OPENSEQ.org - 1433418960 - GREMLIN Submission

May 4, 2021 - We are working on upgrading the webserver, some pages may not work.

HaemAggl

ID:	1433418960	Query Sequence SLNDKIVTISCKADTNLFFYQVAGNVSLFQQTRNYLERWRLIYDSNKAAYKIKSMDIHNTNLVLTWNAPTHNISTQQDSNADNQYWLLLKDIGNNSFIIASYKNPNLVLYADTVARNLKLSTLNNSNYIKFIIEDYIISDLNNFTCKISPILDLNKVVQQVDVTNLNVNLYTWDYGRNQKWTIRYNEEKAAYQFFNTILSNGVLTWIFSNGNTVRVSSSNDQNNDAQYWLINPVSDTDETYTITNLRDTTKALDLYGGQTANGTAIQVFNYHGDDNQKWNIRN	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	283 (267)
Sequences:	485 (412.4)
Seq/Len:	1.816
Nf(neff/√len):	25.2

Jackhmmer Results: (2015_01_07)
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: 1.816).

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
252_A	271_Y	4.895	1.00
203_V	219_S	3.989	1.00
269_F	276_N	2.856	1.00
205_T	217_S	2.840	1.00
213_T	265_A	2.746	1.00
157_V	173_W	2.699	1.00
259_Q	264_T	2.532	1.00
254_D	269_F	2.273	1.00
200_S	216_V	2.090	0.99
229_W	253_L	2.059	0.99
210_N	251_K	1.921	0.98
254_D	276_N	1.795	0.97
196_N	199_L	1.792	0.97
159_Q	178_N	1.729	0.96
214_V	253_L	1.700	0.95
245_N	248_D	1.667	0.95
266_I	279_W	1.607	0.93
205_T	226_A	1.589	0.93
249_T	268_V	1.567	0.92
245_N	268_V	1.514	0.90
229_W	245_N	1.505	0.90
205_T	215_R	1.493	0.89
269_F	274_D	1.491	0.89
205_T	227_Q	1.487	0.89
254_D	277_Q	1.479	0.89
217_S	226_A	1.458	0.88
159_Q	171_Y	1.446	0.87
248_D	268_V	1.432	0.87
193_Q	219_S	1.419	0.86
212_N	268_V	1.401	0.85
181_W	279_W	1.387	0.84
128_Y	131_F	1.336	0.81
251_K	270_N	1.327	0.80
202_G	218_S	1.323	0.80
169_N	178_N	1.323	0.80
192_Y	271_Y	1.310	0.79
192_Y	252_A	1.305	0.79
254_D	278_K	1.300	0.78
242_T	278_K	1.296	0.78
44_D	50_Y	1.287	0.77
267_Q	276_N	1.285	0.77
275_D	278_K	1.254	0.75
254_D	267_Q	1.248	0.74
266_I	269_F	1.245	0.74
256_Y	265_A	1.244	0.74
141_L	149_S	1.238	0.73
255_L	259_Q	1.229	0.73
113_T	123_L	1.228	0.73
46_N	51_K	1.224	0.72
204_L	229_W	1.224	0.72
48_A	51_K	1.190	0.69
114_V	122_T	1.188	0.69
166_L	169_N	1.181	0.68
183_I	196_N	1.171	0.67
194_F	204_L	1.169	0.67
272_H	276_N	1.167	0.67
155_N	158_V	1.165	0.67
248_D	251_K	1.156	0.66
93_G	111_A	1.153	0.66
154_L	170_L	1.144	0.65
114_V	117_N	1.135	0.64
243_I	253_L	1.133	0.64
198_I	243_I	1.123	0.63
32_T	38_R	1.117	0.62
256_Y	267_Q	1.114	0.62
241_Y	252_A	1.108	0.61
214_V	265_A	1.107	0.61
42_I	45_S	1.106	0.61
242_T	271_Y	1.104	0.61
138_I	141_L	1.096	0.60
144_F	149_S	1.095	0.60
90_K	102_Y	1.091	0.59
196_N	216_V	1.079	0.58
43_Y	46_N	1.074	0.57
171_Y	178_N	1.070	0.57
61_N	65_T	1.069	0.57
125_N	129_I	1.068	0.57
143_N	146_C	1.065	0.57
220_N	223_N	1.062	0.56
16_N	19_F	1.060	0.56
196_N	229_W	1.058	0.56
94_N	98_I	1.049	0.55
119_K	124_N	1.045	0.54
191_A	246_L	1.043	0.54
92_I	100_A	1.040	0.54
245_N	252_A	1.033	0.53
140_D	146_C	1.027	0.52
126_S	129_I	1.026	0.52
121_S	128_Y	1.023	0.52
159_Q	169_N	1.021	0.52
200_S	205_T	1.019	0.52
42_I	46_N	1.017	0.51
19_F	24_G	1.014	0.51
145_T	150_P	1.013	0.51
41_L	44_D	1.012	0.51
175_Y	273_G	1.012	0.51
154_L	158_V	1.012	0.51
101_S	111_A	1.011	0.51
76_Q	87_L	1.009	0.50
21_Q	27_S	1.007	0.50
123_L	130_K	1.006	0.50
242_T	252_A	1.004	0.50
29_F	34_N	1.003	0.50

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: (31Jan15)
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
4oujA	2	0.9717	100	0.372	Contact Map
3aj6A	2	0.9753	100	0.392	Contact Map
4jp0A	1	0.4629	100	0.443	Contact Map
3ef2A	4	0.4806	100	0.47	Contact Map
3pg0A	1	0.47	100	0.479	Contact Map
3phzA	2	0.4629	100	0.483	Contact Map
3a21A	2	0.8975	100	0.485	Contact Map
4izxA	1	0.477	100	0.496	Contact Map
3vsfA	6	0.9293	99.9	0.502	Contact Map
3wmvA	2	0.4452	99.9	0.505	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.

Page generated in 1.3054 seconds.