OPENSEQ.org - 1408421120 - GREMLIN Submission

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proteorhodopsin

ID:	1408421120	Query Sequence MSLITNFLAVAKMAPDDYVGFTFFVGCMAMMAASVFFFLSMSSFDKKWRTSILVSGLITFIAAVHYWYMRDYWAANAESPTFFRYVDWVLTVPLMCVEFFLILKVAGAKKSLMWRLIFLSVVMLVTGYMGEVLFREQAWFWGLVSGIAYFVIVYDIWLGKAKKLAVAAGGSVLKAHKTLCWFVLVGWAIYPIGYMAGTPGWYESIFGGWNLDVIYNIGDAINKIGFGLVIYNLAVQSSDEIKK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	243 (228)
Sequences:	381 (298.9)
Seq/Len:	1.671
Nf(neff/√len):	19.8

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: 1.671).

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
61_I	90_L	4.351	1.00
87_D	223_K	2.691	1.00
29_A	220_A	2.569	1.00
92_V	120_S	2.295	1.00
91_T	94_L	2.146	0.99
24_F	70_R	1.858	0.97
62_A	87_D	1.820	0.97
87_D	91_T	1.809	0.97
37_F	227_G	1.706	0.95
62_A	95_M	1.682	0.94
68_Y	141_W	1.667	0.94
123_M	127_G	1.665	0.94
34_S	59_T	1.610	0.92
127_G	223_K	1.582	0.91
91_T	223_K	1.581	0.91
65_H	69_M	1.572	0.91
126_T	145_S	1.504	0.88
187_W	223_K	1.477	0.87
120_S	124_L	1.459	0.86
120_S	123_M	1.445	0.86
92_V	223_K	1.439	0.85
122_V	148_A	1.398	0.83
92_V	123_M	1.388	0.82
143_L	209_W	1.382	0.82
55_S	227_G	1.381	0.82
54_V	94_L	1.367	0.81
124_L	223_K	1.365	0.81
62_A	223_K	1.356	0.80
72_Y	82_F	1.356	0.80
194_Y	218_G	1.349	0.80
197_G	214_I	1.348	0.80
62_A	123_M	1.335	0.79
95_M	223_K	1.317	0.77
87_D	222_N	1.311	0.77
88_W	127_G	1.306	0.77
190_Y	215_Y	1.297	0.76
62_A	156_I	1.293	0.76
87_D	94_L	1.289	0.75
198_T	211_L	1.285	0.75
89_V	121_V	1.280	0.75
91_T	222_N	1.280	0.75
38_F	56_G	1.276	0.74
62_A	92_V	1.275	0.74
58_I	91_T	1.274	0.74
130_G	194_Y	1.272	0.74
26_G	29_A	1.261	0.73
149_Y	152_I	1.252	0.72
33_A	36_F	1.242	0.71
62_A	91_T	1.239	0.71
33_A	224_I	1.227	0.70
85_Y	93_P	1.201	0.68
91_T	127_G	1.190	0.67
194_Y	199_P	1.188	0.66
91_T	120_S	1.185	0.66
126_T	222_N	1.183	0.66
144_V	198_T	1.177	0.65
233_L	237_S	1.176	0.65
88_W	190_Y	1.176	0.65
91_T	123_M	1.175	0.65
64_V	176_H	1.174	0.65
30_M	127_G	1.172	0.65
127_G	226_F	1.164	0.64
87_D	92_V	1.161	0.64
62_A	69_M	1.157	0.63
58_I	94_L	1.157	0.63
88_W	93_P	1.153	0.63
37_F	57_L	1.150	0.63
168_A	173_L	1.147	0.62
62_A	94_L	1.144	0.62
128_Y	132_V	1.143	0.62
59_T	227_G	1.136	0.61
127_G	191_P	1.132	0.61
15_P	18_Y	1.124	0.60
25_V	36_F	1.122	0.60
186_G	218_G	1.122	0.60
65_H	131_E	1.105	0.58
26_G	33_A	1.104	0.58
26_G	224_I	1.098	0.57
30_M	62_A	1.091	0.57
36_F	40_S	1.088	0.56
73_W	82_F	1.088	0.56
131_E	194_Y	1.078	0.55
132_V	211_L	1.077	0.55
123_M	126_T	1.075	0.55
28_M	114_W	1.074	0.55
196_A	214_I	1.072	0.55
96_C	120_S	1.071	0.55
138_A	143_L	1.071	0.55
94_L	130_G	1.065	0.54
122_V	142_G	1.062	0.54
22_T	216_N	1.059	0.53
186_G	221_I	1.056	0.53
92_V	186_G	1.055	0.53
67_W	140_F	1.054	0.53
30_M	123_M	1.051	0.52
139_W	216_N	1.050	0.52
35_V	220_A	1.049	0.52
149_Y	153_V	1.039	0.51
164_L	176_H	1.034	0.51
72_Y	132_V	1.032	0.50
67_W	71_D	1.030	0.50
37_F	59_T	1.028	0.50
55_S	152_I	1.024	0.50
37_F	55_S	1.022	0.49
165_A	173_L	1.021	0.49
35_V	39_L	1.021	0.49
62_A	120_S	1.014	0.49
58_I	65_H	1.013	0.48
30_M	92_V	1.013	0.48
74_A	132_V	1.013	0.48
165_A	183_V	1.007	0.48
33_A	228_L	1.007	0.48

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: (17Jul14)
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
4knfA	5	0.9424	100	0.208	Contact Map
4jq6A	3	0.8477	100	0.211	Contact Map
3ddlA	2	0.9506	100	0.215	Contact Map
2ei4A	1	0.9342	100	0.24	Contact Map
1xioA	1	0.8807	100	0.242	Contact Map
1m0kA	1	0.8724	100	0.244	Contact Map
3qapA	1	0.8889	100	0.246	Contact Map
4hyjA	2	0.93	100	0.247	Contact Map
4l35A	1	0.9259	100	0.248	Contact Map
3am6A	4	0.9012	100	0.251	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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