OPENSEQ.org - 1501766726 - GREMLIN Submission

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laobp

ID:	1501766726	Query Sequence ALPQTVRIGTDTTYAPFSSKDAKGEFIGFDIDLGNEMCKRMQVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLESLKGKHVGVLQGSTQEAYANDNWRTKGVDVVAYANQDLIYSDLTAGRLDAALQDEVAASEGFLKQPAGKEYAFAGPSVKDKKYFGDGTGVGLRKDDTELKAAFDKALTELRQDGTYDKMAKKYFDFNVYGD	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	238 (232)
Sequences:	23810 (15893.4)
Seq/Len:	102.629
Nf(neff/√len):	1043.5

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: 102.629).

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	4.421	1.00
9_G	64_I	3.837	1.00
5_T	46_T	3.318	1.00
40_R	216_E	2.925	1.00
140_Y	149_D	2.664	1.00
73_I	78_Q	2.648	1.00
36_E	222_T	2.406	1.00
7_R	46_T	2.335	1.00
58_S	64_I	2.255	1.00
38_C	45_C	2.238	1.00
85_D	215_T	2.236	1.00
146_I	158_A	2.215	1.00
60_K	80_E	2.211	1.00
32_D	229_K	2.131	1.00
36_E	39_K	2.126	1.00
58_S	63_K	2.114	1.00
207_K	211_D	2.042	1.00
160_Q	165_A	2.039	1.00
142_N	145_L	2.037	1.00
40_R	213_A	2.022	1.00
82_A	207_K	2.016	1.00
21_D	27_I	2.003	1.00
7_R	48_V	1.996	1.00
222_T	225_K	1.972	1.00
224_D	228_K	1.966	1.00
81_I	198_G	1.960	1.00
5_T	44_K	1.944	1.00
85_D	211_D	1.920	1.00
84_S	211_D	1.917	1.00
199_L	207_K	1.882	1.00
149_D	154_R	1.875	1.00
97_A	153_G	1.823	1.00
95_I	165_A	1.822	1.00
75_D	78_Q	1.792	1.00
73_I	196_G	1.791	1.00
215_T	219_Q	1.777	1.00
199_L	210_F	1.759	1.00
123_E	127_N	1.757	1.00
36_E	217_L	1.708	1.00
32_D	230_Y	1.685	1.00
105_T	108_S	1.672	1.00
8_I	34_G	1.659	1.00
123_E	139_A	1.653	1.00
37_M	213_A	1.637	1.00
36_E	40_R	1.635	1.00
50_S	58_S	1.618	1.00
113_H	138_V	1.610	1.00
41_M	213_A	1.599	1.00
93_R	162_E	1.593	1.00
114_V	157_A	1.586	1.00
19_S	27_I	1.577	1.00
213_A	217_L	1.563	1.00
113_H	156_D	1.555	1.00
31_I	35_N	1.537	1.00
8_I	66_A	1.536	1.00
40_R	220_D	1.531	1.00
57_P	61_A	1.523	1.00
112_K	156_D	1.521	1.00
96_A	157_A	1.519	1.00
213_A	216_E	1.512	1.00
200_R	203_D	1.486	1.00
94_L	157_A	1.482	1.00
118_Q	141_A	1.477	1.00
82_A	204_T	1.472	1.00
140_Y	146_I	1.466	1.00
115_G	146_I	1.463	1.00
208_A	212_K	1.453	1.00
148_S	152_A	1.452	1.00
113_H	136_D	1.447	1.00
68_I	197_V	1.437	1.00
149_D	155_L	1.432	1.00
209_A	212_K	1.420	1.00
204_T	208_A	1.401	0.99
55_L	67_I	1.388	0.99
148_S	151_T	1.383	0.99
97_A	100_S	1.376	0.99
150_L	158_A	1.376	0.99
91_D	162_E	1.363	0.99
35_N	47_W	1.357	0.99
89_A	194_G	1.356	0.99
57_P	60_K	1.346	0.99
222_T	226_M	1.311	0.99
209_A	213_A	1.274	0.99
30_D	87_L	1.264	0.99
71_L	198_G	1.257	0.99
21_D	25_E	1.242	0.98
40_R	222_T	1.241	0.98
218_R	223_Y	1.230	0.98
20_K	49_A	1.222	0.98
51_D	54_A	1.212	0.98
83_F	198_G	1.210	0.98
66_A	199_L	1.203	0.98
216_E	220_D	1.202	0.98
162_E	166_S	1.200	0.98
115_G	140_Y	1.173	0.98
212_K	216_E	1.172	0.98
104_P	108_S	1.161	0.97
74_T	77_R	1.159	0.97
118_Q	139_A	1.143	0.97
150_L	178_Y	1.131	0.97
96_A	181_A	1.117	0.96
82_A	202_D	1.115	0.96
146_I	149_D	1.109	0.96
151_T	177_E	1.107	0.96
141_A	145_L	1.102	0.96
116_V	123_E	1.100	0.96
4_Q	43_V	1.100	0.96
34_G	68_I	1.097	0.96
211_D	215_T	1.093	0.96
92_S	122_Q	1.088	0.96
54_A	58_S	1.084	0.96
27_I	32_D	1.083	0.96
29_F	227_A	1.078	0.95
98_K	179_A	1.076	0.95
33_L	223_Y	1.052	0.95
56_I	81_I	1.048	0.94
29_F	226_M	1.042	0.94
145_L	148_S	1.041	0.94
138_V	149_D	1.038	0.94
125_Y	129_N	1.032	0.94
82_A	201_K	1.030	0.94
217_L	222_T	1.024	0.93
98_K	177_E	1.023	0.93
9_G	55_L	1.021	0.93
59_L	81_I	1.012	0.93
35_N	39_K	1.012	0.93
99_G	179_A	1.009	0.93
67_I	71_L	1.003	0.93

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
1lstA	1	0.9958	100	0.032	Contact Map
4powA	2	0.9664	100	0.048	Contact Map
3tqlA	1	0.9412	100	0.056	Contact Map
3i6vA	1	0.916	100	0.057	Contact Map
3k4uA	6	0.9664	100	0.061	Contact Map
4ohnA	1	0.9748	100	0.066	Contact Map
4kqpA	1	0.9538	100	0.068	Contact Map
3kzgA	4	0.9328	100	0.07	Contact Map
4g4pA	1	0.9412	100	0.072	Contact Map
3hv1A	2	0.9748	100	0.074	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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