OPENSEQ.org - 1410104363 - GREMLIN Submission

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ASMA

ID:	1410104363	Query Sequence QTIDAGAEGRAVVNLNRFDLAMLKPFMPETTQASGIFTGKADVAWDTTKEGLPQGSITLSGRNVQVTQTVNDAALPVAFQTLNLTAELRNNRAELGWTIRLTNNGQFDGQVQVTDPQGRRNLGGNVNIRNFNLAMINPIFTRGEKAAGMVSANLRLGGDVQSPQLFGQLQVTGVDIDGNF	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	180 (180)
Sequences:	275 (208.3)
Seq/Len:	1.528
Nf(neff/√len):	15.5

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: 1.528).

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
39_G	59_L	2.587	1.00
64_V	79_F	2.259	0.99
156_L	171_V	2.201	0.99
9_G	45_W	1.745	0.95
15_L	20_L	1.527	0.88
57_I	127_N	1.524	0.88
110_Q	125_N	1.514	0.87
59_L	171_V	1.503	0.87
54_Q	160_V	1.496	0.86
113_V	120_R	1.484	0.86
58_T	111_V	1.422	0.82
139_I	142_R	1.408	0.81
89_R	129_R	1.398	0.81
154_L	165_L	1.393	0.80
13_V	41_A	1.392	0.80
56_S	156_L	1.369	0.79
126_V	156_L	1.366	0.79
60_S	126_V	1.346	0.77
97_W	109_G	1.339	0.77
21_A	27_M	1.331	0.76
39_G	166_F	1.316	0.75
55_G	108_D	1.312	0.75
136_I	152_A	1.312	0.75
95_L	153_N	1.307	0.74
14_N	40_K	1.279	0.72
6_G	9_G	1.266	0.71
81_T	113_V	1.264	0.71
55_G	157_G	1.255	0.70
41_A	111_V	1.252	0.70
33_A	79_F	1.250	0.69
101_L	136_I	1.248	0.69
57_I	88_L	1.244	0.69
107_F	151_S	1.239	0.68
53_P	104_N	1.238	0.68
126_V	134_A	1.233	0.68
10_R	42_D	1.227	0.67
124_G	156_L	1.219	0.67
168_Q	178_G	1.217	0.66
147_A	173_G	1.209	0.66
148_G	180_F	1.200	0.65
33_A	99_I	1.200	0.65
139_I	174_V	1.200	0.65
117_Q	122_L	1.199	0.65
39_G	68_Q	1.181	0.63
17_R	156_L	1.174	0.62
39_G	111_V	1.171	0.62
20_L	35_G	1.171	0.62
124_G	157_G	1.167	0.62
26_F	65_Q	1.151	0.60
96_G	110_Q	1.147	0.60
122_L	157_G	1.145	0.59
18_F	105_G	1.140	0.59
16_N	147_A	1.138	0.59
104_N	160_V	1.129	0.58
43_V	55_G	1.127	0.58
124_G	175_D	1.126	0.58
144_E	148_G	1.109	0.56
29_E	113_V	1.107	0.56
96_G	165_L	1.099	0.55
81_T	101_L	1.098	0.55
39_G	146_A	1.096	0.55
134_A	137_N	1.092	0.54
120_R	128_I	1.090	0.54
85_T	96_G	1.089	0.54
138_P	178_G	1.086	0.53
27_M	143_G	1.081	0.53
109_G	154_L	1.080	0.53
21_A	122_L	1.079	0.53
146_A	176_I	1.078	0.53
34_S	107_F	1.074	0.52
79_F	148_G	1.069	0.52
83_N	103_N	1.069	0.52
66_V	80_Q	1.068	0.52
21_A	35_G	1.066	0.51
137_N	146_A	1.065	0.51
171_V	174_V	1.064	0.51
2_T	171_V	1.063	0.51
1_Q	180_F	1.060	0.51
73_A	132_N	1.055	0.50
94_E	150_V	1.052	0.50
9_G	140_F	1.045	0.49
17_R	87_E	1.045	0.49
152_A	157_G	1.040	0.49
79_F	135_M	1.033	0.48
82_L	143_G	1.033	0.48
1_Q	56_S	1.021	0.47
45_W	53_P	1.021	0.47
20_L	82_L	1.020	0.47
30_T	129_R	1.020	0.47
18_F	53_P	1.019	0.47
81_T	166_F	1.016	0.46
19_D	152_A	1.016	0.46
31_T	104_N	1.015	0.46
41_A	150_V	1.013	0.46
128_I	131_F	1.005	0.45
73_A	99_I	1.003	0.45
30_T	126_V	1.001	0.45

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: (17Jul14)
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
3qs3A	12	0.3722	3.7	0.946	Contact Map
1h54A	2	0.4333	3.1	0.948	Contact Map
1v8hA	2	0.3278	3.1	0.948	Contact Map
2oxgZ	4	0.3333	2.7	0.95	Contact Map
4n2oA	8	0.3444	2.1	0.952	Contact Map
3wirA	4	0.4111	1.9	0.953	Contact Map
3g4nA	2	0.4611	1.6	0.955	Contact Map
3lycA	16	0.6944	1.6	0.955	Contact Map
4opwA	2	0.35	1.3	0.957	Contact Map
4m4dA	2	0.8222	1.3	0.957	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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