OPENSEQ.org - 1493219040 - GREMLIN Submission

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NKP2

ID:	1493219040	Query Sequence GKLLSDFLLAPAPLRDFMTLRQFTEIFPKGHRTNPAVQDLYRELQRLREKDIDLVRRAIAEEIARSKRLRREYASERRQLDDATVAGLDSNALRMEEEVHNIPDSAVNTMLTSSQLSNNGRKKPHTLASVHSSIEEACHSLESQIAEIEVENARALAEVQEVVGALSDLRHGRFAQPASGEDLGEEVLATLKRLEAACTKTPG	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	203 (166)
Sequences:	194 (144.2)
Seq/Len:	1.169
Nf(neff/√len):	11.2

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: 1.169).

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
13_P	16_D	2.310	0.99
169_L	172_G	1.963	0.96
38_Q	57_R	1.844	0.94
20_L	37_V	1.711	0.90
14_L	17_F	1.707	0.90
3_L	18_M	1.655	0.88
42_R	45_Q	1.645	0.88
14_L	41_Y	1.645	0.88
11_P	42_R	1.633	0.87
18_M	33_T	1.587	0.85
13_P	17_F	1.571	0.85
2_K	6_D	1.518	0.82
13_P	41_Y	1.501	0.81
16_D	41_Y	1.446	0.77
169_L	173_R	1.430	0.76
7_F	10_A	1.426	0.76
24_T	37_V	1.423	0.76
7_F	24_T	1.406	0.74
20_L	27_F	1.401	0.74
23_F	44_L	1.396	0.74
170_R	173_R	1.396	0.74
12_A	49_E	1.392	0.73
152_N	161_E	1.375	0.72
12_A	44_L	1.367	0.71
163_V	167_S	1.359	0.71
7_F	39_D	1.356	0.71
21_R	24_T	1.333	0.69
32_R	35_P	1.311	0.67
107_V	124_P	1.311	0.67
4_L	59_I	1.303	0.66
66_S	78_R	1.296	0.65
29_K	46_R	1.285	0.65
11_P	53_D	1.281	0.64
4_L	62_E	1.277	0.64
7_F	149_E	1.272	0.63
1_G	63_I	1.256	0.62
20_L	45_Q	1.249	0.61
19_T	27_F	1.237	0.60
72_E	76_E	1.235	0.60
105_S	108_N	1.227	0.59
71_R	78_R	1.216	0.58
93_L	98_E	1.213	0.58
37_V	71_R	1.204	0.57
19_T	46_R	1.194	0.56
20_L	35_P	1.193	0.56
140_S	147_E	1.193	0.56
152_N	155_A	1.186	0.55
73_Y	76_E	1.185	0.55
126_T	134_I	1.168	0.54
71_R	77_R	1.166	0.53
93_L	100_H	1.159	0.53
12_A	52_I	1.156	0.52
10_A	24_T	1.155	0.52
5_S	25_E	1.154	0.52
6_D	38_Q	1.148	0.52
19_T	56_R	1.147	0.52
99_V	103_P	1.144	0.51
158_E	162_V	1.138	0.51
152_N	158_E	1.133	0.50
12_A	22_Q	1.130	0.50
35_P	66_S	1.128	0.50
106_A	124_P	1.115	0.48
107_V	122_K	1.111	0.48
3_L	15_R	1.107	0.48
152_N	159_V	1.098	0.47
170_R	174_F	1.095	0.47
15_R	34_N	1.093	0.46
19_T	41_Y	1.091	0.46
164_G	167_S	1.090	0.46
21_R	38_Q	1.089	0.46
95_M	129_S	1.087	0.46
18_M	25_E	1.086	0.46
126_T	133_S	1.079	0.45
107_V	123_K	1.078	0.45
10_A	22_Q	1.068	0.44
131_H	137_A	1.062	0.43
125_H	138_C	1.059	0.43
105_S	124_P	1.058	0.43
18_M	34_N	1.052	0.42
2_K	24_T	1.045	0.42
61_E	64_A	1.043	0.42
35_P	62_E	1.042	0.42
20_L	24_T	1.028	0.40
25_E	29_K	1.024	0.40
126_T	137_A	1.019	0.39
37_V	69_L	1.019	0.39
106_A	123_K	1.011	0.39
131_H	134_I	1.008	0.38
104_D	128_A	1.007	0.38
24_T	51_D	1.006	0.38
84_T	102_I	1.004	0.38
93_L	126_T	1.003	0.38
126_T	131_H	1.002	0.38
14_L	19_T	1.001	0.38
108_N	122_K	1.001	0.38

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
1ge9A	1	0.3103	29.9	0.95	Contact Map
3ghgA	4	0.665	25.4	0.952	Contact Map
2zqmA	1	0.5616	22.7	0.953	Contact Map
1fxkA	1	0.4877	20.6	0.954	Contact Map
1deqA	4	0.6847	15.7	0.957	Contact Map
4iloA	2	0.8128	14.7	0.957	Contact Map
4rh7A	1	0.7931	14.6	0.957	Contact Map
4uxvA	1	0.9409	14.3	0.957	Contact Map
3mq9A	8	0.7389	13.7	0.958	Contact Map
3frrA	1	0.7192	12.9	0.958	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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