OPENSEQ.org - 1489408723 - GREMLIN Submission

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spc7_trial 10-150

ID:	1489408723	Query Sequence EPISLSDFLKMTGIEFLDNLTIAKRRETLLPNAEENKKCSIQELLESFYIQFPLLELYKFSCQQLQDYIAEGKDFVTKIEEETLKENPLLFYEYRKASSDMRVLMDSQFLMMKTFARLQAKGDWYEWREGLMQGIKHELNL	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	141 (138)
Sequences:	296 (206.6)
Seq/Len:	2.145
Nf(neff/√len):	17.6

Jackhmmer Results: (2016_04)
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: 2.145).

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 > 50% 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
25_R	28_T	2.378	1.00
124_W	127_W	2.149	1.00
87_N	131_L	1.552	0.94
14_I	53_P	1.548	0.94
64_Q	67_D	1.543	0.93
19_N	28_T	1.459	0.91
81_E	135_I	1.451	0.90
39_C	139_L	1.442	0.90
81_E	91_F	1.377	0.87
120_A	123_D	1.371	0.87
14_I	70_A	1.360	0.86
69_I	91_F	1.356	0.86
108_Q	120_A	1.329	0.84
16_F	57_L	1.319	0.84
83_T	103_V	1.300	0.82
3_I	11_M	1.291	0.82
34_E	52_F	1.278	0.81
24_K	104_L	1.271	0.80
66_Q	108_Q	1.263	0.80
94_Y	132_M	1.245	0.78
88_P	100_D	1.237	0.78
106_D	110_L	1.218	0.76
34_E	38_K	1.204	0.75
113_K	125_Y	1.198	0.75
60_F	127_W	1.184	0.73
40_S	43_E	1.178	0.73
115_F	126_E	1.170	0.72
65_L	109_F	1.164	0.72
64_Q	79_I	1.153	0.71
55_L	120_A	1.149	0.70
83_T	102_R	1.141	0.69
42_Q	93_E	1.139	0.69
64_Q	127_W	1.137	0.69
2_P	66_Q	1.135	0.69
4_S	42_Q	1.132	0.69
5_L	8_F	1.132	0.69
53_P	90_L	1.131	0.68
36_N	119_Q	1.122	0.68
55_L	78_K	1.121	0.67
11_M	95_R	1.121	0.67
15_E	41_I	1.101	0.65
124_W	128_R	1.101	0.65
29_L	77_T	1.100	0.65
93_E	105_M	1.100	0.65
24_K	121_K	1.097	0.65
16_F	93_E	1.097	0.65
51_Q	76_V	1.096	0.65
87_N	118_L	1.094	0.65
61_S	87_N	1.093	0.65
118_L	128_R	1.093	0.65
62_C	87_N	1.079	0.63
4_S	27_E	1.078	0.63
62_C	121_K	1.076	0.63
72_G	138_E	1.074	0.63
9_L	119_Q	1.073	0.62
4_S	7_D	1.069	0.62
18_D	41_I	1.069	0.62
41_I	44_L	1.063	0.61
43_E	87_N	1.055	0.61
24_K	63_Q	1.053	0.60
61_S	109_F	1.052	0.60
12_T	97_A	1.051	0.60
89_L	105_M	1.050	0.60
98_S	133_Q	1.049	0.60
9_L	131_L	1.048	0.60
51_Q	59_K	1.044	0.59
135_I	138_E	1.041	0.59
26_R	121_K	1.041	0.59
35_E	40_S	1.033	0.58
5_L	22_I	1.032	0.58
52_F	125_Y	1.030	0.58
4_S	84_L	1.024	0.57
24_K	31_P	1.024	0.57
85_K	129_E	1.024	0.57
79_I	82_E	1.020	0.57
46_E	83_T	1.015	0.56
70_A	135_I	1.013	0.56

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
1vw41	1	0.8298	8.1	0.932	Contact Map
3d5aX	1	0.5248	6.9	0.934	Contact Map
2b3tB	1	0.383	6.7	0.935	Contact Map
3fhnA	4	0.9716	6.6	0.935	Contact Map
4jbuA	1	0.4113	6.6	0.935	Contact Map
1o5hA	2	0.8865	6.2	0.936	Contact Map
2qklB	1	0.5035	5.8	0.936	Contact Map
4kqtA	1	0.766	5.4	0.937	Contact Map
4wbhA	2	0	4.9	0.939	Contact Map
4a1nA	1	0.5461	4.9	0.939	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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