OPENSEQ.org - 1405072058 - GREMLIN Submission

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rhodopsin

ID:	1405072058	Query Sequence MVGLTTLFWLGAIGMLVGTLAFAWAGRDAGSGERRYYVTLVGISGIAAVAYAVMALGVGWVPVAERTVFVPRYIDWILTTPLIVYFLGLLAGLDSREFGIVITLNTVVMLAGFAGAMVPGIERYALFGMGAVAFIGLVYYLVGPMTESASQRSSGIKSLYVRLRNLTVVLWAIYPFIWLLGPPGVALLTPTVDVALIVYLDLVTKVGFGFIALDAAATL	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	219 (214)
Sequences:	396 (311.6)
Seq/Len:	1.850
Nf(neff/√len):	21.3

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: 1.850).

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	4.439	1.00
75_D	205_K	2.427	1.00
14_G	202_L	2.319	1.00
80_T	105_N	2.200	0.99
9_W	55_A	2.172	0.99
22_F	209_G	1.959	0.99
79_T	82_L	1.912	0.98
60_W	69_F	1.792	0.97
53_V	126_L	1.713	0.96
79_T	205_K	1.702	0.96
75_D	79_T	1.681	0.95
178_W	184_G	1.623	0.94
47_A	75_D	1.611	0.94
19_T	44_S	1.568	0.92
47_A	83_I	1.550	0.92
107_V	133_A	1.530	0.91
50_A	54_M	1.529	0.91
108_V	112_G	1.490	0.90
105_N	108_V	1.454	0.88
183_P	193_D	1.451	0.88
80_T	108_V	1.445	0.88
178_W	200_L	1.445	0.88
112_G	205_K	1.442	0.87
178_W	193_D	1.424	0.86
47_A	205_K	1.376	0.84
18_G	206_V	1.352	0.82
79_T	112_G	1.329	0.81
40_L	86_F	1.327	0.81
50_A	116_A	1.327	0.81
16_L	48_A	1.315	0.80
76_W	112_G	1.304	0.79
153_S	157_K	1.292	0.78
70_V	74_I	1.291	0.78
105_N	109_M	1.290	0.78
40_L	209_G	1.284	0.78
76_W	174_Y	1.275	0.77
109_M	205_K	1.267	0.76
188_L	195_A	1.253	0.75
23_A	41_V	1.241	0.74
80_T	205_K	1.228	0.73
51_Y	82_L	1.218	0.72
76_W	81_P	1.216	0.72
73_Y	76_W	1.212	0.72
171_W	205_K	1.210	0.71
75_D	82_L	1.209	0.71
77_I	106_T	1.195	0.70
115_G	178_W	1.195	0.70
111_A	204_T	1.186	0.69
117_M	183_P	1.182	0.69
61_V	117_M	1.181	0.69
121_I	128_G	1.179	0.69
142_V	199_Y	1.178	0.69
67_T	190_P	1.178	0.69
11_G	206_V	1.175	0.68
11_G	106_T	1.175	0.68
8_F	135_I	1.172	0.68
85_Y	102_I	1.171	0.68
180_L	188_L	1.170	0.68
11_G	15_M	1.169	0.68
80_T	200_L	1.169	0.68
80_T	112_G	1.169	0.68
135_I	165_N	1.168	0.68
73_Y	208_F	1.167	0.67
117_M	132_V	1.166	0.67
47_A	82_L	1.166	0.67
31_S	168_V	1.162	0.67
47_A	108_V	1.158	0.67
20_L	45_G	1.140	0.65
16_L	45_G	1.135	0.64
158_S	162_R	1.131	0.64
43_I	82_L	1.125	0.63
9_W	12_A	1.115	0.62
43_I	79_T	1.112	0.62
142_V	168_V	1.112	0.62
75_D	80_T	1.111	0.62
40_L	137_L	1.108	0.62
47_A	80_T	1.108	0.62
82_L	175_P	1.107	0.61
113_F	117_M	1.103	0.61
19_T	45_G	1.095	0.60
39_T	82_L	1.090	0.60
12_A	52_A	1.089	0.60
128_G	191_T	1.088	0.60
79_T	204_T	1.087	0.59
107_V	127_F	1.085	0.59
73_Y	81_P	1.084	0.59
17_V	202_L	1.072	0.58
60_W	67_T	1.063	0.57
122_E	186_A	1.054	0.56
185_V	188_L	1.050	0.55
80_T	170_L	1.049	0.55
37_Y	94_D	1.046	0.55
87_L	146_T	1.040	0.54
116_A	178_W	1.038	0.54
20_L	23_A	1.036	0.54
54_M	72_R	1.033	0.54
47_A	79_T	1.028	0.53
43_I	50_A	1.026	0.53
79_T	105_N	1.025	0.53
44_S	209_G	1.025	0.53
47_A	141_L	1.022	0.52
86_F	212_A	1.021	0.52
115_G	136_G	1.016	0.52
58_V	122_E	1.015	0.52
73_Y	105_N	1.010	0.51
18_G	210_F	1.009	0.51
43_I	163_L	1.008	0.51
15_M	112_G	1.007	0.51
84_V	128_G	1.004	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: (05Jul14)
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	1	100	0.056	Contact Map
4l35A	1	1	100	0.077	Contact Map
1xioA	1	0.9589	100	0.08	Contact Map
1m0kA	1	0.9589	100	0.097	Contact Map
4fbzA	1	1	100	0.102	Contact Map
2ei4A	1	0.9954	100	0.102	Contact Map
3am6A	4	0.9772	100	0.108	Contact Map
3qbgA	3	0.9863	100	0.134	Contact Map
2jafA	1	0.9772	100	0.141	Contact Map
3ddlA	2	0.9863	100	0.163	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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