GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0831 -force run

ID: 1403741859 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 419 (419)
Sequences: 67 (58.1)
Seq/Len: 0.160
Nf(neff/√len): 2.8

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: 0.160).

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.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

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.

ij Scaled score Prob
242_C245_C1.9970.54
22_R30_G1.8580.46
49_R90_T1.7560.41
414_L417_L1.7350.39
12_K18_E1.6910.37
70_L103_L1.6870.37
70_L93_D1.6740.36
49_R68_Q1.6640.36
63_K348_N1.6630.36
6_L16_E1.6450.35
230_C242_C1.6360.34
230_C245_C1.6360.34
322_G333_K1.6110.33
244_F350_V1.6060.33
32_A48_Y1.5900.32
71_H354_D1.5770.31
48_Y71_H1.5740.31
18_E33_G1.5560.30
22_R358_M1.5560.30
32_A414_L1.5510.30
65_D362_R1.5450.30
96_L404_L1.5400.29
108_M381_I1.5290.29
224_I305_I1.5270.29
21_H370_E1.5250.29
305_I325_S1.5150.28
412_L416_N1.5120.28
22_R355_E1.5100.28
70_L360_T1.5080.28
261_N326_M1.5000.28
143_W335_E1.4850.27
194_L400_A1.4740.26
65_D355_E1.4640.26
189_G279_G1.4600.26
364_R370_E1.4590.26
22_R65_D1.4570.26
205_Q335_E1.4450.25
21_H58_H1.4330.25
32_A413_Y1.3990.23
13_C21_H1.3860.23
75_N107_Y1.3770.22
167_I224_I1.3750.22
259_F362_R1.3720.22
309_A363_L1.3690.22
29_N354_D1.3640.22
33_G330_E1.3630.22
33_G71_H1.3570.22
13_C70_L1.3390.21
167_I194_L1.3170.20
68_Q370_E1.3160.20
142_W230_C1.3130.20
223_V410_Q1.3010.20
22_R71_H1.3000.19
13_C104_R1.2960.19
6_L31_L1.2890.19
29_N75_N1.2850.19
258_L396_D1.2820.19
70_L410_Q1.2780.19
5_L343_W1.2760.19
5_L416_N1.2740.19
12_K19_E1.2740.19
21_H244_F1.2670.18
70_L104_R1.2650.18
146_V163_V1.2640.18
4_E162_R1.2600.18
259_F358_M1.2570.18
89_P92_R1.2510.18
12_K33_G1.2500.18
104_R360_T1.2500.18
107_Y355_E1.2500.18
104_R301_S1.2490.18
355_E362_R1.2470.18
21_H70_L1.2420.18
29_N259_F1.2400.17
71_H355_E1.2380.17
25_V79_L1.2380.17
149_R225_E1.2370.17
72_A350_V1.2330.17
355_E358_M1.2300.17
70_L370_E1.2280.17
50_E342_Y1.2260.17
22_R362_R1.2240.17
30_G358_M1.2190.17
9_L37_I1.2130.17
186_D396_D1.2070.16
258_L360_T1.2040.16
22_R33_G1.1950.16
33_G381_I1.1950.16
90_T93_D1.1930.16
94_G167_I1.1900.16
97_E303_K1.1760.15
70_L364_R1.1750.15
74_H159_L1.1740.15
31_L102_Q1.1680.15
44_A48_Y1.1650.15
7_T134_R1.1640.15
213_K264_K1.1630.15
76_L96_L1.1630.15
44_A71_H1.1590.15
33_G255_E1.1550.15
165_N170_N1.1520.15
21_H34_I1.1480.15
249_E409_G1.1480.15
13_C62_L1.1470.15
68_Q107_Y1.1450.15
132_L350_V1.1450.15
142_W242_C1.1440.15
142_W245_C1.1440.15
14_G363_L1.1420.14
51_V96_L1.1410.14
206_K303_K1.1380.14
29_N76_L1.1340.14
143_W254_Y1.1330.14
101_K296_S1.1330.14
