GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
ccr6 40-340

ID: 1515684879 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 301 (285)
Sequences: 27381 (14332.5)
Seq/Len: 96.074
Nf(neff/√len): 849.0

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: 96.074).

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
21_G57_V4.6361.00
48_N133_W3.9651.00
193_F197_F3.4571.00
48_N96_L2.8421.00
99_C132_V2.4291.00
123_P127_I2.4231.00
196_T200_K2.3861.00
52_A92_C2.3221.00
77_A81_L2.2761.00
88_I137_V2.2531.00
105_Y110_Q2.1851.00
190_F194_C2.1611.00
29_V47_L2.1541.00
105_Y197_F2.1321.00
99_C128_I2.1041.00
76_N80_K2.0781.00
79_C158_C2.0601.00
55_L89_N2.0341.00
110_Q113_K2.0241.00
216_V280_I2.0151.00
32_F47_L1.9631.00
92_C136_S1.9541.00
105_Y109_V1.9501.00
44_V129_C1.9321.00
96_L129_C1.9141.00
197_F200_K1.8381.00
26_I30_I1.8191.00
197_F201_T1.8191.00
127_I131_V1.7821.00
21_G271_C1.7821.00
48_N129_C1.7791.00
109_V201_T1.7661.00
84_G88_I1.7441.00
72_W75_S1.7411.00
233_M237_V1.7361.00
200_K204_Q1.7161.00
98_T194_C1.6791.00
35_Y287_Y1.6401.00
105_Y194_C1.6151.00
53_D273_N1.5901.00
45_Y125_S1.5821.00
8_L12_I1.5561.00
47_L51_I1.5401.00
287_Y290_K1.5391.00
22_L54_I1.5251.00
223_V276_L1.4981.00
26_I54_I1.4831.00
126_K130_L1.4711.00
106_I117_L1.4641.00
38_A43_D1.4621.00
228_Q266_A1.4451.00
44_V126_K1.4401.00
128_I132_V1.4391.00
123_P126_K1.4361.00
98_T190_F1.4181.00
33_A47_L1.4141.00
199_V203_V1.4050.99
103_D107_A1.3850.99
201_T204_Q1.3800.99
62_F66_S1.3730.99
92_C133_W1.3680.99
52_A93_G1.3590.99
178_L182_F1.3390.99
75_S78_T1.3360.99
258_T262_T1.3330.99
24_G271_C1.3290.99
53_D93_G1.3270.99
18_C64_A1.3260.99
102_M194_C1.3200.99
119_S124_R1.3080.99
192_I196_T1.3070.99
50_A53_D1.3060.99
254_L258_T1.3040.99
188_L225_L1.3030.99
23_L26_I1.2990.99
107_A111_A1.2980.99
45_Y100_I1.2820.99
141_S145_V1.2670.99
22_L57_V1.2640.99
92_C96_L1.2620.99
113_K117_L1.2590.99
268_L272_L1.2540.99
113_K116_R1.2520.99
257_Y261_V1.2510.99
273_N277_Y1.2360.98
41_M125_S1.2340.98
95_L187_P1.2320.98
122_L126_K1.2280.98
136_S140_S1.2240.98
29_V51_I1.2180.98
229_I233_M1.2030.98
210_R214_I1.1990.98
52_A89_N1.1980.98
30_I291_I1.1860.98
101_S195_Y1.1810.98
65_V74_F1.1780.98
29_V50_A1.1740.98
91_N183_G1.1710.98
97_L191_M1.1700.97
56_F270_C1.1690.97
96_L133_W1.1610.97
195_Y198_I1.1570.97
29_V54_I1.1570.97
84_G144_F1.1570.97
24_G275_V1.1540.97
49_M96_L1.1460.97
119_S123_P1.1420.97
76_N148_Q1.1420.97
106_I110_Q1.1370.97
211_H215_R1.1310.97
199_V214_I1.1310.97
11_P15_S1.1280.97
91_N136_S1.1210.97
32_F38_A1.1210.97
223_V272_L1.1200.96
94_M187_P1.1180.96
20_F23_L1.1160.96
88_I140_S1.1140.96
61_P64_A1.1130.96
127_I130_L1.1120.96
234_V262_T1.1090.96
30_I34_F1.1020.96
49_M53_D1.1010.96
103_D118_R1.0990.96
95_L132_V1.0960.96
77_A80_K1.0930.96
28_V32_F1.0900.96
20_F271_C1.0860.96
284_F288_F1.0800.95
105_Y193_F1.0750.95
98_T191_M1.0710.95
11_P64_A1.0660.95
62_F78_T1.0550.95
102_M106_I1.0540.95
109_V197_F1.0480.94
225_L229_I1.0470.94
95_L135_L1.0460.94
132_V136_S1.0400.94
45_Y99_C1.0380.94
114_S118_R1.0340.94
44_V48_N1.0320.94
107_A112_T1.0290.94
40_S43_D1.0270.94
18_C57_V1.0240.93
35_Y38_A1.0200.93
213_A216_V1.0160.93
218_I222_L1.0100.93
92_C132_V1.0090.93
87_A140_S1.0070.93
237_V241_N1.0050.93
199_V202_L1.0040.93
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)).
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  
4pxzA10.9071000.042Contact Map
3oduA20.97671000.048Contact Map
3vw7A10.90371000.061Contact Map
2rh1A10.92361000.068Contact Map
4iarA10.8871000.069Contact Map
3uonA10.90371000.071Contact Map
4mbsA20.96011000.072Contact Map
4grvA10.92031000.083Contact Map
4dklA10.92691000.088Contact Map
4xnvA10.93691000.089Contact 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 0.0388 seconds.