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T0819

ID: 1402693020 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 373 (340)
Sequences: 44268 (30478.1)
Seq/Len: 130.200
Nf(neff/√len): 1652.9

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: 130.200).

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
56_R60_G3.8371.00
288_R357_D3.8221.00
330_H365_E3.6891.00
76_A270_A3.5761.00
149_L187_E3.0891.00
292_I360_A2.9551.00
182_A186_P2.8141.00
325_R329_D2.6721.00
53_L57_Q2.6271.00
288_R353_D2.5711.00
267_A270_A2.5361.00
91_G97_L2.5061.00
49_P53_L2.4591.00
145_L180_A2.4361.00
358_L362_A2.3011.00
111_P132_R2.2311.00
283_A287_Q2.2291.00
174_P177_R2.2011.00
292_I295_D2.1981.00
111_P134_V2.1711.00
284_N353_D2.1711.00
240_S245_A2.1561.00
281_K285_S2.1251.00
288_R292_I2.1141.00
110_A158_P2.0981.00
287_Q291_R2.0811.00
76_A266_I2.0111.00
111_P153_G2.0111.00
50_S267_A2.0071.00
52_L56_R1.9841.00
147_G150_A1.9571.00
299_A311_D1.9531.00
111_P156_N1.9531.00
111_P157_A1.9381.00
292_I357_D1.9241.00
38_I359_L1.9181.00
147_G151_A1.9181.00
137_P147_G1.8861.00
75_Q79_R1.8731.00
180_A183_Q1.8561.00
159_L192_V1.8441.00
72_D266_I1.7951.00
149_L184_A1.7841.00
179_V183_Q1.7831.00
175_A179_V1.7821.00
116_L137_P1.7771.00
183_Q187_E1.7701.00
145_L184_A1.7671.00
87_N242_P1.7321.00
291_R295_D1.7101.00
352_P355_E1.7071.00
149_L153_G1.7031.00
50_S271_D1.6971.00
185_L191_L1.6951.00
277_E280_L1.6771.00
185_L189_T1.6741.00
290_G294_A1.6491.00
235_I265_A1.6301.00
325_R330_H1.6271.00
332_I362_A1.6241.00
258_S261_G1.6201.00
106_V131_G1.6091.00
326_L334_I1.5931.00
222_R237_Y1.5811.00
86_A242_P1.5601.00
144_D147_G1.5521.00
292_I361_A1.5411.00
57_Q61_D1.5371.00
358_L361_A1.5331.00
48_A271_D1.5151.00
330_H362_A1.5121.00
149_L180_A1.5111.00
348_I359_L1.5091.00
53_L56_R1.5041.00
101_I219_I1.4981.00
160_V185_L1.4901.00
318_Y321_A1.4881.00
54_A267_A1.4751.00
146_E150_A1.4651.00
325_R366_V1.4651.00
292_I296_S1.4631.00
113_V157_A1.4521.00
72_D270_A1.4491.00
55_I264_A1.4441.00
280_L284_N1.4421.00
292_I364_P1.4401.00
55_I59_A1.4401.00
296_S364_P1.4361.00
76_A79_R1.4231.00
176_E179_V1.4131.00
161_Y192_V1.4111.00
321_A325_R1.4081.00
361_A365_E1.4060.99
310_V348_I1.3940.99
99_G103_R1.3840.99
75_Q85_P1.3780.99
92_E96_G1.3780.99
52_L60_G1.3760.99
160_V189_T1.3720.99
88_I239_L1.3570.99
94_I221_A1.3550.99
267_A271_D1.3520.99
146_E149_L1.3450.99
192_V221_A1.3430.99
152_V184_A1.3430.99
266_I270_A1.3190.99
195_E220_R1.3170.99
290_G308_V1.3150.99
182_A191_L1.3060.99
281_K284_N1.2980.99
146_E180_A1.2960.99
332_I359_L1.2920.99
77_L237_Y1.2920.99
152_V189_T1.2910.99
285_S353_D1.2770.99
116_L135_T1.2720.99
224_F265_A1.2580.99
32_R331_G1.2510.99
353_D357_D1.2490.99
286_R290_G1.2490.99
126_V131_G1.2410.98
101_I192_V1.2400.98
177_R180_A1.2280.98
364_P368_R1.2260.98
359_L362_A1.2110.98
242_P246_Q1.2030.98
81_L239_L1.2000.98
291_R294_A1.1950.98
325_R369_S1.1920.98
52_L59_A1.1840.98
71_H75_Q1.1820.98
164_N198_C1.1790.98
153_G157_A1.1690.97
110_A156_N1.1690.97
330_H369_S1.1620.97
91_G236_G1.1590.97
50_S275_L1.1520.97
285_S356_M1.1410.97
136_V151_A1.1360.97
285_S288_R1.1330.97
289_I292_I1.1290.97
134_V151_A1.1210.97
323_V334_I1.1130.96
196_A223_T1.1130.96
357_D361_A1.1100.96
142_R177_R1.1050.96
188_T217_N1.0990.96
113_V151_A1.0920.96
295_D364_P1.0890.96
176_E180_A1.0890.96
139_A177_R1.0880.96
183_Q186_P1.0880.96
84_S242_P1.0840.96
162_L178_V1.0830.96
294_A300_P1.0810.95
150_A154_R1.0790.95
73_L266_I1.0740.95
280_L283_A1.0740.95
102_V161_Y1.0700.95
184_A189_T1.0690.95
324_D329_D1.0680.95
49_P52_L1.0670.95
326_L363_L1.0580.95
355_E358_L1.0570.95
57_Q60_G1.0540.95
321_A324_D1.0520.95
284_N288_R1.0470.94
98_L192_V1.0430.94
152_V157_A1.0420.94
112_V159_L1.0370.94
323_V336_M1.0360.94
83_T239_L1.0310.94
334_I346_I1.0300.94
153_G156_N1.0270.94
326_L362_A1.0250.93
77_L90_I1.0180.93
112_V126_V1.0120.93
78_A85_P1.0110.93
359_L363_L1.0100.93
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: (07Jun14)
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  
3getA20.95171000.297Contact Map
3ffhA20.93831000.301Contact Map
3ly1A40.93571000.322Contact Map
3hdoA20.92231000.325Contact Map
3eucA20.9331000.328Contact Map
1fg7A10.93031000.332Contact Map
3ftbA40.87671000.334Contact Map
2o1bA10.94641000.335Contact Map
3b46A20.97051000.336Contact Map
1b5pA20.95711000.338Contact 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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