OPENSEQ.org - 1455703479 - GREMLIN Submission

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KNL1 22-160

ID:	1455703479	Query Sequence LREFIDEVGVGFLDTKLIDDLDKKVNFPLNSLNLMEIQRIDNVLSAYYIDIPILEVEAFRCKELWRSINESKNKFKDFETQIDRSHPPLLLQEYFSSSEKMKQLMKDQLQLVKGYSKLEAAMEWYEWRKKQLNGLELIL	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	139 (135)
Sequences:	205 (150.6)
Seq/Len:	1.519
Nf(neff/√len):	13.0

Jackhmmer Results: (2015_08)
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: 1.519).

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
124_W	127_W	1.767	0.95
86_H	131_Q	1.620	0.91
11_G	40_I	1.595	0.90
20_D	23_K	1.559	0.89
63_E	66_R	1.553	0.89
14_D	40_I	1.524	0.88
66_R	135_L	1.512	0.87
10_V	52_P	1.467	0.85
63_E	120_A	1.449	0.84
86_H	130_K	1.444	0.83
80_T	96_S	1.420	0.82
113_K	125_Y	1.406	0.81
130_K	134_G	1.385	0.80
93_E	105_M	1.376	0.79
8_V	97_S	1.360	0.78
60_R	86_H	1.330	0.76
80_T	135_L	1.312	0.74
30_N	73_N	1.294	0.73
99_E	106_K	1.293	0.73
80_T	91_L	1.275	0.71
47_Y	112_V	1.272	0.71
4_F	12_F	1.264	0.70
88_P	128_R	1.242	0.69
45_S	48_Y	1.241	0.68
63_E	78_F	1.238	0.68
106_K	110_Q	1.235	0.68
93_E	109_L	1.233	0.68
64_L	124_W	1.220	0.67
105_M	108_Q	1.217	0.66
115_Y	126_E	1.213	0.66
42_N	128_R	1.207	0.65
52_P	55_E	1.196	0.64
33_N	92_Q	1.182	0.63
49_I	123_E	1.174	0.62
33_N	51_I	1.166	0.61
18_I	58_A	1.165	0.61
71_S	131_Q	1.154	0.60
13_L	40_I	1.152	0.60
94_Y	132_L	1.144	0.59
78_F	86_H	1.135	0.58
102_K	130_K	1.126	0.57
60_R	109_L	1.124	0.57
71_S	134_G	1.121	0.57
67_S	71_S	1.114	0.56
92_Q	95_F	1.104	0.55
50_D	58_A	1.102	0.55
113_K	124_W	1.100	0.55
58_A	103_Q	1.099	0.55
50_D	75_F	1.097	0.54
90_L	108_Q	1.094	0.54
80_T	104_L	1.089	0.54
70_E	95_F	1.085	0.53
110_Q	113_K	1.084	0.53
94_Y	102_K	1.083	0.53
97_S	131_Q	1.077	0.52
32_L	76_K	1.073	0.52
63_E	84_R	1.070	0.52
59_F	127_W	1.061	0.51
64_L	98_S	1.046	0.49
68_I	91_L	1.042	0.49
5_I	19_D	1.041	0.49
5_I	109_L	1.039	0.48
119_E	129_K	1.035	0.48
13_L	17_L	1.032	0.48
30_N	70_E	1.030	0.47
92_Q	110_Q	1.029	0.47
16_K	120_A	1.026	0.47
34_L	84_R	1.025	0.47
90_L	124_W	1.025	0.47
7_E	95_F	1.025	0.47
54_L	77_D	1.021	0.47
80_T	120_A	1.019	0.46
70_E	122_M	1.015	0.46
69_N	96_S	1.007	0.45
62_K	109_L	1.004	0.45
64_L	109_L	1.002	0.45

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	0.741	14.1	0.931	Contact Map
3fhnA	4	0.9712	10.2	0.935	Contact Map
3p8lA	2	0.518	8.1	0.938	Contact Map
4lfgA	2	0.6403	6.9	0.94	Contact Map
4eveA	1	0.7338	5.8	0.942	Contact Map
3kevA	1	0.8201	5.4	0.943	Contact Map
4j2cA	2	0.6763	4.8	0.944	Contact Map
3fd9A	3	0.9065	4.7	0.944	Contact Map
4kkmA	2	0.4964	4.6	0.945	Contact Map
3ucaA	2	0.5108	4.5	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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