OPENSEQ.org - 1482457391 - GREMLIN Submission

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FKRP-48-280 -force run

ID:	1482457391	Query Sequence RVTVLVREFEAFDNAVPELVDSFLQQDPAQPVVVAADTLPYPPLALPRIPNVRLALLQPALDRPAAASRPETYVATEFVALVPDGARAEAPGLLERMVEALRAGSARLVAAPVATANPARCLALNVSLREWTARYGAAPAAPRCDALDGDAVVLLRARDLFNLSAPLARPVGTSLFLQTALRGWAVQLLDLTFAAARQPPLATAHARWKAEREGRARRAALLRALGIRLVSWE	Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length:	233 (229)
Sequences:	104 (74.1)
Seq/Len:	0.454
Nf(neff/√len):	4.9

Jackhmmer Results: (2016_04)
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: 0.454).

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 > 50% 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
151_A	176_F	2.206	0.91
209_K	230_V	1.974	0.83
15_A	87_R	1.914	0.80
179_T	186_V	1.778	0.73
6_V	19_L	1.746	0.71
163_L	226_G	1.685	0.67
174_S	180_A	1.660	0.65
2_V	76_T	1.637	0.63
70_P	83_P	1.636	0.63
28_P	51_N	1.591	0.60
85_G	176_F	1.549	0.57
80_A	152_V	1.486	0.52
55_A	73_Y	1.484	0.52
207_R	222_L	1.460	0.50
198_Q	229_L	1.452	0.50
109_V	183_G	1.396	0.46
206_A	215_R	1.393	0.45
153_V	218_R	1.393	0.45
9_F	14_N	1.361	0.43
69_R	160_L	1.358	0.43
135_Y	164_S	1.345	0.42
74_V	133_A	1.337	0.41
47_P	85_G	1.308	0.39
81_L	185_A	1.290	0.38
185_A	198_Q	1.287	0.38
33_V	75_A	1.282	0.37
159_D	184_W	1.281	0.37
111_A	147_L	1.279	0.37
148_D	157_A	1.275	0.37
20_V	179_T	1.273	0.37
7_R	14_N	1.257	0.36
52_V	87_R	1.245	0.35
97_M	118_P	1.238	0.34
80_A	154_L	1.234	0.34
74_V	104_G	1.229	0.34
151_A	222_L	1.219	0.33
42_P	84_D	1.217	0.33
78_F	113_V	1.215	0.33
57_L	149_G	1.213	0.33
97_M	111_A	1.211	0.32
57_L	83_P	1.206	0.32
16_V	70_P	1.205	0.32
127_S	130_E	1.197	0.31
111_A	122_L	1.196	0.31
4_V	20_V	1.191	0.31
12_F	41_Y	1.190	0.31
61_L	85_G	1.186	0.31
16_V	31_P	1.185	0.31
5_L	36_A	1.179	0.30
11_A	86_A	1.177	0.30
9_F	43_P	1.175	0.30
113_V	146_A	1.170	0.30
175_L	179_T	1.164	0.29
19_L	86_A	1.161	0.29
156_R	182_R	1.160	0.29
113_V	199_P	1.158	0.29
10_E	20_V	1.157	0.29
90_A	201_L	1.156	0.29
6_V	160_L	1.154	0.29
14_N	70_P	1.148	0.28
182_R	221_L	1.142	0.28
10_E	41_Y	1.141	0.28
33_V	72_T	1.140	0.28
159_D	176_F	1.137	0.28
86_A	154_L	1.134	0.28
71_E	176_F	1.133	0.28
79_V	163_L	1.132	0.27
95_E	111_A	1.122	0.27
14_N	43_P	1.116	0.26
80_A	94_L	1.112	0.26
40_P	43_P	1.111	0.26
174_S	225_L	1.110	0.26
200_P	207_R	1.107	0.26
33_V	55_A	1.099	0.26
74_V	81_L	1.097	0.25
152_V	199_P	1.097	0.25
54_L	59_P	1.093	0.25
110_A	220_A	1.090	0.25
15_A	19_L	1.085	0.25
23_F	179_T	1.083	0.25
82_V	96_R	1.083	0.25
30_Q	68_S	1.072	0.24
9_F	84_D	1.070	0.24
4_V	26_Q	1.067	0.24
199_P	223_R	1.066	0.24
208_W	226_G	1.065	0.24
177_L	203_T	1.065	0.24
159_D	181_L	1.062	0.23
15_A	25_Q	1.061	0.23
155_L	175_L	1.057	0.23
79_V	209_K	1.054	0.23
127_S	152_V	1.054	0.23
8_E	36_A	1.052	0.23
167_L	171_V	1.052	0.23
211_E	227_I	1.052	0.23
186_V	206_A	1.051	0.23
160_L	178_Q	1.049	0.23
20_V	149_G	1.048	0.23
22_S	97_M	1.047	0.23
34_V	127_S	1.045	0.23
17_P	110_A	1.043	0.22
59_P	74_V	1.042	0.22
173_T	184_W	1.041	0.22
80_A	89_E	1.041	0.22
8_E	205_H	1.038	0.22
7_R	57_L	1.034	0.22
35_A	185_A	1.032	0.22
203_T	228_R	1.032	0.22
112_P	126_V	1.031	0.22
75_A	220_A	1.030	0.22
91_P	132_T	1.028	0.22
86_A	206_A	1.028	0.22
3_T	33_V	1.028	0.22
127_S	154_L	1.027	0.22
147_L	152_V	1.027	0.22
31_P	95_E	1.024	0.21
127_S	179_T	1.023	0.21
20_V	34_V	1.020	0.21
23_F	55_A	1.018	0.21
124_L	181_L	1.018	0.21
66_A	230_V	1.016	0.21
172_G	223_R	1.013	0.21
2_V	16_V	1.012	0.21
16_V	34_V	1.010	0.21
78_F	220_A	1.010	0.21
55_A	123_A	1.009	0.21
175_L	207_R	1.006	0.21
221_L	225_L	1.002	0.20
74_V	167_L	1.001	0.20
37_D	161_F	1.001	0.20

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
5ajoA	1	0.9785	97.9	0.907	Contact Map
2d7iA	1	0.9785	97.8	0.909	Contact Map
3bcvA	2	0.7339	97.7	0.91	Contact Map
1xhbA	1	0.9356	97.7	0.911	Contact Map
2z86A	4	0.9528	97.6	0.912	Contact Map
3l7iA	4	0	97.5	0.914	Contact Map
3ckjA	1	0.9185	97.5	0.914	Contact Map
1qg8A	1	0.867	97.3	0.917	Contact Map
4fixA	2	0.9828	97.1	0.92	Contact Map
3f1yA	2	0.9485	97	0.922	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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