OPENSEQ.org - 1399787609 - GREMLIN Submission

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babushka

ID:	1399787609	Query Sequence MDVQRVGKAGLHRVDSKKQQTAAGVSFSEVMGKQRDEKAYERLQALMSKIDDQGKLLSETRTIEELRKYKELVKEFVGDAVELGLRLEERRGFNRRGRTKIYKIVKEVDRKLLDLTDAVLAKEKKGLDILNMVGEIKGLLINIYA	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	145 (144)
Sequences:	290 (236.5)
Seq/Len:	2.014
Nf(neff/√len):	19.7

Jackhmmer Results: (2014_04_16)
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: 2.014).

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
74_K	109_D	2.192	1.00
113_L	117_D	1.901	0.98
88_E	106_K	1.841	0.98
84_G	144_Y	1.828	0.98
84_G	113_L	1.751	0.97
84_G	142_N	1.663	0.96
134_G	137_K	1.638	0.95
70_K	116_T	1.602	0.94
31_M	142_N	1.568	0.93
113_L	142_N	1.552	0.93
123_E	134_G	1.537	0.92
65_E	100_K	1.483	0.91
130_L	134_G	1.479	0.90
130_L	135_E	1.472	0.90
108_V	140_L	1.454	0.89
54_G	119_V	1.410	0.87
111_K	135_E	1.385	0.86
62_T	65_E	1.370	0.85
109_D	134_G	1.358	0.85
81_V	106_K	1.331	0.83
108_V	143_I	1.330	0.83
118_A	132_M	1.304	0.81
2_D	5_R	1.284	0.80
111_K	127_L	1.271	0.79
58_S	109_D	1.270	0.79
70_K	83_L	1.250	0.77
118_A	121_A	1.238	0.76
62_T	133_V	1.225	0.75
36_D	49_K	1.222	0.75
53_Q	63_I	1.217	0.74
2_D	6_V	1.209	0.74
30_V	134_G	1.188	0.72
96_R	108_V	1.185	0.72
114_D	127_L	1.172	0.70
57_L	89_E	1.171	0.70
92_G	95_R	1.170	0.70
134_G	142_N	1.166	0.70
125_K	128_D	1.162	0.70
56_L	74_K	1.158	0.69
43_L	76_F	1.150	0.68
111_K	114_D	1.150	0.68
85_L	144_Y	1.150	0.68
42_R	56_L	1.149	0.68
129_I	141_I	1.147	0.68
54_G	133_V	1.138	0.67
20_Q	45_A	1.130	0.66
95_R	98_R	1.123	0.66
110_R	114_D	1.119	0.65
104_I	129_I	1.119	0.65
42_R	79_D	1.112	0.65
92_G	101_I	1.100	0.63
61_R	135_E	1.099	0.63
104_I	134_G	1.090	0.62
84_G	141_I	1.084	0.62
137_K	140_L	1.084	0.62
53_Q	72_L	1.076	0.61
65_E	119_V	1.063	0.59
116_T	119_V	1.059	0.59
50_I	102_Y	1.059	0.59
105_V	116_T	1.054	0.58
63_I	120_L	1.051	0.58
52_D	55_K	1.049	0.58
63_I	102_Y	1.047	0.58
51_D	55_K	1.047	0.58
84_G	134_G	1.040	0.57
44_Q	69_Y	1.040	0.57
25_V	29_E	1.034	0.56
53_Q	112_L	1.033	0.56
76_F	97_G	1.032	0.56
63_I	96_R	1.025	0.55
87_L	93_F	1.023	0.55
57_L	125_K	1.022	0.55
14_V	120_L	1.021	0.55
103_K	134_G	1.021	0.55
121_A	131_N	1.020	0.55
5_R	8_K	1.011	0.54
26_S	143_I	1.002	0.53
37_E	108_V	1.000	0.53

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: (01May14)
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
2qupA	1	0.8207	100	0.119	Contact Map
2p61A	1	0.7793	100	0.142	Contact Map
2hc5A	1	0.7517	69.4	0.906	Contact Map
2kw6A	2	0.3862	12.3	0.939	Contact Map
4nsoB	1	0.5862	9.3	0.942	Contact Map
3bghA	2	0.4	8.7	0.942	Contact Map
2oieA	4	0.5655	8	0.944	Contact Map
4nooB	2	0.5724	5.6	0.947	Contact Map
4l6yA	2	0.7862	5.1	0.948	Contact Map
2m1lA	2	0.4138	4.8	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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