OPENSEQ.org - 1428067799 - GREMLIN Submission

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Tim17Pred

ID:	1428067799	Query Sequence MSADHSRDPCPIVILNDFGGAFAMGAIGGVVWHGIKGFRNSPLGERGSGAMSAIKARAPVLGGNFGVWGGLFSTFDCAVKAVRKREDPWNAIIAGFFTGGALAVRGGWRHTRNSSITCACLLGVIEGVGLMFQRYAAWQAKPMAPPLPEAPSSQPLQA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	158 (143)
Sequences:	312 (182.2)
Seq/Len:	2.182
Nf(neff/√len):	15.2

HHblits Results: (2013_03)
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: 2.182).

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
96_F	115_S	3.022	1.00
10_C	77_C	1.890	0.99
57_R	60_V	1.873	0.99
19_G	22_F	1.786	0.98
71_L	75_F	1.617	0.95
11_P	22_F	1.579	0.95
83_R	90_N	1.498	0.92
133_Q	136_A	1.460	0.91
58_A	62_G	1.381	0.87
138_W	141_K	1.378	0.87
92_I	123_G	1.376	0.87
13_V	16_N	1.365	0.87
30_V	34_G	1.342	0.85
100_G	108_W	1.332	0.85
62_G	98_T	1.314	0.84
140_A	144_A	1.289	0.82
51_M	55_K	1.288	0.82
39_R	44_G	1.285	0.82
75_F	97_F	1.284	0.82
132_F	138_W	1.245	0.79
73_S	98_T	1.243	0.79
79_V	94_A	1.236	0.78
65_F	77_C	1.231	0.78
77_C	83_R	1.229	0.78
11_P	14_I	1.223	0.77
133_Q	140_A	1.219	0.77
3_A	139_Q	1.213	0.76
105_R	115_S	1.198	0.75
13_V	66_G	1.197	0.75
54_I	124_V	1.193	0.75
97_F	116_I	1.187	0.74
141_K	144_A	1.187	0.74
131_M	136_A	1.186	0.74
73_S	100_G	1.184	0.74
130_L	137_A	1.184	0.74
137_A	143_M	1.184	0.74
8_D	20_G	1.161	0.72
96_F	112_R	1.148	0.71
69_G	125_I	1.146	0.70
72_F	85_R	1.140	0.70
23_A	62_G	1.140	0.70
101_A	104_V	1.131	0.69
57_R	72_F	1.127	0.69
83_R	87_D	1.116	0.67
29_G	58_A	1.116	0.67
139_Q	145_P	1.112	0.67
75_F	106_G	1.109	0.67
139_Q	144_A	1.090	0.65
65_F	83_R	1.088	0.65
22_F	44_G	1.073	0.63
71_L	91_A	1.073	0.63
55_K	60_V	1.065	0.62
91_A	126_E	1.059	0.61
132_F	135_Y	1.058	0.61
138_W	144_A	1.057	0.61
52_S	55_K	1.056	0.61
66_G	81_A	1.052	0.61
139_Q	142_P	1.051	0.61
33_H	75_F	1.049	0.60
139_Q	143_M	1.049	0.60
138_W	143_M	1.048	0.60
47_G	50_A	1.048	0.60
75_F	101_A	1.046	0.60
94_A	119_A	1.046	0.60
65_F	90_N	1.036	0.59
72_F	92_I	1.033	0.59
79_V	101_A	1.031	0.58
113_N	117_T	1.026	0.58
140_A	143_M	1.026	0.58
96_F	119_A	1.024	0.58
67_V	124_V	1.023	0.57
91_A	110_H	1.021	0.57
25_G	29_G	1.019	0.57
55_K	105_R	1.016	0.57
129_G	137_A	1.009	0.56
79_V	93_I	1.008	0.56
17_D	68_W	1.007	0.56
62_G	70_G	1.006	0.56
13_V	118_C	1.006	0.56
8_D	125_I	1.004	0.55
76_D	121_L	1.000	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
1d2tA	1	0.3418	5.2	0.957	Contact Map
3vemA	4	0.0633	3.9	0.96	Contact Map
4rqoA	2	0.443	3.5	0.96	Contact Map
4oo0A	2	0.3861	2.4	0.964	Contact Map
2e84A	1	0.1646	2.3	0.964	Contact Map
4c9gA	1	0.7532	2.1	0.965	Contact Map
2ls2A	1	0.1582	2.1	0.965	Contact Map
1ex2A	2	0.3608	1.9	0.966	Contact Map
4pw2A	1	0	1.9	0.966	Contact Map
3w9eC	1	0.0949	1.7	0.967	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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