65_D71_H1.1300.14
122_L322_G1.1280.14
57_E215_L1.1260.14
198_M205_Q1.1230.14
34_I387_E1.1220.14
131_E271_E1.1200.14
30_G355_E1.1190.14
63_K412_L1.1190.14
254_Y363_L1.1180.14
370_E386_V1.1170.14
354_D358_M1.1160.14
18_E63_K1.1150.14
48_Y414_L1.1150.14
292_L350_V1.1140.14
9_L355_E1.1130.14
299_E322_G1.1120.14
34_I58_H1.1110.14
336_Y395_N1.1080.14
52_L362_R1.1040.13
299_E335_E1.0980.13
75_N96_L1.0960.13
92_R180_M1.0950.13
32_A296_S1.0950.13
37_I78_E1.0930.13
194_L254_Y1.0920.13
43_L381_I1.0920.13
227_A352_A1.0890.13
29_N358_M1.0880.13
337_K343_W1.0830.13
29_N413_Y1.0820.13
240_N244_F1.0790.13
212_V345_A1.0750.13
96_L212_V1.0750.13
71_H76_L1.0750.13
59_K91_L1.0740.13
2_M404_L1.0710.13
70_L329_F1.0710.13
14_G33_G1.0710.13
5_L35_H1.0690.13
122_L321_E1.0680.12
244_F339_L1.0660.12
244_F360_T1.0650.12
160_V363_L1.0640.12
156_D163_V1.0640.12
143_W194_L1.0630.12
2_M96_L1.0610.12
159_L415_T1.0610.12
234_P363_L1.0580.12
205_Q305_I1.0580.12
12_K363_L1.0560.12
18_E22_R1.0540.12
36_I360_T1.0510.12
66_S343_W1.0510.12
32_A299_E1.0510.12
33_G379_H1.0510.12
29_N48_Y1.0480.12
143_W159_L1.0470.12
92_R364_R1.0460.12
29_N71_H1.0460.12
27_A104_R1.0440.12
4_E25_V1.0440.12
115_V415_T1.0430.12
299_E333_K1.0420.12
197_Q231_H1.0410.12
32_A71_H1.0400.12
5_L231_H1.0390.12
369_R380_I1.0390.12
227_A410_Q1.0390.12
104_R197_Q1.0350.12
291_G358_M1.0330.12
49_R224_I1.0320.12
150_A185_R1.0310.12
115_V330_E1.0300.12
103_L232_L1.0300.12
143_W205_Q1.0280.12
242_C258_L1.0270.12
245_C258_L1.0270.12
29_N44_A1.0260.11
17_C21_H1.0260.11
270_F274_I1.0240.11
1_T315_D1.0220.11
22_R255_E1.0180.11
76_L355_E1.0160.11
2_M29_N1.0160.11
340_H365_V1.0160.11
74_H199_E1.0160.11
5_L232_L1.0160.11
5_L191_Q1.0160.11
5_L17_C1.0150.11
9_L71_H1.0140.11
233_R345_A1.0140.11
49_R93_D1.0130.11
147_I384_H1.0130.11
6_L30_G1.0130.11
32_A417_L1.0120.11
10_Q299_E1.0090.11
22_R48_Y1.0090.11
76_L107_Y1.0090.11
310_K359_A1.0080.11
142_W205_Q1.0070.11
9_L78_E1.0040.11
21_H103_L1.0030.11
63_K236_R1.0030.11
19_E74_H1.0030.11
143_W242_C1.0030.11
143_W245_C1.0030.11
65_D358_M1.0030.11
20_A76_L1.0020.11
163_V199_E1.0020.11
75_N259_F1.0010.11
202_N318_F1.0010.11
9_L22_R1.0000.11
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)).
NEW Features
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  
4qn1A10.88541000.063Contact Map
3qwpA10.295994.40.955Contact Map
3n71A10.329487.40.962Contact Map
4wuyA10.276886.90.963Contact Map
4yvqC1083.60.964Contact Map
4yvoA10800.966Contact Map
4ui9O10790.966Contact Map
3u3wA20.353276.90.967Contact Map
4gpkA120.298376.50.967Contact Map
4jhrA20.410576.30.967Contact 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 0.0431 seconds.