OPENSEQ.org - 1507225013 - GREMLIN Submission

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

KNL1-2-rwd

ID:	1507225013	Query Sequence SLLVHKLIFQYVEEKESWKKTCTTQHQLPKMLEEFSLVVHHCRLLGEEIEYLKRWGPNYNLMNIDINNNELRLLFSSSAAFAKFEITLFLSAYYPSVPLPSTIQNHVGNTSQDDIATILSKVPLENNYLKNVVKQIYQDLFQDCHFYH	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	148 (141)
Sequences:	155 (91.7)
Seq/Len:	1.099
Nf(neff/√len):	7.7

Jackhmmer Results: (2016_04)
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: 1.099).

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 > 50% 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
75_F	84_F	2.427	0.99
22_C	31_M	2.158	0.98
93_Y	115_I	1.810	0.93
7_L	12_V	1.683	0.88
45_L	83_K	1.587	0.84
115_I	136_I	1.576	0.84
98_P	102_T	1.557	0.83
95_P	128_Y	1.551	0.82
2_L	25_Q	1.533	0.81
125_E	131_N	1.504	0.79
8_I	16_E	1.494	0.79
109_N	115_I	1.486	0.78
59_Y	131_N	1.460	0.77
29_P	105_N	1.398	0.72
111_S	114_D	1.377	0.70
118_I	137_Y	1.366	0.70
100_P	117_T	1.351	0.68
4_V	46_G	1.345	0.68
90_L	102_T	1.323	0.66
59_Y	64_I	1.258	0.60
94_Y	128_Y	1.240	0.59
114_D	135_Q	1.233	0.58
45_L	100_P	1.224	0.57
103_I	114_D	1.201	0.55
119_L	123_P	1.190	0.54
31_M	43_R	1.177	0.53
28_L	35_F	1.163	0.51
22_C	32_L	1.153	0.50
48_E	94_Y	1.146	0.50
2_L	16_E	1.141	0.49
31_M	61_L	1.138	0.49
113_D	130_K	1.136	0.49
27_Q	57_P	1.134	0.49
124_L	140_L	1.133	0.48
35_F	130_K	1.131	0.48
49_I	67_N	1.126	0.48
20_K	23_T	1.120	0.47
37_L	47_E	1.120	0.47
11_Y	20_K	1.117	0.47
34_E	79_A	1.113	0.47
117_T	123_P	1.113	0.47
26_H	115_I	1.105	0.46
2_L	5_H	1.102	0.46
21_T	115_I	1.095	0.45
49_I	112_Q	1.086	0.44
48_E	85_E	1.084	0.44
8_I	126_N	1.080	0.43
92_A	102_T	1.076	0.43
43_R	84_F	1.075	0.43
12_V	20_K	1.071	0.43
16_E	24_T	1.071	0.43
77_S	122_V	1.069	0.42
96_S	138_Q	1.067	0.42
37_L	41_H	1.064	0.42
90_L	106_H	1.060	0.42
22_C	43_R	1.059	0.41
62_M	69_N	1.058	0.41
128_Y	140_L	1.056	0.41
35_F	113_D	1.056	0.41
44_L	134_K	1.056	0.41
31_M	79_A	1.054	0.41
63_N	71_L	1.053	0.41
49_I	127_N	1.052	0.41
32_L	36_S	1.051	0.41
92_A	98_P	1.049	0.41
24_T	36_S	1.047	0.40
14_E	57_P	1.038	0.40
69_N	136_I	1.037	0.39
119_L	122_V	1.036	0.39
27_Q	89_F	1.035	0.39
13_E	16_E	1.031	0.39
53_K	114_D	1.031	0.39
57_P	70_E	1.029	0.39
127_N	131_N	1.023	0.38
74_L	85_E	1.020	0.38
51_Y	119_L	1.016	0.38
3_L	20_K	1.012	0.37
46_G	55_W	1.010	0.37
7_L	49_I	1.010	0.37
11_Y	58_N	1.009	0.37
6_K	49_I	1.002	0.36

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
4nfaA	1	0.9459	100	0.051	Contact Map
4y1lC	1	0	59.2	0.922	Contact Map
1jatB	1	0.7095	51.2	0.926	Contact Map
2yz0A	1	0.777	31	0.935	Contact Map
1jatA	1	0.7027	30.4	0.935	Contact Map
4ccgA	2	0.7432	25.7	0.937	Contact Map
2r0jA	1	0.6824	24.4	0.938	Contact Map
2a7lA	2	0.7027	24.1	0.938	Contact Map
1ayzA	3	0.7027	22.3	0.939	Contact Map
1yh2A	1	0.7297	20.9	0.94	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 3.447 seconds.