GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0851

ID: 1405019180 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 456 (435)
Sequences: 3345 (2241.4)
Seq/Len: 7.690
Nf(neff/√len): 107.5

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: 7.690).

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
48_P52_A5.3881.00
142_R215_E4.8261.00
371_F411_F4.6271.00
345_D409_R3.8181.00
189_G192_S3.7391.00
163_A196_A3.3151.00
319_I403_A3.2191.00
334_T367_R2.9921.00
17_K40_E2.7901.00
212_P251_D2.7571.00
19_V91_A2.7311.00
336_A399_A2.7131.00
337_V358_V2.6231.00
53_D58_R2.5871.00
334_T369_R2.5481.00
118_E151_S2.5091.00
243_A318_V2.4741.00
213_S216_S2.4571.00
36_G72_D2.4561.00
161_G189_G2.4471.00
55_R81_A2.3331.00
319_I401_C2.2781.00
224_T256_A2.2611.00
32_V70_V2.2391.00
357_V405_L2.2261.00
341_A375_A2.2081.00
336_A395_A2.1791.00
93_V199_F2.1491.00
52_A56_A2.1421.00
226_W234_I2.1361.00
59_C70_V2.1351.00
118_E148_L2.0931.00
146_A162_L2.0871.00
391_S394_E2.0721.00
125_R128_Q2.0541.00
245_L294_R2.0121.00
369_R399_A2.0111.00
94_V128_Q2.0101.00
219_V242_C1.9741.00
130_V149_L1.9481.00
273_V432_G1.9371.00
248_D251_D1.9281.00
114_V118_E1.9141.00
176_A180_T1.8931.00
299_R306_A1.8891.00
45_D51_V1.8741.00
39_A202_S1.8171.00
335_I366_F1.8061.00
212_P220_V1.7971.00
242_C249_V1.7821.00
115_A118_E1.7811.00
320_A364_S1.7791.00
313_R360_A1.7681.00
23_A43_A1.7601.00
230_A304_A1.7481.00
34_L199_F1.7411.00
404_F435_H1.7231.00
49_G52_A1.7201.00
344_N407_G1.7191.00
40_E80_T1.7131.00
129_L163_A1.7101.00
396_V419_L1.6761.00
227_W231_N1.6741.00
193_A211_V1.6641.00
400_G424_D1.6381.00
52_A55_R1.6191.00
292_R302_E1.6171.00
36_G73_L1.6051.00
18_V199_F1.6021.00
244_V296_V1.5771.00
338_L414_L1.5631.00
51_V81_A1.5591.00
297_P302_E1.5541.00
21_A116_A1.5231.00
300_T307_V1.5171.00
420_A427_C1.5060.99
300_T303_T1.4700.99
314_H318_V1.4510.99
262_G268_L1.4470.99
129_L195_A1.4440.99
194_A198_R1.4420.99
393_D418_A1.4210.99
33_T36_G1.4200.99
243_A314_H1.4190.99
322_E430_F1.4100.99
240_R311_M1.4050.99
50_T60_R1.3910.99
360_A363_D1.3900.99
322_E450_A1.3870.99
47_D50_T1.3690.99
259_L262_G1.3660.99
241_Y298_L1.3580.99
193_A197_E1.3560.99
146_A150_E1.3550.99
103_D107_E1.3390.99
216_S247_V1.3300.98
361_L366_F1.3270.98
23_A31_A1.3270.98
240_R314_H1.3200.98
48_P83_T1.3160.98
229_D305_R1.3160.98
316_A357_V1.3150.98
32_V69_A1.3150.98
438_P442_R1.3130.98
216_S252_V1.3120.98
51_V83_T1.3070.98
124_L149_L1.2980.98
155_V158_R1.2960.98
319_I430_F1.2890.98
71_R75_A1.2870.98
86_D89_G1.2840.98
275_V305_R1.2810.98
238_L249_V1.2780.98
230_A300_T1.2780.98
288_W302_E1.2770.98
127_G161_G1.2740.98
114_V144_L1.2720.98
17_K42_V1.2700.98
165_C200_W1.2700.98
194_A210_Q1.2690.98
114_V148_L1.2650.98
223_A238_L1.2610.98
93_V129_L1.2490.97
93_V195_A1.2460.97
358_V362_R1.2440.97
124_L128_Q1.2380.97
19_V87_P1.2320.97
230_A234_I1.2290.97
19_V94_V1.2250.97
54_L81_A1.2150.97
336_A402_L1.2140.97
53_D60_R1.2100.97
369_R389_A1.2080.97
55_R80_T1.2070.97
70_V79_L1.2070.97
33_T178_V1.2010.96
44_V82_S1.2010.96
397_S422_R1.1930.96
441_I444_L1.1930.96
190_P194_A1.1830.96
120_I130_V1.1760.96
18_V34_L1.1740.96
96_V113_L1.1740.96
197_E211_V1.1670.96
70_V74_A1.1650.96
340_A370_I1.1610.96
335_I401_C1.1560.95
118_E122_P1.1560.95
356_G359_A1.1560.95
149_L152_G1.1510.95
131_I199_F1.1460.95
441_I449_F1.1450.95
453_G456_R1.1400.95
298_L301_V1.1370.95
262_G267_N1.1360.95
85_Y122_P1.1360.95
401_C430_F1.1340.95
235_A253_I1.1310.95
42_V82_S1.1310.95
340_A352_T1.1280.95
42_V80_T1.1230.94
42_V91_A1.1220.94
161_G192_S1.1210.94
69_A175_L1.1180.94
82_S87_P1.1170.94
36_G179_R1.1170.94
42_V87_P1.1060.94
261_K267_N1.0990.93
355_R359_A1.0950.93
404_F436_L1.0940.93
407_G433_R1.0900.93
418_A422_R1.0810.93
438_P456_R1.0780.93
89_G125_R1.0760.93
319_I335_I1.0750.92
17_K90_A1.0710.92
92_D128_Q1.0670.92
318_V430_F1.0660.92
415_D418_A1.0650.92
30_L183_V1.0630.92
261_K268_L1.0620.92
73_L78_R1.0590.92
159_D191_R1.0570.92
111_D115_A1.0540.91
31_A43_A1.0510.91
124_L160_F1.0500.91
349_V354_V1.0500.91
340_A349_V1.0490.91
33_T179_R1.0490.91
51_V55_R1.0490.91
251_D254_G1.0450.91
54_L79_L1.0380.91
108_M137_S1.0330.90
231_N269_L1.0330.90
340_A380_I1.0320.90
316_A364_S1.0300.90
260_P267_N1.0280.90
336_A369_R1.0250.90
231_N235_A1.0250.90
80_T86_D1.0240.90
313_R317_A1.0220.90
40_E78_R1.0220.90
30_L178_V1.0200.90
187_G193_A1.0140.89
429_V436_L1.0130.89
338_L402_L1.0120.89
396_V402_L1.0070.89
127_G191_R1.0000.88
173_V176_A1.0000.88
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: (05Jul14)
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  
2y0cA40.94961000.278Contact Map
3g79A20.96491000.301Contact Map
4a7pA20.93421000.309Contact Map
3gg2A40.9321000.31Contact Map
2q3eA120.95181000.312Contact Map
2o3jA30.95181000.313Contact Map
3ojoA20.89911000.322Contact Map
3vtfA10.92761000.33Contact Map
1mv8A40.91451000.358Contact Map
3pidA10.83991000.406Contact 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 0.0384 seconds.