OPENSEQ.org - 1389647934 - GREMLIN Submission

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2lao_no_eukarya_141013

ID:	1389647934	Query Sequence ALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGTYDKMAKKYFDFNVYGD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	238 (233)
Sequences:	14078 (10642)
Seq/Len:	60.421
Nf(neff/√len):	697.2

HHblits Results: (2013_03)
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: 60.421).

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
115_G	155_L	3.986	1.00
9_G	64_I	3.757	1.00
5_T	46_T	3.202	1.00
40_R	216_E	3.193	1.00
85_D	215_T	2.589	1.00
7_R	46_T	2.447	1.00
140_Y	149_D	2.421	1.00
75_D	78_Q	2.363	1.00
38_C	45_C	2.323	1.00
73_I	196_G	2.312	1.00
73_I	78_Q	2.303	1.00
222_T	225_K	2.291	1.00
207_K	211_D	2.243	1.00
224_D	228_K	2.237	1.00
5_T	44_K	2.191	1.00
58_S	64_I	2.139	1.00
36_E	222_T	2.074	1.00
123_E	127_N	2.072	1.00
7_R	48_V	2.069	1.00
36_E	39_K	2.067	1.00
142_N	145_L	2.053	1.00
215_T	219_Q	2.050	1.00
160_Q	165_A	2.008	1.00
81_I	198_G	1.989	1.00
21_D	27_I	1.982	1.00
82_A	207_K	1.979	1.00
60_K	80_E	1.960	1.00
123_E	139_A	1.944	1.00
85_D	211_D	1.928	1.00
199_L	207_K	1.910	1.00
113_H	138_V	1.901	1.00
36_E	217_L	1.862	1.00
40_R	213_A	1.852	1.00
84_S	211_D	1.809	1.00
204_T	208_A	1.805	1.00
199_L	210_F	1.792	1.00
36_E	40_R	1.788	1.00
32_D	229_K	1.780	1.00
200_R	203_D	1.775	1.00
40_R	220_D	1.719	1.00
146_I	158_A	1.718	1.00
58_S	63_K	1.686	1.00
68_I	197_V	1.685	1.00
208_A	212_K	1.612	1.00
32_D	230_Y	1.562	1.00
82_A	202_D	1.546	1.00
21_D	25_E	1.546	1.00
113_H	136_D	1.530	1.00
95_I	165_A	1.521	1.00
8_I	34_G	1.518	1.00
112_K	156_D	1.500	1.00
149_D	154_R	1.493	1.00
118_Q	141_A	1.474	1.00
114_V	157_A	1.464	1.00
8_I	66_A	1.463	1.00
35_N	47_W	1.452	1.00
162_E	166_S	1.441	1.00
41_M	213_A	1.440	1.00
209_A	212_K	1.422	1.00
150_L	158_A	1.401	0.99
56_I	81_I	1.386	0.99
50_S	58_S	1.385	0.99
19_S	27_I	1.382	0.99
30_D	87_L	1.380	0.99
105_T	108_S	1.375	0.99
141_A	145_L	1.352	0.99
104_P	108_S	1.347	0.99
37_M	213_A	1.338	0.99
97_A	153_G	1.321	0.99
149_D	155_L	1.306	0.99
113_H	156_D	1.306	0.99
212_K	216_E	1.305	0.99
216_E	220_D	1.302	0.99
55_L	67_I	1.298	0.99
29_F	226_M	1.291	0.99
209_A	213_A	1.270	0.99
94_L	157_A	1.269	0.99
62_K	200_R	1.262	0.99
213_A	217_L	1.251	0.99
31_I	35_N	1.242	0.98
97_A	100_S	1.237	0.98
43_V	209_A	1.237	0.98
213_A	216_E	1.234	0.98
29_F	227_A	1.234	0.98
150_L	155_L	1.229	0.98
4_Q	43_V	1.215	0.98
89_A	194_G	1.213	0.98
99_G	179_A	1.213	0.98
115_G	146_I	1.203	0.98
222_T	226_M	1.191	0.98
66_A	199_L	1.189	0.98
124_A	128_D	1.189	0.98
57_P	60_K	1.170	0.97
218_R	223_Y	1.163	0.97
148_S	152_A	1.160	0.97
84_S	210_F	1.157	0.97
117_L	120_S	1.157	0.97
67_I	71_L	1.154	0.97
98_K	179_A	1.153	0.97
74_T	77_R	1.151	0.97
20_K	49_A	1.150	0.97
82_A	204_T	1.142	0.97
140_Y	146_I	1.142	0.97
125_Y	129_N	1.142	0.97
127_N	139_A	1.141	0.97
103_Q	108_S	1.128	0.97
51_D	54_A	1.121	0.97
8_I	45_C	1.121	0.97
76_K	79_Q	1.119	0.96
91_D	162_E	1.116	0.96
66_A	210_F	1.114	0.96
25_E	35_N	1.111	0.96
115_G	140_Y	1.102	0.96
98_K	177_E	1.101	0.96
33_L	223_Y	1.101	0.96
40_R	217_L	1.100	0.96
40_R	222_T	1.099	0.96
35_N	39_K	1.089	0.96
71_L	198_G	1.086	0.96
32_D	35_N	1.077	0.95
148_S	151_T	1.072	0.95
29_F	231_F	1.064	0.95
34_G	197_V	1.042	0.94
96_A	157_A	1.037	0.94
225_K	228_K	1.034	0.94
34_G	68_I	1.024	0.93
93_R	162_E	1.018	0.93
33_L	217_L	1.009	0.93
85_D	218_R	1.001	0.92

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: (08Feb14)
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
1wdnA	1	0.937	100	0.134	Contact Map
4oenA	2	0.9286	100	0.143	Contact Map
1lstA	1	0.9958	100	0.161	Contact Map
2ylnA	1	0.9538	100	0.191	Contact Map
4g4pA	1	0.9412	100	0.194	Contact Map
3vv5A	2	0.9538	100	0.196	Contact Map
3i6vA	1	0.916	100	0.2	Contact Map
3kzgA	4	0.9328	100	0.205	Contact Map
3k4uA	6	0.9622	100	0.205	Contact Map
2y7iA	2	0.9454	100	0.205	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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