OPENSEQ.org - 1482007746 - GREMLIN Submission

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VTE6_noSignalPeptide

ID:	1482007746	Query Sequence ASMEGVMTEAMKLIQSASPTWKSAVANNLLIFVLGSPLLVTGLSASGIAAAFLLGTLTWRAYGSAGFLLVAAYFVIGTAATKVKMTQKEAQGVAEKRKGRRGPRSVIGSSAAGCVCAFLSIYQVGGAAFSQLFRLGFVSSFCTKVSDTVSSEIGKAYGKTTYLATTFKIVPRGTEGAMSLEGTLAGLLASFFLASVGCFLGQITPPEAAVCVLASQIANLGESIIGASFQDKEGFKWLNNDVVNVINISLGSIVAILMQQFILQNWVK	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	268 (230)
Sequences:	873 (640.6)
Seq/Len:	3.796
Nf(neff/√len):	42.2

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: 3.796).

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
72_A	196_V	3.005	1.00
80_A	149_V	2.801	1.00
150_S	186_G	2.672	1.00
143_T	251_G	2.630	1.00
76_I	149_V	2.518	1.00
77_G	149_V	2.466	1.00
144_K	248_I	2.317	1.00
84_K	87_Q	2.305	1.00
170_V	174_T	2.271	1.00
191_F	212_V	2.227	1.00
43_L	51_A	2.173	1.00
194_A	211_C	2.151	1.00
76_I	192_F	2.023	1.00
230_Q	240_N	1.997	1.00
143_T	247_N	1.953	1.00
160_T	169_I	1.947	1.00
186_G	219_N	1.912	1.00
72_A	192_F	1.901	1.00
50_A	103_P	1.896	1.00
178_M	183_T	1.709	0.99
136_G	256_I	1.708	0.99
50_A	107_I	1.651	0.99
146_S	190_S	1.635	0.99
163_L	170_V	1.634	0.99
62_Y	66_G	1.596	0.98
183_T	220_L	1.552	0.98
162_Y	169_I	1.488	0.97
149_V	189_A	1.467	0.97
238_L	243_V	1.424	0.96
153_I	185_A	1.421	0.96
51_A	55_G	1.368	0.95
116_C	136_G	1.346	0.94
221_G	250_L	1.340	0.94
138_V	211_C	1.337	0.94
76_I	145_V	1.336	0.94
187_L	216_Q	1.314	0.93
108_G	146_S	1.306	0.93
245_V	249_S	1.266	0.91
113_G	141_F	1.258	0.91
171_P	174_T	1.255	0.91
246_I	250_L	1.249	0.90
85_M	105_S	1.247	0.90
153_I	181_E	1.242	0.90
157_Y	181_E	1.241	0.90
178_M	200_L	1.238	0.90
187_L	213_L	1.235	0.90
111_A	115_V	1.221	0.89
190_S	194_A	1.216	0.89
72_A	76_I	1.214	0.89
145_V	149_V	1.208	0.88
112_A	248_I	1.201	0.88
164_A	227_A	1.193	0.88
108_G	156_A	1.191	0.87
51_A	185_A	1.186	0.87
74_F	111_A	1.185	0.87
190_S	211_C	1.182	0.87
246_I	249_S	1.180	0.87
114_C	141_F	1.172	0.86
158_G	181_E	1.165	0.86
139_S	251_G	1.165	0.86
163_L	174_T	1.165	0.86
187_L	253_I	1.164	0.86
189_A	193_L	1.162	0.86
109_S	241_D	1.155	0.85
110_S	140_S	1.154	0.85
194_A	250_L	1.149	0.85
218_A	222_E	1.147	0.85
238_L	242_V	1.147	0.85
102_G	105_S	1.143	0.84
112_A	245_V	1.141	0.84
77_G	80_A	1.137	0.84
175_E	231_D	1.133	0.84
73_Y	109_S	1.128	0.83
62_Y	223_S	1.127	0.83
96_K	100_R	1.125	0.83
81_T	88_K	1.125	0.83
44_S	164_A	1.121	0.83
247_N	251_G	1.117	0.82
110_S	141_F	1.116	0.82
54_L	114_C	1.110	0.82
53_L	254_V	1.102	0.81
164_A	177_A	1.099	0.81
168_K	221_G	1.098	0.81
165_T	227_A	1.095	0.81
44_S	165_T	1.094	0.81
116_C	252_S	1.090	0.80
150_S	220_L	1.075	0.79
248_I	252_S	1.073	0.79
70_V	141_F	1.072	0.79
81_T	95_E	1.065	0.78
195_S	208_A	1.058	0.77
217_I	220_L	1.057	0.77
210_V	214_A	1.049	0.77
41_T	250_L	1.046	0.76
140_S	144_K	1.043	0.76
179_S	183_T	1.042	0.76
143_T	211_C	1.042	0.76
115_V	119_L	1.036	0.75
45_A	49_A	1.034	0.75
43_L	47_G	1.031	0.75
186_G	220_L	1.028	0.75
225_I	229_F	1.027	0.74
177_A	223_S	1.026	0.74
81_T	108_G	1.025	0.74
104_R	241_D	1.021	0.74
214_A	255_A	1.021	0.74
170_V	177_A	1.021	0.74
55_G	186_G	1.017	0.73
249_S	253_I	1.016	0.73
191_F	208_A	1.016	0.73
139_S	214_A	1.014	0.73
107_I	110_S	1.008	0.72
194_A	207_E	1.007	0.72
81_T	99_G	1.007	0.72
77_G	94_A	1.004	0.72
112_A	252_S	1.004	0.72
45_A	166_T	1.000	0.72
69_L	193_L	1.000	0.72

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

See coupling matrix (for protein design or mutagenesis)
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
3dh4A	4	0.4739	35.5	0.96	Contact Map
2xq2A	1	0.5709	33	0.961	Contact Map
3qnqA	4	0.3694	10.8	0.969	Contact Map
2ks1B	1	0.1642	8	0.971	Contact Map
2jwaA	2	0.1642	7.8	0.971	Contact Map
2gfpA	2	0.8955	6.4	0.972	Contact Map
4w6vA	1	0	5.9	0.972	Contact Map
4q2eA	2	0.8657	5.5	0.973	Contact Map
4px7A	1	0.3358	5.2	0.973	Contact Map
1pw4A	1	0.3731	4.9	0.973	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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