F	1.166	0.84
5_R	9_F	1.163	0.83
6_V	15_S	1.162	0.83
187_V	194_Y	1.162	0.83
194_Y	198_R	1.161	0.83
182_L	189_N	1.160	0.83
80_H	151_F	1.158	0.83
57_L	68_R	1.157	0.83
57_L	124_G	1.153	0.83
109_S	144_F	1.150	0.82
5_R	192_W	1.144	0.82
164_P	167_L	1.142	0.82
64_L	77_L	1.140	0.82
94_N	109_S	1.135	0.81
5_R	196_I	1.133	0.81
27_P	30_W	1.132	0.81
139_F	192_W	1.128	0.81
134_F	198_R	1.123	0.80
40_Y	130_S	1.122	0.80
120_K	136_G	1.120	0.80
63_M	99_G	1.112	0.79
4_N	8_S	1.105	0.79
179_L	183_L	1.105	0.79
159_Y	163_W	1.104	0.79
119_L	131_L	1.100	0.78
63_M	151_F	1.092	0.78
118_F	148_I	1.091	0.78
103_F	186_F	1.088	0.77
103_F	139_F	1.083	0.77
80_H	119_L	1.078	0.76
89_F	93_Y	1.075	0.76
145_V	149_V	1.074	0.76
30_W	36_D	1.070	0.76
114_N	117_W	1.068	0.75
18_W	48_Y	1.067	0.75
48_Y	73_F	1.063	0.75
113_L	136_G	1.054	0.74
55_Y	59_D	1.047	0.73
55_Y	193_F	1.046	0.73
110_T	136_G	1.037	0.72
140_A	152_P	1.037	0.72
11_H	97_R	1.034	0.72
31_S	34_P	1.031	0.72
52_S	185_L	1.030	0.72
77_L	161_D	1.027	0.71
153_Y	193_F	1.027	0.71
115_L	131_L	1.025	0.71
83_T	86_L	1.023	0.71
111_P	135_N	1.019	0.70
58_Y	94_N	1.017	0.70
54_G	117_W	1.016	0.70
109_S	146_F	1.014	0.70
58_Y	63_M	1.008	0.69
9_F	115_L	1.007	0.69
116_R	189_N	1.000	0.68

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: (10May14)
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
3omdA	2	0.2475	0.8	0.966	Contact Map
2lx0A	1	0.1616	0.7	0.967	Contact Map
3wguG	2	0.1364	0.7	0.968	Contact Map
2l8sA	1	0.1768	0.6	0.969	Contact Map
1scfA	4	0	0.6	0.969	Contact Map
4gh4D	1	0.101	0.6	0.969	Contact Map
1b44D	5	0.1061	0.6	0.97	Contact Map
2rnzA	1	0.1616	0.6	0.97	Contact Map
2rspA	2	0.2121	0.5	0.97	Contact Map
2k2wA	1	0.202	0.5	0.97	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 6.0868 seconds.