OPENSEQ.org - 1443085258 - GREMLIN Submission

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Rv3835 81-339 -force run 5-159

ID:	1443085258	Query Sequence GAKINASFNRVASGDCLMWPDGTPESAAIVSCADEHRFEVAESIDMRTFPGMEYGQNAAPPSPARIQQISEEQCEAAVRRYLGTKFDPNSKFTISMLWPGDRAWRQAGERRMLCGLQSPGPNNQQLAFKGKVADIDQSKVWPAGTCLGIDATTNQ	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	155 (149)
Sequences:	171 (129.4)
Seq/Len:	1.148
Nf(neff/√len):	10.6

HHblits Results: (2015_06)
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: 1.148).

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
41_A	78_V	2.665	1.00
53_E	65_R	1.680	0.89
39_E	104_W	1.644	0.88
38_F	115_G	1.636	0.87
80_R	134_D	1.595	0.85
37_R	78_V	1.556	0.83
92_F	132_V	1.482	0.79
38_F	87_D	1.478	0.79
92_F	128_F	1.471	0.78
119_P	125_Q	1.430	0.76
104_W	110_R	1.403	0.74
50_P	65_R	1.398	0.73
132_V	135_I	1.397	0.73
127_A	138_S	1.365	0.71
142_P	145_T	1.364	0.71
141_W	145_T	1.363	0.71
17_L	40_V	1.352	0.70
50_P	54_Y	1.333	0.68
61_P	87_D	1.330	0.68
48_T	140_V	1.308	0.66
35_E	127_A	1.290	0.64
117_Q	144_G	1.285	0.64
26_S	103_A	1.277	0.63
141_W	148_G	1.266	0.62
116_L	124_Q	1.262	0.62
40_V	115_G	1.262	0.62
135_I	147_L	1.257	0.61
87_D	115_G	1.254	0.61
116_L	132_V	1.249	0.61
97_L	100_G	1.243	0.60
116_L	126_L	1.235	0.59
7_S	79_R	1.233	0.59
42_E	77_A	1.233	0.59
33_A	151_A	1.225	0.58
11_V	40_V	1.225	0.58
45_D	50_P	1.214	0.57
46_M	97_L	1.150	0.51
14_G	82_L	1.145	0.51
144_G	148_G	1.144	0.51
138_S	149_I	1.141	0.50
5_N	10_R	1.116	0.48
46_M	69_I	1.113	0.48
103_A	112_M	1.108	0.47
38_F	61_P	1.106	0.47
19_W	61_P	1.105	0.47
22_G	26_S	1.104	0.47
91_K	127_A	1.103	0.47
27_A	113_L	1.103	0.47
142_P	147_L	1.101	0.47
138_S	148_G	1.094	0.46
19_W	87_D	1.084	0.45
39_E	110_R	1.080	0.45
7_S	33_A	1.074	0.44
138_S	141_W	1.073	0.44
118_S	126_L	1.071	0.44
48_T	151_A	1.069	0.44
139_K	150_D	1.065	0.43
25_E	147_L	1.055	0.42
150_D	153_T	1.054	0.42
96_M	141_W	1.054	0.42
54_Y	66_I	1.052	0.42
68_Q	151_A	1.052	0.42
47_R	67_Q	1.040	0.41
103_A	109_E	1.037	0.41
54_Y	97_L	1.036	0.40
46_M	139_K	1.035	0.40
31_S	78_V	1.034	0.40
92_F	129_K	1.030	0.40
40_V	45_D	1.029	0.40
8_F	81_Y	1.028	0.40
60_P	148_G	1.026	0.40
48_T	105_R	1.022	0.39
131_K	134_D	1.021	0.39
33_A	121_P	1.021	0.39
47_R	124_Q	1.020	0.39
58_A	152_T	1.018	0.39
59_A	143_A	1.018	0.39
81_Y	130_G	1.016	0.39
49_F	140_V	1.016	0.39
25_E	105_R	1.015	0.39
18_M	102_R	1.014	0.38
8_F	65_R	1.013	0.38
117_Q	140_V	1.013	0.38
139_K	149_I	1.012	0.38
9_N	27_A	1.009	0.38
69_I	111_R	1.007	0.38
66_I	97_L	1.002	0.37

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: (06Aug15)
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
4drrA	1	0.3419	2.5	0.964	Contact Map
2gpiA	1	0.5613	2.3	0.964	Contact Map
1yi8B	3	0.4645	1.8	0.967	Contact Map
3alzB	1	0.1742	1.7	0.967	Contact Map
3tzlA	2	0.4581	1.4	0.969	Contact Map
2mvoA	1	0	1.4	0.969	Contact Map
3hqxA	1	0.529	1.3	0.97	Contact Map
2zibA	1	0.2903	1.3	0.97	Contact Map
2oyzA	1	0.4645	1	0.971	Contact Map
3eo6A	2	0.5484	1	0.972	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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