OPENSEQ.org - 1400522176 - GREMLIN Submission

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

Welcome: casp11@openseq.org

T0783 1-275 -force run

ID:	1400522176	Query Sequence SMHPQAVAAVLPAGGCGERMGVPTPKQFCPILERPLISYTLQALERVCWIKDIVVAVTGENMEVMKSIIQKYQHKRISLVEAGVTRHRSIFNGLKALAEDQINSKLSKPEVVIIHDAVRPFVEEGVLLKVVTAAKEHGAAGAIRPLVSTVVSPSADGCLDYSLERARHRASEMPQAFLFDVIYEAYQQCSDYDLEFGTECLQLALKYCCTKAKLVEGSPDLWKVTYKRDLYAAESIIKERISQEICVVMDTEEDNKHVGHLLEEVLKSELNHVKV	Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length:	275 (249)
Sequences:	204 (89.1)
Seq/Len:	0.819
Nf(neff/√len):	5.6

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: 0.819).

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
84_V	88_R	2.895	1.00
203_L	206_K	2.342	0.98
199_E	202_Q	2.289	0.98
184_E	200_C	2.148	0.96
52_D	75_K	2.129	0.96
80_V	92_N	2.123	0.96
153_P	244_E	2.120	0.96
188_Q	199_E	2.043	0.94
153_P	245_I	2.015	0.94
41_L	69_I	1.989	0.93
153_P	246_C	1.969	0.93
98_A	109_P	1.913	0.91
184_E	203_L	1.856	0.90
232_A	239_E	1.826	0.89
211_K	235_S	1.800	0.88
158_C	211_K	1.761	0.86
247_V	266_L	1.755	0.86
88_R	195_E	1.744	0.85
148_S	151_V	1.735	0.85
133_A	213_K	1.707	0.84
180_D	207_Y	1.637	0.80
159_L	214_L	1.634	0.80
151_V	229_D	1.558	0.75
55_V	77_I	1.526	0.73
177_F	201_L	1.503	0.71
249_M	252_E	1.499	0.71
202_Q	206_K	1.497	0.71
65_M	229_D	1.483	0.70
173_M	256_K	1.459	0.68
186_Y	246_C	1.449	0.67
173_M	243_Q	1.445	0.67
163_L	185_A	1.438	0.67
151_V	173_M	1.427	0.66
63_E	77_I	1.425	0.65
228_R	239_E	1.402	0.64
153_P	186_Y	1.399	0.63
143_I	152_S	1.380	0.62
152_S	214_L	1.374	0.61
112_V	179_F	1.364	0.60
16_C	255_N	1.358	0.60
57_V	112_V	1.351	0.59
111_V	127_L	1.347	0.59
125_G	152_S	1.337	0.58
159_L	215_V	1.315	0.56
141_G	159_L	1.306	0.56
109_P	112_V	1.290	0.54
98_A	179_F	1.286	0.54
150_V	229_D	1.286	0.54
66_K	228_R	1.277	0.53
163_L	189_C	1.261	0.52
72_Y	143_I	1.247	0.50
22_V	246_C	1.247	0.50
200_C	203_L	1.239	0.50
173_M	219_P	1.235	0.49
28_F	67_S	1.234	0.49
98_A	112_V	1.225	0.48
182_I	219_P	1.222	0.48
185_A	246_C	1.213	0.47
81_E	92_N	1.209	0.47
185_A	189_C	1.208	0.47
74_H	77_I	1.206	0.47
53_I	74_H	1.206	0.47
31_I	214_L	1.195	0.46
64_V	67_S	1.194	0.46
95_K	260_H	1.192	0.46
22_V	244_E	1.189	0.45
131_V	170_A	1.186	0.45
115_H	199_E	1.183	0.45
137_H	209_C	1.178	0.44
51_K	234_E	1.175	0.44
208_C	236_I	1.169	0.44
185_A	245_I	1.167	0.43
162_S	246_C	1.164	0.43
31_I	43_A	1.163	0.43
29_C	57_V	1.162	0.43
186_Y	244_E	1.159	0.43
148_S	229_D	1.158	0.43
184_E	242_S	1.157	0.42
29_C	152_S	1.151	0.42
62_M	81_E	1.139	0.41
28_F	151_V	1.139	0.41
130_V	147_V	1.131	0.40
180_D	209_C	1.126	0.40
95_K	109_P	1.124	0.40
186_Y	245_I	1.124	0.40
163_L	246_C	1.116	0.39
128_L	228_R	1.114	0.39
57_V	63_E	1.110	0.38
136_E	140_A	1.105	0.38
148_S	228_R	1.101	0.38
88_R	229_D	1.092	0.37
247_V	260_H	1.087	0.37
24_T	29_C	1.077	0.36
217_G	240_R	1.074	0.36
94_L	186_Y	1.067	0.35
114_I	184_E	1.064	0.35
151_V	243_Q	1.064	0.35
60_E	206_K	1.063	0.35
132_T	264_E	1.059	0.34
156_D	164_E	1.059	0.34
200_C	267_K	1.059	0.34
57_V	143_I	1.059	0.34
16_C	92_N	1.058	0.34
227_K	249_M	1.057	0.34
24_T	200_C	1.055	0.34
72_Y	249_M	1.050	0.34
199_E	243_Q	1.047	0.33
22_V	162_S	1.047	0.33
248_V	266_L	1.041	0.33
43_A	112_V	1.022	0.31
153_P	162_S	1.021	0.31
22_V	245_I	1.021	0.31
62_M	77_I	1.021	0.31
165_R	264_E	1.018	0.31
248_V	263_E	1.015	0.31
188_Q	202_Q	1.012	0.31
180_D	214_L	1.011	0.31
173_M	211_K	1.008	0.30
7_V	29_C	1.006	0.30
145_P	237_I	1.002	0.30

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
4ho4A	2	0.9309	100	0.544	Contact Map
1lvwA	4	0.9309	100	0.546	Contact Map
1iimA	2	0.9091	100	0.549	Contact Map
1mc3A	2	0.9164	100	0.553	Contact Map
4cvhA	1	0.9709	100	0.66	Contact Map
4kt7A	2	0.8109	100	0.714	Contact Map
4zdqA	4	0	100	0.721	Contact Map
4jisA	2	0.7964	100	0.721	Contact Map
2yc3A	1	0.7927	100	0.724	Contact Map
2xwlA	2	0.8036	100	0.726	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 0.634 seconds.