OPENSEQ.org - 1403893667 - GREMLIN Submission

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T0834 -force run

ID:	1403893667	Query Sequence DSLPERIDLFVSLFDYNSATTSYDIRSIQTDFPTRLLTPDSMLPQTSEYPLKDIQLLYKLAQSCTGKLPLSPLITEPLVFTRSLCKGSSLSPRWFARSGLIHPGGGTYAFRYAEKYPAQFANLLPYMHIQERPNAAEGTLLYHLQNMGEDAINALVSGASMFGSGSDLWLRKGDIYYLFNEETWLTNANKAGLSYSLLSADNTCFIQRGNICWDVEDHS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	219 (218)
Sequences:	61 (52.3)
Seq/Len:	0.280
Nf(neff/√len):	3.5

Jackhmmer Results: (2014_04_16)
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: 0.280).

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
48_E	196_S	1.779	0.58
102_H	210_N	1.735	0.55
37_L	89_S	1.679	0.51
58_Y	123_L	1.635	0.49
138_G	175_I	1.630	0.48
32_F	118_A	1.602	0.46
37_L	168_L	1.595	0.46
13_L	191_A	1.583	0.45
55_Q	70_L	1.573	0.45
185_L	211_I	1.537	0.42
136_A	211_I	1.521	0.41
114_E	157_S	1.519	0.41
32_F	164_S	1.518	0.41
101_I	128_H	1.405	0.34
14_F	127_M	1.396	0.33
3_L	111_R	1.389	0.33
90_L	102_H	1.386	0.33
128_H	131_E	1.386	0.33
160_S	164_S	1.361	0.31
134_N	146_N	1.346	0.31
80_F	184_W	1.339	0.30
2_S	37_L	1.338	0.30
58_Y	209_G	1.317	0.29
14_F	19_A	1.307	0.28
25_I	207_Q	1.297	0.28
113_A	118_A	1.296	0.28
30_T	37_L	1.287	0.27
31_D	193_L	1.274	0.27
130_Q	149_E	1.272	0.27
2_S	73_L	1.261	0.26
2_S	56_L	1.259	0.26
84_L	163_G	1.256	0.26
155_L	184_W	1.242	0.25
17_N	62_Q	1.242	0.25
83_S	109_A	1.237	0.25
77_P	104_G	1.235	0.25
90_L	109_A	1.222	0.24
151_A	197_L	1.220	0.24
61_A	211_I	1.215	0.24
74_I	116_Y	1.214	0.24
17_N	59_K	1.214	0.24
39_P	117_P	1.213	0.24
60_L	174_D	1.212	0.24
90_L	108_Y	1.198	0.23
110_F	138_G	1.194	0.23
122_N	157_S	1.194	0.23
91_S	207_Q	1.193	0.23
116_Y	126_Y	1.191	0.23
136_A	185_L	1.185	0.22
11_V	47_S	1.161	0.21
215_V	218_H	1.157	0.21
156_V	168_L	1.154	0.21
133_P	201_D	1.153	0.21
135_A	139_T	1.142	0.20
19_A	127_M	1.136	0.20
29_Q	152_I	1.126	0.20
188_A	211_I	1.125	0.20
114_E	202_N	1.114	0.19
140_L	155_L	1.112	0.19
18_S	54_I	1.112	0.19
110_F	173_G	1.110	0.19
9_L	59_K	1.105	0.19
88_S	167_D	1.103	0.19
28_I	122_N	1.102	0.19
51_L	81_T	1.102	0.19
173_G	177_Y	1.099	0.19
91_S	160_S	1.098	0.19
80_F	155_L	1.096	0.19
188_A	198_L	1.091	0.18
5_E	216_E	1.090	0.18
72_P	123_L	1.090	0.18
61_A	108_Y	1.086	0.18
136_A	166_S	1.085	0.18
98_S	176_Y	1.080	0.18
196_S	199_S	1.076	0.18
166_S	189_N	1.072	0.18
20_T	91_S	1.070	0.18
207_Q	218_H	1.070	0.18
33_P	106_G	1.070	0.18
148_G	175_I	1.068	0.17
56_L	87_G	1.067	0.17
22_S	216_E	1.065	0.17
72_P	141_L	1.063	0.17
2_S	129_I	1.063	0.17
99_G	163_G	1.054	0.17
136_A	168_L	1.054	0.17
72_P	131_E	1.050	0.17
35_R	163_G	1.049	0.17
13_L	194_S	1.045	0.17
20_T	61_A	1.042	0.16
65_T	139_T	1.041	0.16
168_L	184_W	1.038	0.16
51_L	77_P	1.037	0.16
16_Y	166_S	1.036	0.16
174_D	205_F	1.035	0.16
74_I	218_H	1.032	0.16
133_P	198_L	1.032	0.16
177_Y	203_T	1.031	0.16
18_S	61_A	1.030	0.16
140_L	193_L	1.030	0.16
154_A	194_S	1.029	0.16
160_S	188_A	1.029	0.16
12_S	201_D	1.028	0.16
17_N	84_L	1.025	0.16
116_Y	178_L	1.024	0.16
168_L	200_A	1.024	0.16
10_F	123_L	1.021	0.16
31_D	107_T	1.020	0.16
67_K	70_L	1.017	0.16
59_K	146_N	1.016	0.16
83_S	107_T	1.015	0.16
151_A	178_L	1.013	0.15
4_P	51_L	1.010	0.15
156_V	188_A	1.005	0.15
90_L	210_N	1.005	0.15
65_T	207_Q	1.003	0.15
41_S	155_L	1.003	0.15
136_A	150_D	1.001	0.15
67_K	100_L	1.001	0.15
74_I	172_K	1.000	0.15
16_Y	27_S	1.000	0.15

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
4r7qA	1	0.968	100	0.046	Contact Map
2eboA	3	0.274	9.5	0.973	Contact Map
1s3cA	1	0.589	8.3	0.973	Contact Map
3rdwA	2	0.484	7.1	0.974	Contact Map
3hshA	6	0.2557	6.6	0.975	Contact Map
3fz4A	1	0.4932	6.6	0.975	Contact Map
3n3fA	2	0.2466	6.4	0.975	Contact Map
2izyA	8	0.2192	5.2	0.976	Contact Map
3gkxA	2	0.4977	4.9	0.976	Contact Map
4n21A	6	0.3562	4.6	0.976	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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