OPENSEQ.org - 1430137675 - GREMLIN Submission

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ID:	1430137675	Query Sequence RVAPPGPDRRASLKRLYLQQNWLSLLEQCDDMFARGASHLWLDLQWYIHQALLQTGKENYAAIIQYDLKGLLLRLPGLETLAFNDGMPFADDVTLSWIQQQVMECGERWAEEPSVTITAAPGDNDILSLEPEALQIADNEGTEAALSWLQARPGIQSDRSNWLLRLLMARVAEQTGKNDLALHLLAELDERATRLTLSQWEPELVFEVKARRLKLLRMKSAKTESDRVRLQPDMEHLLAGLIAIDAARAAVLCNSGSS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	258 (252)
Sequences:	403 (278)
Seq/Len:	1.599
Nf(neff/√len):	17.5

Jackhmmer Results: (2015_01_07)
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: 1.599).

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
159_R	201_E	2.562	1.00
91_D	94_T	2.109	0.99
46_W	91_D	2.049	0.99
26_L	48_I	2.029	0.98
90_A	94_T	1.954	0.98
151_A	164_L	1.919	0.98
72_L	78_L	1.873	0.97
126_I	164_L	1.845	0.97
29_C	51_A	1.823	0.96
169_A	181_A	1.786	0.96
33_F	45_Q	1.779	0.96
83_F	89_F	1.749	0.95
126_I	151_A	1.686	0.94
39_H	44_L	1.681	0.94
43_D	94_T	1.645	0.93
6_G	39_H	1.619	0.92
7_P	203_E	1.590	0.91
32_M	44_L	1.565	0.90
46_W	50_Q	1.562	0.90
46_W	94_T	1.559	0.90
78_L	157_S	1.540	0.89
53_L	64_I	1.528	0.89
43_D	91_D	1.527	0.89
40_L	83_F	1.504	0.88
43_D	90_A	1.486	0.87
13_L	44_L	1.485	0.87
77_G	91_D	1.443	0.85
77_G	81_L	1.433	0.84
52_L	64_I	1.396	0.82
52_L	60_Y	1.395	0.82
130_E	167_L	1.394	0.82
9_R	32_M	1.390	0.81
2_V	32_M	1.380	0.81
39_H	89_F	1.373	0.80
29_C	44_L	1.373	0.80
108_R	111_E	1.363	0.80
75_L	202_P	1.356	0.79
121_P	125_D	1.352	0.79
49_H	65_Q	1.332	0.77
24_S	207_E	1.332	0.77
5_P	13_L	1.324	0.77
55_T	247_A	1.311	0.76
8_D	71_L	1.302	0.75
185_L	211_R	1.302	0.75
39_H	246_A	1.298	0.75
2_V	9_R	1.290	0.74
137_A	149_L	1.281	0.73
212_R	233_D	1.279	0.73
43_D	87_M	1.246	0.70
48_I	83_F	1.235	0.69
41_W	89_F	1.235	0.69
42_L	94_T	1.221	0.68
185_L	212_R	1.217	0.68
113_P	116_T	1.215	0.68
4_P	45_Q	1.212	0.67
172_A	245_D	1.211	0.67
141_G	144_A	1.211	0.67
71_L	78_L	1.210	0.67
68_L	166_L	1.205	0.67
215_L	219_K	1.198	0.66
169_A	212_R	1.197	0.66
13_L	252_L	1.192	0.65
71_L	235_E	1.186	0.65
56_G	133_A	1.176	0.64
25_L	159_R	1.173	0.64
150_Q	199_Q	1.158	0.62
109_W	112_E	1.157	0.62
6_G	35_R	1.157	0.62
57_K	175_T	1.148	0.61
60_Y	133_A	1.145	0.61
110_A	114_S	1.145	0.61
32_M	169_A	1.144	0.61
234_M	238_L	1.143	0.61
59_N	106_G	1.137	0.60
165_R	177_K	1.137	0.60
15_R	19_Q	1.125	0.59
96_S	203_E	1.125	0.59
40_L	90_A	1.120	0.58
160_S	172_A	1.119	0.58
12_S	71_L	1.117	0.58
133_A	145_A	1.110	0.57
220_S	243_A	1.109	0.57
114_S	198_S	1.104	0.57
2_V	40_L	1.102	0.57
50_Q	78_L	1.102	0.57
56_G	145_A	1.099	0.56
27_E	176_G	1.098	0.56
71_L	109_W	1.094	0.56
92_D	127_L	1.083	0.55
108_R	115_V	1.079	0.54
147_S	192_A	1.078	0.54
13_L	47_Y	1.073	0.53
165_R	183_H	1.073	0.53
229_R	233_D	1.072	0.53
11_A	42_L	1.066	0.53
169_A	185_L	1.062	0.52
33_F	71_L	1.061	0.52
33_F	39_H	1.054	0.52
104_E	107_E	1.052	0.51
131_P	134_L	1.050	0.51
216_L	249_A	1.050	0.51
83_F	221_A	1.047	0.51
161_N	176_G	1.047	0.51
24_S	140_E	1.047	0.51
74_R	202_P	1.046	0.51
42_L	79_E	1.046	0.51
68_L	98_I	1.044	0.50
6_G	45_Q	1.042	0.50
5_P	44_L	1.039	0.50
4_P	84_N	1.036	0.50
208_V	235_E	1.031	0.49
37_A	44_L	1.028	0.49
69_K	104_E	1.025	0.48
223_T	232_P	1.021	0.48
217_R	238_L	1.018	0.48
122_G	174_Q	1.018	0.48
46_W	93_V	1.014	0.47
40_L	70_G	1.014	0.47
151_A	205_V	1.013	0.47
9_R	44_L	1.012	0.47
13_L	241_L	1.011	0.47
94_T	97_W	1.010	0.47
163_L	248_R	1.009	0.47
188_L	192_A	1.008	0.47
122_G	135_Q	1.006	0.46
2_V	31_D	1.001	0.46

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: (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
3mv2B	3	0.7984	89	0.927	Contact Map
3mkrA	1	0.7752	85.8	0.931	Contact Map
4kvmA	4	0.8953	85.4	0.931	Contact Map
3qouA	1	0.6395	85.3	0.931	Contact Map
4uzyA	1	0.7946	84.9	0.932	Contact Map
4f3vA	2	0.9031	83.1	0.933	Contact Map
2r5sA	2	0.6628	82	0.934	Contact Map
4hnyA	2	0.7326	81.2	0.934	Contact Map
2pl2A	2	0.6938	79.1	0.936	Contact Map
1w3bA	2	0.8411	76.6	0.937	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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