OPENSEQ.org - 1508961640 - GREMLIN Submission

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dhcfl_cut2

ID:	1508961640	Query Sequence NHHLGKMDETDTSPAPTVRITLLQGRPSPKRTPFYMMADGTGTIATYIHLPAFKSKMPVYGIDSPFLRCPSRLTKDVGIPGVAKLIVDALVTAQPTGPLMIGGFSAGSIVAYEVTRQLGALGRQVTGLVLIDMCCPRSSLLDEDAMNSEDDASFAIFENAVSKDGLWSLASTTQDHFRAYHVAMHAYHPPYMTAQERPSHTAVIWAEKGMVNRVVGNDRLMQMLADQGIPTTSYPGYMEDPRLGAFACLVPDRTAADLGPNGWEKYTAGEVLALSVAGDHLDLPMPGHVHLLQREMEKAFAY	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	302 (277)
Sequences:	1317 (1026)
Seq/Len:	4.755
Nf(neff/√len):	61.6

HHblits Results: (2016_02)
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: 4.755).

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
91_V	123_R	3.718	1.00
100_M	126_T	3.490	1.00
37_M	114_V	3.478	1.00
84_K	117_Q	3.283	1.00
192_M	199_S	3.269	1.00
36_M	102_G	3.133	1.00
87_V	114_V	3.078	1.00
96_T	123_R	2.781	1.00
108_S	133_M	2.780	1.00
94_Q	99_L	2.777	1.00
113_E	117_Q	2.777	1.00
106_A	110_V	2.557	1.00
99_L	123_R	2.521	1.00
47_Y	104_F	2.459	1.00
38_A	86_I	2.407	1.00
119_G	198_P	2.352	1.00
91_V	121_L	2.298	1.00
33_P	58_P	2.213	1.00
39_D	47_Y	2.204	1.00
113_E	116_R	2.192	1.00
90_L	114_V	2.177	1.00
34_F	102_G	2.170	1.00
91_V	99_L	2.076	1.00
39_D	104_F	2.055	1.00
39_D	46_T	2.010	1.00
44_I	61_G	1.965	1.00
38_A	104_F	1.951	1.00
65_P	85_L	1.900	1.00
94_Q	123_R	1.883	1.00
279_D	282_D	1.862	1.00
29_P	58_P	1.811	1.00
35_Y	99_L	1.789	1.00
102_G	129_V	1.787	1.00
34_F	59_V	1.776	1.00
78_G	81_G	1.752	1.00
208_K	277_A	1.746	1.00
35_Y	94_Q	1.691	0.99
33_P	57_M	1.690	0.99
24_Q	54_K	1.680	0.99
79_I	83_A	1.678	0.99
100_M	127_G	1.606	0.99
205_W	275_S	1.599	0.99
94_Q	97_G	1.550	0.99
87_V	90_L	1.541	0.99
105_S	132_D	1.531	0.99
94_Q	98_P	1.514	0.98
19_R	89_A	1.503	0.98
95_P	99_L	1.484	0.98
278_G	288_H	1.477	0.98
207_E	277_A	1.476	0.98
37_M	83_A	1.457	0.98
54_K	297_E	1.443	0.98
243_L	246_F	1.424	0.97
32_T	100_M	1.419	0.97
83_A	113_E	1.406	0.97
80_P	187_Y	1.405	0.97
53_F	59_V	1.401	0.97
110_V	114_V	1.400	0.97
83_A	114_V	1.398	0.97
278_G	282_D	1.395	0.97
88_D	121_L	1.382	0.97
57_M	100_M	1.370	0.97
80_P	113_E	1.369	0.97
112_Y	116_R	1.368	0.97
106_A	180_Y	1.359	0.96
33_P	60_Y	1.355	0.96
31_R	56_K	1.353	0.96
35_Y	93_A	1.321	0.96
274_L	295_E	1.316	0.95
65_P	82_V	1.313	0.95
38_A	82_V	1.302	0.95
129_V	296_M	1.297	0.95
32_T	126_T	1.290	0.95
176_H	180_Y	1.288	0.95
89_A	92_T	1.287	0.95
83_A	117_Q	1.285	0.95
98_P	123_R	1.270	0.94
39_D	42_G	1.252	0.94
112_Y	187_Y	1.249	0.93
80_P	117_Q	1.243	0.93
35_Y	97_G	1.222	0.92
64_S	176_H	1.219	0.92
79_I	110_V	1.219	0.92
37_M	62_I	1.216	0.92
208_K	278_G	1.200	0.92
46_T	104_F	1.196	0.91
34_F	100_M	1.189	0.91
105_S	280_H	1.182	0.91
208_K	279_D	1.182	0.91
35_Y	90_L	1.176	0.90
131_I	283_L	1.174	0.90
19_R	22_L	1.173	0.90
22_L	25_G	1.168	0.90
36_M	59_V	1.157	0.89
25_G	58_P	1.156	0.89
127_G	296_M	1.155	0.89
207_E	275_S	1.154	0.89
179_A	183_A	1.142	0.89
117_Q	121_L	1.137	0.88
66_F	82_V	1.133	0.88
7_M	11_D	1.124	0.88
244_G	247_A	1.114	0.87
91_V	94_Q	1.109	0.87
60_Y	93_A	1.108	0.87
51_P	293_Q	1.102	0.86
116_R	119_G	1.098	0.86
38_A	47_Y	1.089	0.85
129_V	204_I	1.079	0.85
117_Q	120_A	1.075	0.84
87_V	117_Q	1.074	0.84
41_T	104_F	1.065	0.83
23_L	47_Y	1.053	0.83
127_G	202_A	1.051	0.82
40_G	281_L	1.045	0.82
116_R	120_A	1.045	0.82
277_A	288_H	1.038	0.81
260_P	264_E	1.023	0.80
80_P	186_A	1.021	0.80
103_G	107_G	1.014	0.79
131_I	278_G	1.005	0.78
97_G	123_R	1.002	0.78
242_R	246_F	1.001	0.78
22_L	29_P	1.000	0.78

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
2vz8A	2	0	100	0.352	Contact Map
2cb9A	1	0.6954	100	0.548	Contact Map
1jmkC	2	0.745	100	0.566	Contact Map
3tejA	2	0.8046	99.9	0.577	Contact Map
1kezA	3	0.7881	99.9	0.581	Contact Map
3ilsA	1	0.8411	99.9	0.587	Contact Map
2vsqA	1	0.7285	99.9	0.623	Contact Map
3tjmA	1	0.7649	99.9	0.635	Contact Map
2k2qB	1	0.7583	99.9	0.641	Contact Map
2px6A	2	0.7384	99.9	0.649	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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