OPENSEQ.org - 1492603444 - GREMLIN Submission

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1k40 -force run

ID:	1492603444	Query Sequence NDKVYENVTGLVKAVIEMSSKIQPAPPEEYVPMVKEVGLALRTLLATVDETIPALPASTHREIEMAQKLLNSDLGELISKMKLAQQYVMTSLQQEYKKQMLTAAHALAVDAKNLLDVIDQARLKML	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	126 (126)
Sequences:	93 (53.9)
Seq/Len:	0.738
Nf(neff/√len):	4.8

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: 0.738).

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
101_L	105_H	1.734	0.83
8_V	11_L	1.614	0.76
107_L	119_D	1.544	0.71
113_N	116_D	1.541	0.71
8_V	69_L	1.510	0.69
18_M	42_R	1.508	0.69
119_D	122_R	1.437	0.63
100_M	103_A	1.436	0.63
71_N	74_L	1.432	0.63
107_L	110_D	1.402	0.60
19_S	63_I	1.395	0.60
14_A	61_R	1.386	0.59
70_L	101_L	1.382	0.59
38_G	49_D	1.381	0.59
68_K	85_Q	1.366	0.57
35_K	121_A	1.349	0.56
15_V	23_Q	1.335	0.55
55_L	78_I	1.301	0.52
8_V	71_N	1.292	0.51
101_L	112_K	1.291	0.51
101_L	104_A	1.285	0.51
37_V	48_V	1.283	0.50
31_V	72_S	1.260	0.48
70_L	112_K	1.247	0.47
20_S	72_S	1.236	0.46
87_Y	117_V	1.215	0.45
15_V	75_G	1.211	0.44
115_L	119_D	1.209	0.44
18_M	72_S	1.187	0.42
112_K	119_D	1.180	0.42
84_A	104_A	1.178	0.41
98_K	109_V	1.175	0.41
70_L	105_H	1.165	0.40
2_D	34_V	1.163	0.40
98_K	122_R	1.152	0.39
16_I	71_N	1.151	0.39
115_L	122_R	1.148	0.39
18_M	78_I	1.138	0.38
112_K	122_R	1.138	0.38
84_A	105_H	1.136	0.38
56_P	96_Y	1.131	0.38
69_L	91_S	1.121	0.37
19_S	25_A	1.108	0.36
107_L	112_K	1.104	0.36
83_L	117_V	1.104	0.36
101_L	107_L	1.099	0.35
105_H	112_K	1.098	0.35
18_M	31_V	1.097	0.35
16_I	74_L	1.097	0.35
45_L	65_M	1.095	0.35
100_M	110_D	1.088	0.34
30_Y	47_T	1.087	0.34
51_T	57_A	1.085	0.34
4_V	14_A	1.076	0.33
19_S	120_Q	1.074	0.33
3_K	58_S	1.074	0.33
100_M	113_N	1.070	0.33
38_G	73_D	1.063	0.32
37_V	42_R	1.046	0.31
65_M	96_Y	1.040	0.31
88_V	95_E	1.039	0.31
105_H	108_A	1.038	0.31
112_K	116_D	1.036	0.30
50_E	54_A	1.033	0.30
83_L	90_T	1.033	0.30
110_D	116_D	1.031	0.30
117_V	121_A	1.030	0.30
66_A	96_Y	1.028	0.30
7_N	63_I	1.025	0.30
116_D	119_D	1.023	0.29
84_A	118_I	1.023	0.29
22_I	47_T	1.021	0.29
40_A	97_K	1.018	0.29
14_A	24_P	1.016	0.29
59_T	79_S	1.016	0.29
81_M	84_A	1.015	0.29
29_E	43_T	1.011	0.29
64_E	84_A	1.010	0.29
78_I	121_A	1.008	0.28
13_K	16_I	1.003	0.28
68_K	110_D	1.000	0.28

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
3gm3A	1	1	100	0.023	Contact Map
1k04A	1	1	100	0.032	Contact Map
2l6fA	1	1	100	0.109	Contact Map
2jx0A	1	0.9206	48.2	0.925	Contact Map
3dyjA	2	0.9286	40.3	0.929	Contact Map
4w8pA	1	0.9762	17.2	0.941	Contact Map
4gehA	2	0.881	15.1	0.942	Contact Map
4jkvA	2	0.4524	13.8	0.943	Contact Map
3zccA	2	0.8571	13.4	0.943	Contact Map
2ozbB	2	0.9444	13.2	0.944	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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