OPENSEQ.org - 1430742575 - GREMLIN Submission

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Ant2

ID:	1430742575	Query Sequence ALSAITSGQELLSQARVLAKYLRDQPEGWLAAHRLMKSVRHDTLHQLPPLSADGRTRIAPPGPDRRASLKRLYLQQNWLSLLEQCDDMFARGASHLWLDLQWYIHQALLQTGKENYAAIIQYDLKGLLLRLPGLETLAFNDGMPFADDVTLSWIQQQVMECGERWAEEPSVTIT	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	174 (172)
Sequences:	182 (118)
Seq/Len:	1.058
Nf(neff/√len):	9.0

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: 1.058).

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
147_D	150_T	1.772	0.91
102_W	147_D	1.711	0.89
9_Q	13_S	1.677	0.87
146_A	150_T	1.676	0.87
37_K	86_D	1.663	0.87
75_Q	147_D	1.646	0.86
139_F	145_F	1.625	0.85
133_G	147_D	1.607	0.84
166_A	172_T	1.584	0.83
166_A	171_V	1.577	0.83
69_L	100_L	1.508	0.79
61_P	69_L	1.504	0.78
164_R	168_E	1.495	0.78
44_L	96_L	1.486	0.77
2_L	171_V	1.482	0.77
82_L	104_I	1.462	0.76
168_E	171_V	1.449	0.75
69_L	72_L	1.416	0.72
169_P	172_T	1.406	0.72
167_E	171_V	1.390	0.70
88_M	100_L	1.386	0.70
109_L	120_I	1.371	0.69
77_N	99_D	1.368	0.69
48_P	56_T	1.365	0.68
11_L	15_A	1.361	0.68
99_D	143_M	1.356	0.68
61_P	101_Q	1.331	0.65
99_D	146_A	1.314	0.64
3_S	167_E	1.314	0.64
163_E	166_A	1.313	0.64
123_D	154_I	1.306	0.63
165_W	168_E	1.286	0.62
99_D	147_D	1.276	0.61
108_L	120_I	1.272	0.60
163_E	172_T	1.266	0.60
2_L	170_S	1.264	0.60
97_W	145_F	1.259	0.59
99_D	150_T	1.241	0.57
166_A	169_P	1.239	0.57
164_R	171_V	1.235	0.57
48_P	145_F	1.229	0.56
2_L	167_E	1.219	0.55
95_H	100_L	1.212	0.55
164_R	170_S	1.201	0.54
41_H	91_R	1.172	0.51
33_H	101_Q	1.171	0.51
30_L	33_H	1.166	0.50
166_A	170_S	1.161	0.50
30_L	150_T	1.158	0.50
60_P	94_S	1.155	0.49
4_A	169_P	1.150	0.49
41_H	58_I	1.133	0.47
2_L	168_E	1.133	0.47
167_E	170_S	1.132	0.47
22_L	119_I	1.131	0.47
128_L	134_L	1.129	0.47
16_R	32_A	1.129	0.47
2_L	169_P	1.119	0.46
3_S	169_P	1.119	0.46
167_E	173_I	1.111	0.45
18_L	144_P	1.111	0.45
67_A	98_L	1.109	0.45
162_G	172_T	1.103	0.45
32_A	141_D	1.101	0.44
162_G	171_V	1.097	0.44
40_R	101_Q	1.086	0.43
40_R	89_F	1.085	0.43
159_M	167_E	1.083	0.43
3_S	166_A	1.081	0.43
168_E	172_T	1.080	0.42
2_L	172_T	1.064	0.41
110_Q	155_Q	1.064	0.41
98_L	148_D	1.063	0.41
69_L	103_Y	1.060	0.41
165_W	171_V	1.056	0.40
4_A	171_V	1.056	0.40
34_R	123_D	1.049	0.40
157_Q	165_W	1.042	0.39
3_S	173_I	1.040	0.39
40_R	62_G	1.040	0.39
79_L	104_I	1.039	0.39
16_R	93_A	1.035	0.38
163_E	168_E	1.027	0.38
159_M	162_G	1.026	0.38
55_R	141_D	1.022	0.37
95_H	145_F	1.021	0.37
2_L	164_R	1.013	0.36
164_R	169_P	1.009	0.36
62_G	91_R	1.008	0.36
4_A	164_R	1.005	0.36
166_A	173_I	1.005	0.36
70_K	99_D	1.004	0.36

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
3b0pA	2	0.454	26.2	0.943	Contact Map
4ky9A	2	0.431	21.9	0.945	Contact Map
2kc7A	1	0.546	15.9	0.948	Contact Map
2a3qA	2	0.5862	14.5	0.949	Contact Map
2yxhA	2	0.6609	12.4	0.951	Contact Map
2jrtA	1	0.2816	9.6	0.953	Contact Map
4lixA	1	0.4138	9.1	0.954	Contact Map
1vccA	1	0.2241	8.3	0.955	Contact Map
2qv5A	2	0.7356	7.4	0.956	Contact Map
3bkxA	2	0.7586	5.8	0.958	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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