OPENSEQ.org - 1446022657 - GREMLIN Submission

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sp2_L

ID:	1446022657	Query Sequence MPGRAPLRTVPGALGAWLLGGLWAWTLCGLCSLGAVGAPRPCQAPQQWEGRQVMYQQSSGRNSRALLSYDGLNQRVRVLDERKALIPCKRLFEYILLYKDGVMFQIDQATKQCSKMTLTQLWDPLDIPQNSTFEDQYSIGGPQEQITVQEWSDRKSARSYETWIGIYTVKDCYPVQETFTINYSVILSTRFFDIQLGIKDPSVFTPPSTCQMAQLEKMSEDCSW	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	224 (204)
Sequences:	266 (214.3)
Seq/Len:	1.304
Nf(neff/√len):	15.0

Jackhmmer Results: (2015_08)
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: 1.304).

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
42_C	172_C	2.866	1.00
43_Q	126_D	2.709	1.00
102_V	115_K	2.111	0.98
48_W	194_I	1.830	0.95
25_W	29_G	1.794	0.94
77_R	93_E	1.641	0.90
128_P	131_S	1.536	0.85
140_G	172_C	1.535	0.85
148_V	175_V	1.499	0.83
118_L	175_V	1.499	0.83
127_I	148_V	1.481	0.82
145_Q	171_D	1.467	0.81
126_D	167_Y	1.467	0.81
217_K	220_E	1.406	0.77
24_A	29_G	1.406	0.77
71_G	122_W	1.387	0.76
67_L	78_V	1.385	0.76
106_I	128_P	1.337	0.72
88_C	173_Y	1.330	0.72
65_A	80_D	1.326	0.71
39_P	151_W	1.319	0.71
141_G	201_P	1.314	0.70
42_C	140_G	1.312	0.70
153_D	163_W	1.309	0.70
156_S	179_F	1.303	0.69
93_E	124_P	1.300	0.69
117_T	175_V	1.292	0.68
161_E	183_Y	1.286	0.68
97_L	206_P	1.266	0.66
51_R	193_D	1.263	0.66
36_V	39_P	1.263	0.66
50_G	194_I	1.257	0.65
68_S	79_L	1.256	0.65
56_Q	204_F	1.254	0.65
107_D	110_T	1.229	0.63
161_E	175_V	1.225	0.62
67_L	89_K	1.221	0.62
29_G	64_R	1.215	0.61
118_L	143_Q	1.214	0.61
125_L	167_Y	1.206	0.61
28_C	34_G	1.202	0.60
70_D	204_F	1.200	0.60
49_E	68_S	1.191	0.59
97_L	126_D	1.187	0.59
42_C	45_P	1.187	0.59
137_Y	150_E	1.185	0.59
45_P	69_Y	1.179	0.58
49_E	198_I	1.179	0.58
82_R	90_R	1.178	0.58
63_S	184_S	1.168	0.57
133_F	200_D	1.162	0.56
101_G	104_F	1.156	0.56
205_T	216_E	1.156	0.56
27_L	33_L	1.155	0.56
26_T	109_A	1.145	0.55
45_P	50_G	1.142	0.54
27_L	173_Y	1.135	0.54
93_E	153_D	1.121	0.52
78_V	123_D	1.121	0.52
167_Y	204_F	1.117	0.52
45_P	201_P	1.117	0.52
87_P	130_N	1.115	0.52
102_V	216_E	1.115	0.52
128_P	168_T	1.115	0.52
98_Y	103_M	1.114	0.52
97_L	100_D	1.114	0.52
104_F	131_S	1.113	0.51
131_S	199_K	1.110	0.51
41_P	151_W	1.105	0.51
64_R	204_F	1.102	0.50
128_P	153_D	1.098	0.50
63_S	80_D	1.097	0.50
79_L	193_D	1.097	0.50
56_Q	193_D	1.087	0.49
33_L	143_Q	1.082	0.48
37_G	97_L	1.082	0.48
97_L	124_P	1.081	0.48
72_L	151_W	1.080	0.48
71_G	76_V	1.075	0.48
96_L	103_M	1.074	0.48
39_P	149_Q	1.070	0.47
106_I	151_W	1.068	0.47
68_S	197_G	1.067	0.47
68_S	195_Q	1.066	0.47
47_Q	163_W	1.064	0.47
27_L	32_S	1.060	0.46
50_G	128_P	1.059	0.46
44_A	71_G	1.056	0.46
85_L	101_G	1.054	0.46
71_G	106_I	1.052	0.45
97_L	114_S	1.051	0.45
100_D	145_Q	1.048	0.45
146_I	160_Y	1.048	0.45
31_C	40_R	1.047	0.45
77_R	95_I	1.046	0.45
214_Q	220_E	1.044	0.45
191_F	213_A	1.041	0.44
182_N	200_D	1.039	0.44
147_T	169_V	1.038	0.44
82_R	212_M	1.036	0.44
214_Q	217_K	1.036	0.44
127_I	131_S	1.033	0.44
79_L	182_N	1.033	0.44
49_E	203_V	1.029	0.43
26_T	34_G	1.029	0.43
42_C	69_Y	1.029	0.43
43_Q	129_Q	1.025	0.43
65_A	141_G	1.020	0.42
78_V	98_Y	1.015	0.42
19_L	24_A	1.014	0.42
95_I	106_I	1.011	0.41
73_N	92_F	1.011	0.41
68_S	92_F	1.009	0.41
105_Q	114_S	1.008	0.41
109_A	182_N	1.003	0.41
50_G	98_Y	1.001	0.40
100_D	193_D	1.001	0.40
44_A	124_P	1.000	0.40

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: (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
3bmzA	2	0.7411	78	0.927	Contact Map
4mxtA	1	0.7545	29.4	0.947	Contact Map
1co7I	1	0.183	22.6	0.95	Contact Map
1iwlA	1	0.7232	19.4	0.952	Contact Map
4orrA	1	0.6116	16.9	0.953	Contact Map
2w7qA	2	0.7902	10.4	0.957	Contact Map
2ab9A	1	0.1384	9.9	0.957	Contact Map
3zbiC	14	0.125	8.2	0.959	Contact Map
2oqcA	2	0.4688	4.4	0.964	Contact Map
1agqA	4	0.3125	4.3	0.964	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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