OPENSEQ.org - 1405064903 - GREMLIN Submission

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T0848 165-354 -force run

ID:	1405064903	Query Sequence LATADKLQDSAKALSAYVDVLLFGKDNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKDEAIVEATVKPVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVKMKKNDIDQWQLDMDDYRAAELVEAFIKE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	190 (184)
Sequences:	128 (116.8)
Seq/Len:	0.696
Nf(neff/√len):	8.6

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: 0.696).

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
14_L	163_M	1.849	0.86
13_A	25_K	1.785	0.84
39_N	43_N	1.738	0.81
104_V	159_V	1.679	0.78
87_Q	103_T	1.646	0.76
89_K	101_E	1.623	0.75
34_T	161_V	1.598	0.73
131_S	134_E	1.531	0.69
7_L	10_S	1.495	0.66
23_F	35_G	1.449	0.62
12_K	16_A	1.442	0.62
162_K	174_D	1.412	0.59
163_M	173_L	1.400	0.58
115_R	162_K	1.390	0.58
68_A	81_S	1.389	0.58
161_V	169_D	1.387	0.57
20_V	23_F	1.381	0.57
39_N	48_S	1.362	0.55
131_S	158_T	1.349	0.54
96_D	140_L	1.330	0.53
85_S	105_K	1.328	0.52
109_A	143_Y	1.314	0.51
144_P	153_A	1.295	0.50
101_E	158_T	1.284	0.49
13_A	23_F	1.273	0.48
44_D	51_D	1.253	0.46
117_E	161_V	1.236	0.45
13_A	30_F	1.232	0.44
67_K	162_K	1.231	0.44
85_S	107_V	1.222	0.44
112_L	163_M	1.221	0.43
26_D	94_S	1.218	0.43
31_E	69_L	1.213	0.43
45_F	105_K	1.199	0.42
46_N	131_S	1.175	0.40
24_G	112_L	1.174	0.40
106_P	156_E	1.173	0.40
53_Y	132_Y	1.168	0.39
40_E	70_D	1.168	0.39
69_L	102_A	1.164	0.39
71_N	87_Q	1.164	0.39
154_S	183_L	1.162	0.39
61_S	129_S	1.160	0.39
49_A	90_T	1.159	0.38
9_D	16_A	1.152	0.38
51_D	100_V	1.132	0.36
67_K	134_E	1.129	0.36
86_I	135_A	1.123	0.36
36_A	64_A	1.120	0.35
37_N	40_E	1.117	0.35
24_G	169_D	1.117	0.35
106_P	154_S	1.116	0.35
69_L	126_K	1.114	0.35
116_I	120_V	1.113	0.35
57_S	102_A	1.110	0.35
66_S	120_V	1.103	0.34
83_N	155_S	1.098	0.34
43_N	97_E	1.096	0.34
13_A	24_G	1.094	0.33
134_E	137_K	1.093	0.33
54_L	78_E	1.093	0.33
36_A	80_L	1.084	0.33
28_A	40_E	1.084	0.33
7_L	14_L	1.081	0.32
70_D	83_N	1.075	0.32
48_S	124_Y	1.075	0.32
63_Y	165_K	1.075	0.32
76_I	147_F	1.073	0.32
154_S	159_V	1.069	0.32
71_N	138_Y	1.069	0.32
32_K	100_V	1.065	0.31
26_D	47_E	1.063	0.31
147_F	150_L	1.060	0.31
11_A	15_S	1.058	0.31
181_A	184_V	1.057	0.31
13_A	16_A	1.056	0.31
57_S	145_E	1.051	0.30
17_Y	20_V	1.050	0.30
4_A	7_L	1.048	0.30
122_D	126_K	1.048	0.30
88_A	179_R	1.044	0.30
167_D	172_Q	1.044	0.30
46_N	73_V	1.042	0.30
24_G	33_I	1.041	0.30
67_K	183_L	1.040	0.29
170_Q	173_L	1.039	0.29
53_Y	182_E	1.037	0.29
49_A	84_S	1.036	0.29
153_A	161_V	1.035	0.29
117_E	121_K	1.032	0.29
96_D	114_D	1.028	0.29
11_A	16_A	1.022	0.28
167_D	184_V	1.022	0.28
60_S	82_K	1.022	0.28
95_K	182_E	1.012	0.28
95_K	128_S	1.008	0.27
46_N	94_S	1.006	0.27
121_K	125_S	1.004	0.27
33_I	47_E	1.003	0.27
89_K	148_K	1.003	0.27
67_K	109_A	1.002	0.27
23_F	29_D	1.000	0.27

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: (05Jul14)
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
3k7cA	4	0.5316	90.1	0.875	Contact Map
4hz9B	2	0.6316	59.6	0.907	Contact Map
4fczB	2	0.7789	6.4	0.943	Contact Map
3fkaA	4	0.6158	5.6	0.944	Contact Map
2qguA	1	0.7632	5.5	0.944	Contact Map
3fwcB	4	0.2842	5.4	0.945	Contact Map
3robA	4	0.6789	4.8	0.946	Contact Map
1s94A	2	0.2947	3	0.951	Contact Map
4orlA	1	0.5789	2.7	0.952	Contact Map
1vqqA	2	0.6	2.6	0.952	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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