OPENSEQ.org - 1501723953 - GREMLIN Submission

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bbs_7_sheet1 -force run

ID:	1501723953	Query Sequence SSKAKSAVPSFSVNDKFTLNKDDASYSLILEVQTAIDNVLIQSDVPIDLLDVDKNSAVVSFSSCDSESNDNFLLATYRCQANTTRLELKIRSIEGQYGTLQAYVTPRIQPKTCQVRQYHIKPLSLHQRTH	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	130 (127)
Sequences:	108 (76.7)
Seq/Len:	0.850
Nf(neff/√len):	6.8

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: 0.850).

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
11_F	114_Q	1.955	0.93
95_G	98_G	1.816	0.89
44_D	99_T	1.745	0.86
79_C	83_T	1.652	0.82
36_I	47_I	1.633	0.81
94_E	126_H	1.625	0.80
36_I	55_N	1.497	0.72
32_V	48_D	1.462	0.69
86_L	104_V	1.436	0.67
6_S	9_P	1.430	0.67
14_N	46_P	1.420	0.66
41_I	122_P	1.374	0.62
9_P	13_V	1.356	0.61
92_S	124_S	1.350	0.60
15_D	118_Y	1.344	0.60
95_G	122_P	1.338	0.59
85_R	94_E	1.328	0.59
77_Y	120_I	1.324	0.58
49_L	55_N	1.323	0.58
103_Y	106_P	1.319	0.58
28_L	100_L	1.289	0.55
19_L	62_S	1.285	0.55
55_N	80_Q	1.249	0.52
95_G	125_L	1.217	0.49
98_G	124_S	1.208	0.48
95_G	126_H	1.184	0.46
51_D	80_Q	1.182	0.46
31_E	111_K	1.175	0.45
51_D	113_C	1.170	0.45
55_N	77_Y	1.164	0.44
75_A	110_P	1.160	0.44
82_N	103_Y	1.160	0.44
36_I	39_V	1.152	0.43
9_P	15_D	1.141	0.42
30_L	116_R	1.135	0.42
37_D	103_Y	1.134	0.41
98_G	121_K	1.134	0.41
24_A	38_N	1.131	0.41
36_I	79_C	1.130	0.41
106_P	122_P	1.125	0.41
73_L	106_P	1.123	0.41
24_A	91_R	1.120	0.40
10_S	115_V	1.119	0.40
19_L	45_V	1.118	0.40
65_D	84_T	1.115	0.40
29_I	93_I	1.113	0.40
29_I	70_D	1.110	0.39
55_N	88_L	1.109	0.39
114_Q	121_K	1.108	0.39
76_T	86_L	1.108	0.39
25_S	51_D	1.107	0.39
49_L	80_Q	1.107	0.39
96_Q	125_L	1.104	0.39
26_Y	126_H	1.104	0.39
120_I	124_S	1.098	0.38
37_D	116_R	1.083	0.37
15_D	116_R	1.080	0.37
91_R	124_S	1.078	0.37
47_I	68_S	1.072	0.36
60_S	103_Y	1.069	0.36
55_N	83_T	1.064	0.36
6_S	30_L	1.063	0.36
22_D	90_I	1.055	0.35
9_P	37_D	1.054	0.35
13_V	90_I	1.049	0.34
87_E	94_E	1.049	0.34
80_Q	83_T	1.047	0.34
62_S	81_A	1.040	0.34
41_I	127_Q	1.033	0.33
76_T	128_R	1.027	0.33
16_K	47_I	1.025	0.32
55_N	79_C	1.025	0.32
6_S	28_L	1.020	0.32
87_E	128_R	1.017	0.32
42_Q	71_N	1.007	0.31

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
4p6zM	1	0.9231	18.7	0.94	Contact Map
4en2M	2	0.9231	18.6	0.94	Contact Map
4iknA	1	0.9308	17.6	0.941	Contact Map
3l81A	1	0.9385	13.3	0.944	Contact Map
1i31A	1	0.8154	9.3	0.948	Contact Map
3ml6A	6	0.9	7.4	0.95	Contact Map
2vglM	1	0.8077	7.3	0.95	Contact Map
4fruA	1	0.4231	5	0.954	Contact Map
1qngA	1	0.3769	4.5	0.955	Contact Map
2l0lA	1	0.0769	3.4	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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