OPENSEQ.org - 1476355239 - GREMLIN Submission

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ccdc84 -force run

ID:	1476355239	Query Sequence YCKVCRLHHDHGSRHKYFPRHKDLLSTFLDRFRTKIADVRFFLKNPSVLRPQEQSQNRVWCVFCDEDIVELGSSFACSKAINHFASSDHLKNVKQFLSKNGPAMDCIDDFRISEANVATWRRKCQSLGSE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	130 (127)
Sequences:	116 (84.3)
Seq/Len:	0.913
Nf(neff/√len):	7.5

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: 0.913).

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
36_I	48_V	1.838	0.91
29_L	40_R	1.827	0.90
36_I	59_V	1.789	0.89
89_H	96_F	1.653	0.83
57_N	70_E	1.622	0.82
23_D	30_D	1.540	0.77
13_S	16_K	1.528	0.76
1_Y	31_R	1.484	0.73
91_K	98_S	1.460	0.71
6_R	13_S	1.448	0.70
48_V	63_F	1.445	0.70
4_V	13_S	1.444	0.70
25_L	40_R	1.440	0.70
44_K	98_S	1.427	0.69
7_L	20_R	1.414	0.68
59_V	68_I	1.393	0.66
73_S	90_L	1.381	0.65
55_S	115_A	1.378	0.65
115_A	118_A	1.328	0.61
114_E	117_V	1.296	0.58
80_A	100_N	1.269	0.56
108_D	119_T	1.258	0.55
8_H	11_H	1.254	0.54
59_V	115_A	1.248	0.54
4_V	74_S	1.235	0.52
60_W	64_C	1.229	0.52
12_G	60_W	1.226	0.52
35_K	98_S	1.211	0.50
41_F	51_P	1.187	0.48
8_H	12_G	1.175	0.47
102_P	110_F	1.163	0.46
121_R	124_C	1.160	0.46
28_F	78_S	1.158	0.46
122_R	125_Q	1.143	0.44
6_R	113_S	1.136	0.44
16_K	41_F	1.133	0.43
79_K	99_K	1.131	0.43
98_S	116_N	1.123	0.42
95_Q	100_N	1.119	0.42
68_I	127_L	1.119	0.42
31_R	46_P	1.114	0.42
91_K	116_N	1.113	0.42
44_K	68_I	1.109	0.41
79_K	120_W	1.106	0.41
78_S	82_N	1.100	0.40
33_R	112_I	1.096	0.40
14_R	18_F	1.093	0.40
62_V	65_D	1.087	0.39
67_D	81_I	1.086	0.39
50_R	63_F	1.085	0.39
29_L	51_P	1.081	0.39
28_F	65_D	1.080	0.39
4_V	17_Y	1.078	0.38
54_Q	123_K	1.077	0.38
95_Q	109_D	1.074	0.38
56_Q	66_E	1.073	0.38
19_P	31_R	1.072	0.38
106_C	115_A	1.065	0.37
4_V	28_F	1.063	0.37
13_S	95_Q	1.058	0.37
16_K	22_K	1.050	0.36
34_T	71_L	1.043	0.36
28_F	74_S	1.037	0.35
71_L	113_S	1.024	0.34
107_I	117_V	1.023	0.34
88_D	110_F	1.022	0.34
17_Y	21_H	1.021	0.34
20_R	23_D	1.012	0.33
25_L	60_W	1.008	0.33

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
1zu1A	1	0.6769	95	0.882	Contact Map
4f9cB	1	0.3692	77.4	0.915	Contact Map
2mkdA	1	0.4462	64.7	0.922	Contact Map
3cw1L	4	0.4385	50.3	0.929	Contact Map
2yrkA	1	0.2923	36.7	0.934	Contact Map
3ihpA	2	0.5538	24.7	0.94	Contact Map
2jobA	1	0.6923	15.9	0.945	Contact Map
2uzgA	1	0.4385	11.7	0.948	Contact Map
2mdlA	1	0.1846	11.5	0.948	Contact Map
3cuqA	1	0.7385	10.8	0.949	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.

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