OPENSEQ.org - 1489136015 - GREMLIN Submission

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KNL1 22-160

ID:	1489136015	Query Sequence LREFIDEVGVGFLDTKLIDDLDKKVNFPLNSLNLMEIQRIDNVLSAYYIDIPILEVEAFRCKELWRSINESKNKFKDFETQIDRSHPPLLLQEYFSSSEKMKQLMKDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELIL	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	139 (135)
Sequences:	301 (204)
Seq/Len:	2.230
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: 2.230).

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
20_D	23_K	2.032	0.99
124_W	127_W	2.008	0.99
63_E	66_R	1.745	0.97
80_T	135_L	1.734	0.97
10_V	52_P	1.548	0.94
12_F	87_P	1.495	0.92
120_A	123_E	1.419	0.90
60_R	109_L	1.407	0.89
65_W	108_Q	1.400	0.89
39_R	42_N	1.398	0.89
68_I	91_L	1.396	0.89
86_H	131_Q	1.346	0.86
50_D	75_F	1.326	0.85
20_D	25_V	1.325	0.85
52_P	90_L	1.324	0.85
113_K	125_Y	1.309	0.84
106_K	110_Q	1.287	0.82
80_T	91_L	1.282	0.82
12_F	93_E	1.268	0.81
118_L	128_R	1.267	0.81
108_Q	120_A	1.264	0.81
93_E	105_M	1.248	0.80
94_Y	132_L	1.245	0.79
7_E	95_F	1.238	0.79
17_L	23_K	1.227	0.78
5_I	19_D	1.218	0.77
10_V	37_I	1.204	0.76
21_L	110_Q	1.189	0.75
34_L	39_R	1.183	0.74
61_C	121_A	1.182	0.74
59_F	127_W	1.165	0.73
63_E	78_F	1.162	0.72
10_V	69_N	1.160	0.72
54_L	61_C	1.158	0.72
54_L	120_A	1.156	0.72
64_L	109_L	1.148	0.71
61_C	86_H	1.147	0.71
30_N	73_N	1.141	0.71
69_N	135_L	1.114	0.68
63_E	127_W	1.113	0.68
14_D	40_I	1.107	0.67
66_R	135_L	1.105	0.67
62_K	134_G	1.103	0.67
8_V	97_S	1.099	0.66
40_I	45_S	1.099	0.66
35_M	119_E	1.078	0.64
78_F	81_Q	1.076	0.64
54_L	77_D	1.071	0.63
24_K	101_M	1.067	0.63
45_S	82_I	1.067	0.63
84_R	107_D	1.065	0.63
97_S	115_Y	1.062	0.62
57_E	132_L	1.055	0.62
11_G	40_I	1.053	0.61
33_N	103_Q	1.046	0.61
12_F	56_V	1.044	0.60
8_V	20_D	1.044	0.60
57_E	131_Q	1.041	0.60
60_R	116_S	1.040	0.60
109_L	128_R	1.038	0.60
84_R	129_K	1.038	0.60
10_V	113_K	1.038	0.60
124_W	128_R	1.036	0.60
130_K	134_G	1.035	0.59
56_V	83_D	1.032	0.59
5_I	119_E	1.031	0.59
3_E	29_L	1.027	0.59
78_F	86_H	1.026	0.58
24_K	28_P	1.024	0.58
50_D	58_A	1.023	0.58
86_H	130_K	1.016	0.57
115_Y	126_E	1.016	0.57
103_Q	126_E	1.012	0.57
26_N	52_P	1.006	0.56
80_T	100_K	1.002	0.56
24_K	98_S	1.002	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
2ve7C	2	0.7626	19.3	0.919	Contact Map
3fhnA	4	0.9065	16.5	0.922	Contact Map
3er9B	1	0.7266	10.4	0.929	Contact Map
3fd9A	3	0.9209	7.7	0.933	Contact Map
4j2cA	2	0.6763	7.6	0.933	Contact Map
4a1nA	1	0.5612	5.3	0.937	Contact Map
1o5hA	2	0.8561	5.3	0.937	Contact Map
4eveA	1	0.7338	5	0.938	Contact Map
4wbdA	1	0.9137	4.5	0.939	Contact Map
4ux3A	1	0.8417	4.4	0.94	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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