OPENSEQ.org - 1426262700 - GREMLIN Submission

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rhodopsin

ID:	1426262700	Query Sequence MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYAVMALGVGWVPVAERTVFVPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATLRAEHGE	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	225 (219)
Sequences:	395 (311.9)
Seq/Len:	1.804
Nf(neff/√len):	21.1

HHblits Results: (2013_03)
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: 1.804).

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
46_I	78_L	4.433	1.00
14_G	202_L	2.485	1.00
75_D	205_K	2.355	1.00
80_T	105_N	2.179	0.99
9_W	55_A	2.069	0.99
79_T	82_L	1.917	0.98
22_F	209_G	1.913	0.98
53_V	126_L	1.769	0.96
60_W	69_F	1.726	0.96
79_T	205_K	1.647	0.94
75_D	79_T	1.634	0.94
178_W	184_G	1.622	0.94
47_A	75_D	1.592	0.93
47_A	83_I	1.565	0.92
19_T	44_S	1.563	0.92
50_A	54_M	1.562	0.92
107_V	133_A	1.498	0.89
108_V	112_G	1.473	0.88
80_T	108_V	1.429	0.86
183_P	193_D	1.424	0.86
105_N	108_V	1.422	0.86
112_G	205_K	1.407	0.85
40_L	86_F	1.352	0.82
16_L	48_A	1.338	0.81
76_W	174_Y	1.333	0.80
178_W	200_L	1.327	0.80
70_V	74_I	1.327	0.80
18_G	206_V	1.321	0.80
47_A	205_K	1.314	0.79
76_W	112_G	1.301	0.78
50_A	116_A	1.298	0.78
188_L	195_A	1.298	0.78
79_T	112_G	1.289	0.77
178_W	193_D	1.286	0.77
111_A	204_T	1.286	0.77
153_S	157_K	1.280	0.77
76_W	81_P	1.279	0.77
17_V	202_L	1.278	0.76
77_I	106_T	1.277	0.76
8_F	135_I	1.271	0.76
109_M	205_K	1.266	0.76
40_L	209_G	1.248	0.74
23_A	41_V	1.242	0.74
18_G	210_F	1.231	0.73
11_G	206_V	1.224	0.72
80_T	205_K	1.224	0.72
11_G	106_T	1.224	0.72
51_Y	82_L	1.221	0.72
73_Y	81_P	1.212	0.71
67_T	190_P	1.205	0.70
115_G	178_W	1.203	0.70
61_V	117_M	1.203	0.70
180_L	188_L	1.201	0.70
73_Y	76_W	1.199	0.70
20_L	23_A	1.198	0.70
171_W	205_K	1.196	0.69
73_Y	208_F	1.193	0.69
11_G	15_M	1.192	0.69
20_L	45_G	1.185	0.68
85_Y	102_I	1.185	0.68
158_S	162_R	1.169	0.67
43_I	82_L	1.159	0.66
105_N	109_M	1.154	0.65
142_V	168_V	1.152	0.65
31_S	168_V	1.145	0.65
128_G	191_T	1.145	0.65
16_L	45_G	1.140	0.64
12_A	52_A	1.139	0.64
43_I	50_A	1.138	0.64
80_T	112_G	1.132	0.63
39_T	82_L	1.125	0.63
52_A	125_A	1.125	0.63
40_L	137_L	1.123	0.62
47_A	82_L	1.122	0.62
75_D	82_L	1.121	0.62
142_V	199_Y	1.119	0.62
111_A	130_G	1.119	0.62
125_A	185_V	1.117	0.62
60_W	63_V	1.116	0.62
82_L	175_P	1.114	0.61
121_I	128_G	1.112	0.61
54_M	72_R	1.111	0.61
47_A	108_V	1.100	0.60
9_W	12_A	1.099	0.60
117_M	183_P	1.094	0.59
113_F	117_M	1.094	0.59
87_L	146_T	1.073	0.57
75_D	80_T	1.072	0.57
135_I	165_N	1.069	0.57
79_T	204_T	1.069	0.57
107_V	127_F	1.067	0.56
19_T	45_G	1.061	0.56
28_D	147_E	1.059	0.56
102_I	173_I	1.059	0.56
80_T	200_L	1.058	0.56
47_A	80_T	1.056	0.55
43_I	79_T	1.056	0.55
11_G	202_L	1.053	0.55
43_I	163_L	1.045	0.54
117_M	132_V	1.043	0.54
47_A	79_T	1.039	0.53
44_S	209_G	1.032	0.53
43_I	208_F	1.032	0.53
116_A	178_W	1.028	0.52
58_V	122_E	1.024	0.52
48_A	52_A	1.024	0.52
122_E	186_A	1.022	0.52
84_V	128_G	1.022	0.52
64_A	169_V	1.007	0.50
37_Y	94_D	1.000	0.49

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

See coupling matrix (for protein design or mutagenesis)
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: (31Jan15)
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
3qapA	1	0.9733	100	0.067	Contact Map
1xioA	1	0.9422	100	0.093	Contact Map
4l35A	1	1	100	0.122	Contact Map
3wqjA	1	0.9689	100	0.122	Contact Map
4fbzA	1	1	100	0.127	Contact Map
1m0kA	1	0.9511	100	0.128	Contact Map
3am6A	4	0.9644	100	0.176	Contact Map
3qbgA	3	0.9911	100	0.185	Contact Map
2jafA	1	0.9911	100	0.189	Contact Map
3ddlA	2	0.9911	100	0.203	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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