OPENSEQ.org - 1481239159 - GREMLIN Submission

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3cax_1e33

ID:	1481239159	Query Sequence LKTLYQENKEIMKDAEMLNLYAKTLATTKDERMREEILGVLEEIVSSLRMVGFTHYNREEMLIFPYIERRGLTVIATVLWTKHDEIRAMIKQLAELLRKREEMPWEEFVEKFKAKAGEVAFALSDMVFRENNIFYPTLKAL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	141 (140)
Sequences:	230 (203.4)
Seq/Len:	1.643
Nf(neff/√len):	17.2

HHblits Results: (2016_02)
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: 1.643).

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
9_K	12_M	2.488	1.00
10_E	13_K	2.321	1.00
46_S	50_M	2.231	0.99
75_I	79_L	2.000	0.98
75_I	129_R	1.930	0.98
8_N	126_M	1.759	0.96
79_L	129_R	1.747	0.95
3_T	58_R	1.680	0.94
21_Y	44_I	1.576	0.91
8_N	59_E	1.523	0.89
2_K	6_Q	1.491	0.87
74_V	138_L	1.477	0.87
19_N	124_S	1.438	0.85
59_E	126_M	1.423	0.84
63_I	129_R	1.419	0.84
4_L	135_Y	1.416	0.84
1_L	135_Y	1.401	0.83
18_L	45_V	1.396	0.82
59_E	131_N	1.393	0.82
82_K	86_I	1.380	0.81
60_E	87_R	1.378	0.81
85_E	122_A	1.371	0.81
51_V	90_I	1.360	0.80
64_F	68_E	1.356	0.80
57_N	61_M	1.334	0.78
92_Q	96_L	1.326	0.78
61_M	91_K	1.325	0.78
78_V	129_R	1.287	0.75
56_Y	80_W	1.286	0.75
8_N	78_V	1.278	0.74
82_K	126_M	1.271	0.73
68_E	87_R	1.268	0.73
64_F	87_R	1.266	0.73
62_L	81_T	1.259	0.72
67_I	74_V	1.259	0.72
3_T	63_I	1.241	0.71
36_E	99_K	1.236	0.70
72_L	137_T	1.214	0.68
67_I	138_L	1.213	0.68
15_A	85_E	1.203	0.67
46_S	54_T	1.201	0.67
77_T	129_R	1.200	0.67
22_A	127_V	1.196	0.67
58_R	87_R	1.196	0.67
78_V	126_M	1.187	0.66
93_L	116_A	1.164	0.64
48_L	71_G	1.159	0.63
78_V	82_K	1.158	0.63
17_M	20_L	1.157	0.63
72_L	76_A	1.146	0.62
11_I	51_V	1.143	0.62
8_N	56_Y	1.140	0.61
45_V	97_L	1.139	0.61
83_H	122_A	1.135	0.61
57_N	91_K	1.134	0.61
8_N	82_K	1.114	0.59
92_Q	115_K	1.112	0.58
50_M	54_T	1.110	0.58
96_L	112_F	1.100	0.57
110_E	114_A	1.093	0.56
44_I	47_S	1.091	0.56
112_F	119_V	1.090	0.56
29_K	132_N	1.079	0.55
78_V	81_T	1.077	0.55
51_V	126_M	1.075	0.55
1_L	4_L	1.067	0.54
15_A	121_F	1.065	0.53
80_W	84_D	1.063	0.53
72_L	141_L	1.056	0.53
60_E	79_L	1.047	0.52
93_L	135_Y	1.046	0.51
55_H	58_R	1.045	0.51
2_K	128_F	1.025	0.49
74_V	125_D	1.021	0.49
64_F	76_A	1.017	0.48
53_F	87_R	1.004	0.47

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
3caxA	1	0.9929	99.9	0.491	Contact Map
2p0nA	2	0.9433	99.7	0.64	Contact Map
4xpxA	1	0	80.7	0.908	Contact Map
3agtA	2	0.8369	75.6	0.912	Contact Map
2dfsA	2	0.3972	23.9	0.938	Contact Map
2hmqA	4	0.6809	23.6	0.938	Contact Map
3u9jA	2	0.9149	18.2	0.941	Contact Map
2mhrA	1	0.6879	13.4	0.944	Contact Map
2l7bA	1	0.9504	13.2	0.944	Contact Map
2zxxA	4	0.2128	12.5	0.945	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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