OPENSEQ.org - 1399486638 - GREMLIN Submission

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

Welcome: casp11@openseq.org

T0768

ID:	1399486638	Query Sequence MKKRALSLLLALCLCLSLMPAASASVVESTVQVGPYTFEIWFDGTATLTRYDESLAGSTYADIPASVTDENGQEYPVTVIGEKAFEETNITGVTVPDSVISIGRLAFAYCNSLSDVKLSENLIYINELAFASCDALKEITIPASVEKMDNPFRWSNALDTVYMEGMVAPE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	170 (168)
Sequences:	171 (138)
Seq/Len:	1.018
Nf(neff/√len):	10.6

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: 1.018).

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
125_I	129_A	2.772	1.00
133_C	155_S	2.356	0.99
118_L	122_L	2.187	0.98
110_C	133_C	2.179	0.98
96_P	119_S	1.961	0.95
139_I	161_V	1.922	0.94
106_A	125_I	1.828	0.92
102_I	106_A	1.819	0.92
110_C	155_S	1.805	0.91
106_A	129_A	1.716	0.88
106_A	145_V	1.659	0.86
130_F	152_F	1.631	0.85
136_L	158_L	1.596	0.83
129_A	142_P	1.591	0.83
110_C	145_V	1.556	0.81
72_G	75_Y	1.543	0.80
145_V	166_M	1.535	0.79
106_A	166_M	1.500	0.77
139_I	163_M	1.490	0.77
145_V	168_A	1.431	0.72
103_G	119_S	1.428	0.72
115_D	160_T	1.417	0.71
148_M	151_P	1.374	0.68
123_I	146_E	1.353	0.66
141_I	145_V	1.340	0.65
125_I	166_M	1.336	0.65
114_S	137_K	1.336	0.65
98_S	119_S	1.302	0.62
64_P	116_V	1.291	0.61
113_L	116_V	1.290	0.61
125_I	142_P	1.288	0.61
81_G	141_I	1.286	0.60
93_V	133_C	1.240	0.56
122_L	166_M	1.230	0.55
93_V	106_A	1.229	0.55
116_V	133_C	1.214	0.54
6_L	102_I	1.211	0.54
99_V	145_V	1.207	0.53
119_S	139_I	1.205	0.53
102_I	142_P	1.203	0.53
70_E	93_V	1.195	0.52
121_N	144_S	1.163	0.49
30_T	42_F	1.154	0.48
85_F	130_F	1.154	0.48
89_N	118_L	1.154	0.48
155_S	166_M	1.146	0.47
72_G	76_P	1.145	0.47
151_P	166_M	1.140	0.47
64_P	67_V	1.138	0.47
148_M	166_M	1.133	0.46
78_T	122_L	1.131	0.46
129_A	166_M	1.129	0.46
129_A	148_M	1.126	0.46
122_L	144_S	1.121	0.45
125_I	148_M	1.104	0.44
19_M	132_S	1.101	0.43
78_T	133_C	1.092	0.42
70_E	75_Y	1.083	0.42
92_G	115_D	1.072	0.41
132_S	162_Y	1.071	0.41
99_V	114_S	1.065	0.40
46_A	50_R	1.062	0.40
11_A	14_L	1.056	0.39
88_T	116_V	1.051	0.39
65_A	77_V	1.050	0.39
79_V	124_Y	1.050	0.39
106_A	148_M	1.045	0.38
16_L	95_V	1.043	0.38
20_P	139_I	1.043	0.38
91_T	114_S	1.042	0.38
14_L	23_S	1.042	0.38
70_E	163_M	1.039	0.38
9_L	156_N	1.037	0.38
134_D	156_N	1.034	0.37
45_T	135_A	1.029	0.37
93_V	116_V	1.027	0.37
106_A	151_P	1.021	0.36
59_T	77_V	1.018	0.36
47_T	89_N	1.017	0.36
145_V	148_M	1.015	0.36
47_T	50_R	1.002	0.35

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: (01May14)
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
4gt6A	1	0.8353	99.7	0.519	Contact Map
4fs7A	1	0.8059	99.6	0.552	Contact Map
3t6qA	2	0.7824	99.5	0.6	Contact Map
4fdwA	1	0.9529	99.5	0.601	Contact Map
2lz0A	1	0.5706	99.5	0.604	Contact Map
3zyiA	1	0.8059	99.4	0.607	Contact Map
3zyjA	2	0.8059	99.4	0.608	Contact Map
4kt1A	1	0.8059	99.4	0.609	Contact Map
3sb4A	2	0.9529	99.4	0.619	Contact Map
1ziwA	1	0.7471	99.4	0.624	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 0.9509 seconds.