OPENSEQ.org - 1403892752 - GREMLIN Submission

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T0834 -force run

ID:	1403892752	Query Sequence DSLPERIDLFVSLFDYNSATTSYDIRSIQTDFPTRLLTPDSMLPQTSEYPLKDIQLLYKLAQSCTGKLPLSPLITEPLVFTRSLCKGSSLSPRWFARSGLIHPGGGTYAFRYAEKYPAQFANLLPYMHIQERPNAAEGTLLYHLQNMGEDAINALVSGASMFGSGSDLWLRKGDIYYLFNEETWLTNANKAGLSYSLLSADNTCFIQRGNICWDVEDHS	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	219 (219)
Sequences:	61 (52.3)
Seq/Len:	0.279
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: 0.279).

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
37_L	89_S	1.807	0.60
14_F	19_A	1.805	0.60
102_H	210_N	1.640	0.49
185_L	211_I	1.606	0.47
48_E	196_S	1.558	0.43
2_S	73_L	1.537	0.42
32_F	164_S	1.531	0.42
30_T	37_L	1.509	0.40
55_Q	70_L	1.506	0.40
58_Y	123_L	1.504	0.40
136_A	211_I	1.499	0.40
37_L	168_L	1.492	0.39
3_L	6_R	1.392	0.33
2_S	37_L	1.386	0.33
114_E	157_S	1.381	0.32
113_A	118_A	1.378	0.32
160_S	164_S	1.360	0.31
32_F	118_A	1.348	0.31
77_P	104_G	1.345	0.30
13_L	194_S	1.341	0.30
101_I	128_H	1.322	0.29
138_G	175_I	1.322	0.29
58_Y	209_G	1.313	0.29
136_A	168_L	1.311	0.29
7_I	14_F	1.311	0.29
90_L	102_H	1.307	0.28
3_L	111_R	1.303	0.28
9_L	59_K	1.295	0.28
31_D	193_L	1.286	0.27
74_I	116_Y	1.269	0.26
84_L	163_G	1.264	0.26
134_N	146_N	1.262	0.26
39_P	117_P	1.251	0.25
135_A	139_T	1.247	0.25
116_Y	126_Y	1.238	0.25
60_L	174_D	1.237	0.25
122_N	157_S	1.226	0.24
151_A	197_L	1.222	0.24
23_Y	66_G	1.222	0.24
51_L	81_T	1.221	0.24
80_F	184_W	1.216	0.24
13_L	183_T	1.214	0.24
207_Q	218_H	1.211	0.23
5_E	216_E	1.201	0.23
61_A	211_I	1.194	0.23
70_L	191_A	1.192	0.23
215_V	218_H	1.185	0.22
91_S	160_S	1.169	0.22
88_S	167_D	1.159	0.21
91_S	207_Q	1.146	0.21
188_A	211_I	1.144	0.20
51_L	77_P	1.138	0.20
130_Q	149_E	1.134	0.20
14_F	127_M	1.133	0.20
39_P	131_E	1.124	0.20
117_P	132_R	1.119	0.19
31_D	107_T	1.117	0.19
61_A	108_Y	1.115	0.19
4_P	51_L	1.111	0.19
52_K	173_G	1.105	0.19
17_N	59_K	1.095	0.18
51_L	104_G	1.095	0.18
154_A	194_S	1.095	0.18
148_G	175_I	1.094	0.18
168_L	200_A	1.080	0.18
43_L	46_T	1.078	0.18
155_L	184_W	1.077	0.18
30_T	182_E	1.076	0.18
23_Y	213_W	1.073	0.18
110_F	173_G	1.072	0.18
163_G	188_A	1.070	0.17
128_H	141_L	1.069	0.17
151_A	178_L	1.069	0.17
136_A	150_D	1.067	0.17
160_S	188_A	1.064	0.17
188_A	198_L	1.064	0.17
118_A	186_T	1.062	0.17
130_Q	159_A	1.061	0.17
83_S	142_Y	1.060	0.17
41_S	60_L	1.060	0.17
149_E	154_A	1.058	0.17
8_D	14_F	1.056	0.17
107_T	170_L	1.056	0.17
155_L	207_Q	1.056	0.17
23_Y	82_R	1.054	0.17
166_S	189_N	1.054	0.17
84_L	160_S	1.054	0.17
162_F	217_D	1.053	0.17
108_Y	174_D	1.052	0.17
116_Y	178_L	1.051	0.17
98_S	176_Y	1.050	0.17
26_R	29_Q	1.049	0.17
114_E	202_N	1.049	0.17
21_T	91_S	1.049	0.17
124_L	166_S	1.047	0.17
136_A	185_L	1.046	0.17
128_H	131_E	1.038	0.16
59_K	146_N	1.038	0.16
35_R	163_G	1.035	0.16
15_D	119_Q	1.032	0.16
79_V	104_G	1.032	0.16
173_G	177_Y	1.031	0.16
90_L	108_Y	1.026	0.16
74_I	218_H	1.025	0.16
11_V	47_S	1.025	0.16
5_E	184_W	1.023	0.16
30_T	130_Q	1.020	0.16
80_F	155_L	1.020	0.16
72_P	141_L	1.015	0.15
174_D	205_F	1.014	0.15
83_S	195_Y	1.013	0.15
37_L	133_P	1.009	0.15
2_S	32_F	1.007	0.15
196_S	199_S	1.006	0.15
83_S	107_T	1.005	0.15
56_L	87_G	1.004	0.15
9_L	84_L	1.003	0.15
135_A	171_R	1.002	0.15
107_T	214_D	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: (05Jul14)
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
3f0iA	2	0.5023	25.8	0.967	Contact Map
3rdwA	2	0.484	17.1	0.969	Contact Map
1s3cA	1	0.5845	8.9	0.973	Contact Map
3fz4A	1	0.4932	8.6	0.973	Contact Map
3hshA	6	0.2511	6.2	0.975	Contact Map
3n3fA	2	0.242	5.9	0.975	Contact Map
1pbuA	1	0.6438	5.3	0.976	Contact Map
2eboA	3	0.274	5.3	0.976	Contact Map
1vw4b	1	0.589	5.1	0.976	Contact Map
3gkxA	2	0.4977	4.8	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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