OPENSEQ.org - 1485868285 - GREMLIN Submission

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Kox_NT_TM_and_loop

ID:	1485868285	Query Sequence MRLPQLAGCVIIGILPLLWLPVLPGRWVTWGLMVLALLIAQCRRRPAQYAALITLFFVWGVLSARQTLWPTERLTDKNQRVEVELTATDGQTTHQGKIIRLDGRRLFPAPGISLYGNYLPETPCAGQVWAMTLRARPVHGQLNDGGFDSQRYALAQHRPLTGRFITAEIRERNCSLRARYL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	181 (181)
Sequences:	329 (249)
Seq/Len:	1.818
Nf(neff/√len):	18.5

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: 1.818).

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
147_F	152_Y	2.560	1.00
124_C	174_C	2.124	0.99
78_N	134_R	1.787	0.97
124_C	127_Q	1.747	0.96
142_L	150_Q	1.670	0.95
8_G	12_I	1.613	0.93
17_L	148_D	1.594	0.93
134_R	166_T	1.561	0.92
140_G	146_G	1.553	0.92
150_Q	155_A	1.510	0.90
13_G	68_L	1.471	0.88
158_R	176_L	1.454	0.88
24_P	127_Q	1.451	0.87
156_Q	161_T	1.440	0.87
133_L	162_G	1.439	0.87
54_T	162_G	1.423	0.86
16_P	20_L	1.410	0.85
145_G	150_Q	1.368	0.83
164_F	167_A	1.354	0.82
112_I	135_A	1.348	0.82
78_N	135_A	1.313	0.79
21_P	55_L	1.312	0.79
60_G	131_M	1.312	0.79
17_L	24_P	1.294	0.78
138_V	150_Q	1.290	0.78
78_N	141_Q	1.282	0.77
55_L	156_Q	1.268	0.76
82_E	130_A	1.267	0.76
166_T	176_L	1.262	0.75
17_L	20_L	1.262	0.75
17_L	139_H	1.247	0.74
136_R	153_A	1.247	0.74
12_I	26_R	1.242	0.74
116_G	164_F	1.231	0.73
52_L	85_L	1.228	0.73
17_L	142_L	1.226	0.72
20_L	148_D	1.215	0.71
112_I	181_L	1.213	0.71
3_L	136_R	1.200	0.70
148_D	153_A	1.200	0.70
1_M	114_L	1.194	0.70
133_L	163_R	1.193	0.69
168_E	172_R	1.173	0.68
153_A	160_L	1.162	0.66
140_G	161_T	1.157	0.66
138_V	142_L	1.155	0.66
127_Q	139_H	1.153	0.66
140_G	168_E	1.148	0.65
114_L	162_G	1.143	0.65
89_D	96_G	1.137	0.64
85_L	98_I	1.126	0.63
54_T	173_N	1.118	0.62
139_H	142_L	1.113	0.62
9_C	13_G	1.111	0.61
138_V	160_L	1.110	0.61
178_A	181_L	1.108	0.61
100_R	114_L	1.105	0.61
166_T	170_R	1.104	0.61
81_V	133_L	1.100	0.60
79_Q	102_D	1.100	0.60
129_W	142_L	1.097	0.60
132_T	165_I	1.092	0.59
152_Y	156_Q	1.089	0.59
63_S	139_H	1.085	0.59
3_L	6_L	1.083	0.58
34_V	108_P	1.080	0.58
41_Q	52_L	1.080	0.58
88_T	93_T	1.076	0.58
144_D	154_L	1.076	0.58
98_I	112_I	1.073	0.57
124_C	139_H	1.069	0.57
22_V	154_L	1.069	0.57
2_R	9_C	1.064	0.56
31_G	48_Q	1.059	0.56
21_P	118_Y	1.059	0.56
95_Q	99_I	1.058	0.56
1_M	115_Y	1.054	0.55
24_P	139_H	1.052	0.55
33_M	81_V	1.051	0.55
128_V	176_L	1.046	0.54
78_N	131_M	1.045	0.54
129_W	150_Q	1.037	0.54
20_L	155_A	1.036	0.53
34_V	68_L	1.032	0.53
10_V	61_V	1.030	0.53
106_L	174_C	1.022	0.52
154_L	180_Y	1.020	0.52
69_W	180_Y	1.020	0.52
10_V	38_L	1.020	0.52
13_G	133_L	1.011	0.51
24_P	60_G	1.006	0.50
151_R	177_R	1.003	0.50
133_L	136_R	1.002	0.50

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
3eipA	2	0.3757	8.6	0.941	Contact Map
1hnrA	1	0.2486	2.6	0.954	Contact Map
3ne5A	1	0.3315	1.7	0.958	Contact Map
1dj7B	1	0.2541	1.6	0.959	Contact Map
4tp8I	1	0.5138	1.4	0.96	Contact Map
2juiA	1	0.1823	1.3	0.961	Contact Map
1ynxA	1	0.2983	1.3	0.961	Contact Map
2as0A	2	0.5028	1.2	0.962	Contact Map
4uisB	1	0	1.2	0.962	Contact Map
2l7qA	1	0.4144	1.2	0.962	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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