OPENSEQ.org - 1430310682 - GREMLIN Submission

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ID:	1430310682	Query Sequence AADILSLEPEALQIADNEGTEAALSWLQAAAAGIAQSDRSNWLLRLLMARVAEQTGKNDLALHLLAELDERATRLTLSQWEPELVFEVKARRLKLLRMKSAKTESDRVRLQPDMEHLLAGLIAIDAARAAVLCNSGSAA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	139 (131)
Sequences:	279 (170.6)
Seq/Len:	2.130
Nf(neff/√len):	14.9

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: 2.130).

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	2.744	1.00
92_R	113_D	2.063	0.99
49_A	65_L	1.954	0.99
19_G	22_A	1.830	0.98
49_A	61_A	1.700	0.97
65_L	92_R	1.610	0.95
43_L	128_R	1.569	0.94
15_A	27_L	1.475	0.91
95_L	99_K	1.375	0.87
20_T	55_T	1.358	0.86
69_D	89_K	1.336	0.84
31_A	50_R	1.313	0.83
66_A	113_D	1.310	0.83
41_N	124_I	1.299	0.82
25_S	41_N	1.294	0.82
12_L	19_G	1.291	0.82
73_T	98_M	1.278	0.81
68_L	121_L	1.255	0.79
45_R	57_K	1.250	0.79
4_I	55_T	1.247	0.78
104_E	109_R	1.236	0.78
37_S	106_D	1.221	0.76
48_M	84_L	1.214	0.76
47_L	130_A	1.213	0.76
2_A	44_L	1.209	0.75
96_L	129_A	1.206	0.75
41_N	125_D	1.203	0.75
38_D	51_V	1.202	0.75
11_A	14_I	1.198	0.74
49_A	52_A	1.177	0.73
30_A	91_R	1.175	0.72
64_L	93_L	1.172	0.72
34_I	40_S	1.170	0.72
21_E	52_A	1.164	0.71
27_L	96_L	1.151	0.70
20_T	51_V	1.149	0.70
72_A	116_H	1.148	0.70
55_T	120_G	1.138	0.69
25_S	55_T	1.127	0.68
52_A	92_R	1.125	0.68
48_M	64_L	1.118	0.67
45_R	71_R	1.116	0.67
39_R	80_W	1.113	0.66
34_I	121_L	1.099	0.65
44_L	123_A	1.088	0.64
11_A	81_E	1.086	0.64
15_A	95_L	1.086	0.64
49_A	92_R	1.077	0.63
13_Q	130_A	1.075	0.62
40_S	56_G	1.071	0.62
51_V	89_K	1.069	0.62
81_E	121_L	1.068	0.62
17_N	37_S	1.066	0.61
14_I	18_E	1.060	0.61
24_L	60_L	1.058	0.61
92_R	125_D	1.055	0.60
52_A	125_D	1.052	0.60
19_G	50_R	1.047	0.59
15_A	130_A	1.045	0.59
21_E	50_R	1.045	0.59
80_W	121_L	1.043	0.59
50_R	61_A	1.043	0.59
45_R	48_M	1.038	0.58
61_A	77_L	1.037	0.58
88_V	115_E	1.036	0.58
40_S	45_R	1.036	0.58
37_S	67_E	1.035	0.58
93_L	121_L	1.030	0.58
8_E	47_L	1.025	0.57
72_A	121_L	1.015	0.56
120_G	133_C	1.012	0.56
84_L	124_I	1.012	0.56
76_T	120_G	1.011	0.55
2_A	74_R	1.010	0.55
38_D	79_Q	1.003	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	77.2	0.88	Contact Map
2r5sA	2	0.8129	74.5	0.882	Contact Map
3urzA	2	0.8417	74.3	0.883	Contact Map
4ja7A	1	0.7698	68	0.888	Contact Map
1xnfA	2	0.8489	67.9	0.888	Contact Map
4kvmA	4	0.8345	66.9	0.889	Contact Map
4gywA	2	0.8345	66.1	0.89	Contact Map
4a1sA	2	0.8993	62.7	0.892	Contact Map
3qouA	1	0.8058	62.5	0.892	Contact Map
4i2zA	1	0.8561	60.8	0.893	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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