OPENSEQ.org - 1430312596 - GREMLIN Submission

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

tssaa

ID:	1430312596	Query Sequence AADILSLEPEALQIADNEGTEAALSWLQAARPGIAQSDRSNWLLRLLMARVAEQTGKNDLALHLLAELDERATRLTLSQWEPELVFEVKARRLKLLRMKSAKTESDRVRLQPDMEHLLAGLIAIDAARAAVLCNSGSAA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	139 (131)
Sequences:	281 (172.4)
Seq/Len:	2.145
Nf(neff/√len):	15.1

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: 2.145).

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
39_R	81_E	2.873	1.00
49_A	65_L	1.926	0.99
92_R	113_D	1.926	0.99
19_G	22_A	1.771	0.98
49_A	61_A	1.767	0.98
65_L	92_R	1.576	0.94
43_L	128_R	1.468	0.91
49_A	92_R	1.463	0.91
15_A	27_L	1.451	0.90
25_S	41_N	1.411	0.89
12_L	19_G	1.377	0.87
95_L	99_K	1.373	0.87
52_A	92_R	1.371	0.87
104_E	109_R	1.325	0.84
66_A	113_D	1.318	0.84
20_T	55_T	1.301	0.82
72_A	116_H	1.293	0.82
41_N	125_D	1.268	0.80
4_I	55_T	1.268	0.80
68_L	121_L	1.254	0.79
21_E	52_A	1.248	0.79
49_A	52_A	1.237	0.78
33_G	132_L	1.235	0.78
69_D	89_K	1.226	0.77
2_A	44_L	1.210	0.76
27_L	96_L	1.201	0.75
45_R	57_K	1.198	0.75
15_A	95_L	1.195	0.74
73_T	98_M	1.182	0.73
41_N	124_I	1.157	0.71
81_E	121_L	1.156	0.71
20_T	51_V	1.144	0.70
93_L	121_L	1.114	0.67
40_S	56_G	1.110	0.66
47_L	130_A	1.103	0.66
13_Q	130_A	1.100	0.65
38_D	51_V	1.098	0.65
45_R	48_M	1.098	0.65
64_L	93_L	1.098	0.65
96_L	129_A	1.090	0.64
72_A	121_L	1.077	0.63
44_L	123_A	1.073	0.62
100_S	103_T	1.072	0.62
34_I	40_S	1.070	0.62
48_M	84_L	1.063	0.61
11_A	14_I	1.060	0.61
52_A	125_D	1.060	0.61
39_R	80_W	1.056	0.61
28_Q	48_M	1.055	0.61
88_V	115_E	1.052	0.60
45_R	71_R	1.046	0.60
41_N	96_L	1.046	0.60
22_A	113_D	1.040	0.59
42_W	91_R	1.039	0.59
25_S	55_T	1.037	0.59
37_S	67_E	1.036	0.58
76_T	120_G	1.036	0.58
100_S	123_A	1.034	0.58
26_W	86_F	1.033	0.58
24_L	60_L	1.033	0.58
8_E	47_L	1.027	0.57
92_R	125_D	1.027	0.57
13_Q	60_L	1.019	0.57
48_M	90_A	1.019	0.57
112_P	120_G	1.017	0.56
51_V	89_K	1.016	0.56
21_E	50_R	1.014	0.56
50_R	61_A	1.011	0.56
55_T	120_G	1.010	0.56
108_V	132_L	1.009	0.55
80_W	121_L	1.003	0.55
65_L	91_R	1.002	0.55

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
4r7sA	1	0.8561	82.8	0.869	Contact Map
3urzA	2	0.8417	81.5	0.872	Contact Map
4gywA	2	0.8345	73.9	0.88	Contact Map
4ja7A	1	0.7698	73.9	0.88	Contact Map
2r5sA	2	0.8129	73.8	0.88	Contact Map
4i2zA	1	0.8561	72.4	0.881	Contact Map
4a1sA	2	0.8993	71.4	0.882	Contact Map
1xnfA	2	0.8489	70.2	0.883	Contact Map
2mhkA	1	0.9209	69.4	0.884	Contact Map
2dbaA	1	0.8561	69.2	0.884	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 1.0271 seconds.