OPENSEQ.org - 1415141280 - GREMLIN Submission

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CarO-redo2

ID:	1415141280	Query Sequence MKVLRVLVTTTALLAAGAAMADEAVVHDSYAFDKNQLIPVGARAEVGTTGYGGALLWQANPYVGLALGYNGGDISWSDDVKVNGSTYDLDMDNNNVYLNAEIRPWGASTNRWAQGLYVAAGAAYLDNDYDLTRNVDATRSFRVNNQDFIAGADGVKINGQMSYKNDIAPYLGFGFAPKINKNWGVFGEVGAYYTGNPTVKLVSSGSAVTTGDQTLEEAVNAEARKIANDDKYKWLPVGKVGVNFFW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	246 (246)
Sequences:	246 (218.8)
Seq/Len:	1.000
Nf(neff/√len):	14.0

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: 1.000).

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
148_F	218_A	2.503	0.99
193_Y	234_W	2.479	0.99
45_E	52_G	2.359	0.99
117_Y	188_E	2.318	0.99
66_A	101_E	1.920	0.94
115_G	175_F	1.798	0.91
84_G	131_L	1.757	0.90
172_G	237_V	1.731	0.89
43_R	54_A	1.680	0.87
43_R	68_G	1.659	0.86
186_F	241_G	1.613	0.83
8_V	14_L	1.587	0.82
6_V	11_T	1.535	0.79
85_S	157_I	1.525	0.78
173_F	189_V	1.525	0.78
146_Q	218_A	1.525	0.78
6_V	9_T	1.471	0.75
68_G	97_Y	1.446	0.73
11_T	14_L	1.440	0.73
70_N	127_N	1.430	0.72
183_W	242_V	1.411	0.70
5_R	9_T	1.399	0.69
220_N	223_A	1.395	0.69
131_L	159_G	1.392	0.69
7_L	11_T	1.382	0.68
99_N	188_E	1.360	0.66
8_V	11_T	1.359	0.66
148_F	215_L	1.358	0.66
144_N	218_A	1.355	0.66
184_G	243_N	1.335	0.64
5_R	8_V	1.330	0.64
41_G	182_N	1.320	0.63
123_A	192_Y	1.308	0.62
5_R	11_T	1.294	0.61
101_E	119_A	1.292	0.60
24_A	27_H	1.291	0.60
199_V	220_N	1.289	0.60
3_V	7_L	1.284	0.60
9_T	14_L	1.272	0.59
173_F	188_E	1.235	0.55
43_R	165_N	1.221	0.54
41_G	177_P	1.218	0.54
10_T	16_A	1.215	0.53
5_R	20_M	1.211	0.53
67_L	96_V	1.208	0.53
173_F	245_F	1.208	0.53
5_R	16_A	1.202	0.52
209_T	213_Q	1.201	0.52
170_Y	188_E	1.194	0.51
203_S	206_S	1.193	0.51
193_Y	232_Y	1.192	0.51
215_L	219_V	1.192	0.51
102_I	244_F	1.192	0.51
56_L	103_R	1.189	0.51
41_G	55_L	1.188	0.51
16_A	19_A	1.186	0.51
172_G	188_E	1.184	0.50
62_Y	102_I	1.178	0.50
6_V	14_L	1.177	0.50
158_N	202_V	1.174	0.50
69_Y	122_A	1.174	0.50
101_E	159_G	1.173	0.49
20_M	24_A	1.170	0.49
64_G	177_P	1.165	0.49
161_M	175_F	1.165	0.49
5_R	23_E	1.155	0.48
87_Y	222_E	1.153	0.48
49_T	54_A	1.153	0.48
24_A	28_D	1.147	0.47
153_D	157_I	1.147	0.47
11_T	18_A	1.147	0.47
49_T	127_N	1.143	0.47
5_R	18_A	1.143	0.47
228_N	240_V	1.141	0.47
85_S	133_R	1.135	0.46
188_E	191_A	1.134	0.46
171_L	189_V	1.133	0.46
140_S	145_N	1.132	0.46
6_V	29_S	1.129	0.45
3_V	6_V	1.124	0.45
213_Q	220_N	1.123	0.45
3_V	14_L	1.119	0.44
179_I	188_E	1.116	0.44
135_V	154_G	1.107	0.43
118_V	238_G	1.106	0.43
9_T	12_A	1.104	0.43
57_W	179_I	1.103	0.43
119_A	172_G	1.098	0.43
63_V	100_A	1.094	0.42
17_G	24_A	1.090	0.42
150_A	154_G	1.085	0.41
46_V	114_Q	1.085	0.41
14_L	18_A	1.072	0.40
81_K	92_D	1.071	0.40
161_M	223_A	1.071	0.40
40_V	55_L	1.068	0.40
7_L	10_T	1.066	0.40
3_V	18_A	1.066	0.40
42_A	55_L	1.063	0.39
10_T	18_A	1.062	0.39
79_D	230_D	1.060	0.39
46_V	242_V	1.057	0.39
63_V	102_I	1.050	0.38
99_N	172_G	1.049	0.38
125_L	163_Y	1.046	0.38
8_V	24_A	1.043	0.38
9_T	24_A	1.040	0.37
8_V	16_A	1.040	0.37
7_L	20_M	1.037	0.37
120_A	185_V	1.033	0.37
5_R	10_T	1.033	0.37
212_D	215_L	1.030	0.37
7_L	17_G	1.030	0.37
10_T	17_G	1.029	0.36
232_Y	235_L	1.028	0.36
206_S	209_T	1.023	0.36
119_A	170_Y	1.023	0.36
5_R	24_A	1.022	0.36
47_G	239_K	1.018	0.36
14_L	24_A	1.005	0.34
39_P	60_N	1.004	0.34
11_T	23_E	1.003	0.34
15_A	40_V	1.002	0.34
92_D	166_D	1.000	0.34
68_G	185_V	1.000	0.34

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: (06Sep14)
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
4fuvA	1	0.8659	100	0.202	Contact Map
3nb3A	3	0.5203	98.7	0.845	Contact Map
2f1vA	6	0.7195	97.1	0.894	Contact Map
2k0lA	1	0.7154	97.1	0.895	Contact Map
1qjpA	1	0.5163	96.7	0.9	Contact Map
3qraA	1	0.6057	96.4	0.903	Contact Map
2x27X	1	0.752	96.1	0.906	Contact Map
2jmmA	1	0.5447	95.6	0.91	Contact Map
1p4tA	1	0.5732	94.5	0.915	Contact Map
2lhfA	1	0.6911	94	0.917	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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