OPENSEQ.org - 1488992188 - GREMLIN Submission

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TssM_Cyto_NTP

ID:	1488992188	Query Sequence VMKKYVQELTYRRRARKEQRLPDDEERLAQTPPRYVTVQDIRHTLRRQYGRFWGRKIRILLITGTASEVELLTPGLTEQFWQEEQGTLLLWGGDPSQPENADWLAALRRLRYRPADGIVWVTSGLSETLSAPLTEDALDRVSRAVSSCCERLGWRLPLYVWSLQESPDERGRITQPVGCLLPAECSS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	187 (159)
Sequences:	263 (185)
Seq/Len:	1.654
Nf(neff/√len):	14.7

HHblits Results: (2016_02)
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: 1.654).

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
172_R	175_Q	2.231	0.99
70_E	77_T	2.034	0.99
59_I	161_W	1.998	0.98
83_E	161_W	1.890	0.97
169_E	172_R	1.848	0.97
114_P	156_L	1.743	0.95
158_L	181_L	1.636	0.93
50_G	53_W	1.633	0.93
38_V	41_I	1.596	0.92
91_W	179_C	1.546	0.90
174_T	179_C	1.439	0.85
70_E	75_G	1.422	0.84
58_R	87_T	1.403	0.83
85_Q	156_L	1.380	0.82
72_L	122_T	1.339	0.79
87_T	171_G	1.315	0.77
149_C	156_L	1.310	0.77
71_L	121_V	1.292	0.75
30_Q	33_P	1.280	0.74
96_S	167_P	1.267	0.73
57_I	161_W	1.261	0.73
169_E	177_V	1.244	0.71
80_F	103_W	1.240	0.71
93_G	169_E	1.233	0.70
57_I	88_L	1.233	0.70
49_Y	57_I	1.231	0.70
58_R	119_V	1.225	0.70
139_D	187_S	1.219	0.69
42_R	62_I	1.217	0.69
33_P	38_V	1.216	0.69
81_W	93_G	1.212	0.68
154_W	164_Q	1.209	0.68
118_I	187_S	1.209	0.68
148_C	153_G	1.203	0.68
143_R	160_V	1.195	0.67
31_T	55_R	1.192	0.67
41_I	88_L	1.184	0.66
90_L	181_L	1.184	0.66
41_I	58_R	1.169	0.64
106_A	114_P	1.160	0.63
160_V	174_T	1.155	0.63
119_V	183_A	1.153	0.63
48_Q	147_S	1.139	0.61
120_W	141_V	1.137	0.61
159_Y	181_L	1.136	0.61
72_L	138_L	1.126	0.60
119_V	134_T	1.123	0.60
29_A	33_P	1.117	0.59
32_P	40_D	1.115	0.59
65_T	72_L	1.113	0.59
122_T	141_V	1.112	0.59
31_T	38_V	1.110	0.58
59_I	83_E	1.104	0.58
52_F	184_E	1.101	0.57
97_Q	131_A	1.101	0.57
72_L	163_L	1.095	0.57
83_E	117_G	1.094	0.57
122_T	126_S	1.094	0.57
149_C	155_R	1.090	0.56
84_E	110_L	1.087	0.56
101_A	105_A	1.085	0.56
109_R	150_E	1.081	0.55
61_L	113_R	1.076	0.55
30_Q	102_D	1.066	0.54
119_V	178_G	1.058	0.53
41_I	67_S	1.048	0.52
108_R	187_S	1.047	0.52
61_L	165_E	1.045	0.52
35_Y	38_V	1.045	0.52
118_I	156_L	1.043	0.51
91_W	120_W	1.041	0.51
117_G	161_W	1.036	0.51
59_I	162_S	1.032	0.50
59_I	88_L	1.027	0.50
39_Q	52_F	1.027	0.50
99_E	149_C	1.026	0.50
121_V	135_E	1.025	0.49
51_R	181_L	1.024	0.49
90_L	160_V	1.021	0.49
79_Q	82_Q	1.017	0.49
90_L	156_L	1.016	0.48
120_W	154_W	1.010	0.48
29_A	35_Y	1.009	0.48
30_Q	39_Q	1.006	0.47
61_L	91_W	1.005	0.47

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: (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
3en0A	3	0.5027	20.3	0.953	Contact Map
2lr1B	1	0.1123	9.4	0.96	Contact Map
3qp9A	4	0.7273	3.8	0.966	Contact Map
2pcqA	1	0.7433	3.8	0.966	Contact Map
2l60A	1	0.1925	3.8	0.966	Contact Map
3fhtA	2	0.9091	3.3	0.967	Contact Map
3fmpB	2	0.0802	3.3	0.967	Contact Map
1qbfA	1	0.1711	2.8	0.969	Contact Map
3qzeA	4	0.8235	2.7	0.969	Contact Map
4h33A	1	0.0642	2.7	0.969	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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