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T0808 19-330 -force run

ID: 1405971945 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 312 (309)
Sequences: 83 (71.7)
Seq/Len: 0.269
Nf(neff/√len): 4.1

Jackhmmer Results: (2014_04_16)
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: 0.269).

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
43_F99_I2.2970.84
197_L240_Q2.0310.72
156_W272_Y1.9990.70
221_L287_F1.8790.63
208_N211_E1.8470.61
202_S237_S1.8430.61
172_S227_V1.8060.58
155_E258_Q1.7560.55
243_L284_I1.7130.52
156_W298_R1.7040.52
259_I296_Y1.7020.52
16_T265_G1.6420.48
157_F299_P1.6330.47
257_M271_A1.5940.45
234_N283_L1.5580.42
230_G234_N1.5450.42
251_N275_A1.5410.41
101_L282_K1.4550.36
202_S209_P1.4100.33
16_T40_S1.4050.33
181_E294_T1.3680.31
272_Y299_P1.3620.31
231_E269_Y1.3550.30
202_S212_I1.3390.29
136_W218_I1.3350.29
49_T121_N1.3210.28
7_V155_E1.3210.28
44_Y114_I1.3170.28
91_I186_M1.3120.28
176_A255_F1.3000.27
147_Y159_N1.2880.27
220_L276_T1.2810.26
40_S100_D1.2710.26
157_F272_Y1.2650.26
26_Q274_Y1.2580.25
229_I297_K1.2550.25
168_E171_H1.2460.25
188_Y296_Y1.2440.25
296_Y299_P1.2330.24
171_H207_Q1.2300.24
29_V300_H1.2250.24
168_E188_Y1.2250.24
7_V39_V1.2210.23
129_V137_G1.2190.23
140_G289_R1.2160.23
171_H174_Y1.2140.23
139_R289_R1.2120.23
25_T63_I1.2110.23
43_F119_A1.2060.23
76_L167_G1.2020.23
131_D134_D1.2000.22
141_P240_Q1.1940.22
186_M196_I1.1870.22
7_V29_V1.1850.22
141_P164_P1.1850.22
243_L308_P1.1790.21
103_G111_F1.1780.21
272_Y298_R1.1710.21
140_G203_P1.1700.21
162_T252_T1.1660.21
202_S206_T1.1600.21
200_V284_I1.1590.21
15_V196_I1.1560.21
64_K71_G1.1550.20
137_G287_F1.1540.20
128_Y297_K1.1520.20
10_S272_Y1.1520.20
34_N42_Y1.1500.20
257_M296_Y1.1490.20
128_Y300_H1.1450.20
104_V170_M1.1380.20
7_V84_V1.1330.20
259_I266_N1.1330.20
186_M214_D1.1300.19
14_Y257_M1.1280.19
137_G202_S1.1270.19
14_Y263_G1.1270.19
40_S98_R1.1260.19
30_T76_L1.1240.19
221_L298_R1.1220.19
129_V163_V1.1170.19
45_L99_I1.1160.19
61_S103_G1.1100.19
175_M240_Q1.1080.19
99_I134_D1.1080.19
14_Y310_Q1.1050.18
166_E252_T1.1050.18
66_S125_K1.1020.18
13_G310_Q1.0970.18
24_I103_G1.0950.18
195_R286_S1.0940.18
89_I134_D1.0940.18
125_K161_I1.0920.18
16_T266_N1.0890.18
203_P289_R1.0890.18
135_Y292_T1.0890.18
193_E305_N1.0890.18
270_T287_F1.0850.18
11_G252_T1.0840.18
117_L288_L1.0830.18
40_S102_Q1.0820.18
209_P237_S1.0820.18
164_P271_A1.0800.17
193_E290_P1.0800.17
108_G269_Y1.0780.17
213_P234_N1.0780.17
156_W299_P1.0750.17
158_Y254_K1.0740.17
184_F194_R1.0740.17
212_I237_S1.0740.17
203_P239_G1.0740.17
12_N139_R1.0720.17
207_Q297_K1.0720.17
188_Y223_Q1.0710.17
14_Y121_N1.0700.17
60_H161_I1.0670.17
141_P197_L1.0660.17
197_L242_Y1.0640.17
142_S160_E1.0620.17
139_R203_P1.0600.17
87_G285_A1.0580.17
166_E188_Y1.0580.17
91_I94_A1.0560.17
266_N288_L1.0560.17
35_P191_P1.0550.17
49_T192_T1.0550.17
20_D39_V1.0540.16
136_W150_P1.0520.16
231_E234_N1.0510.16
186_M284_I1.0500.16
72_F89_I1.0480.16
181_E204_F1.0470.16
204_F237_S1.0460.16
218_I230_G1.0460.16
33_T46_H1.0450.16
155_E260_R1.0450.16
137_G212_I1.0430.16
49_T220_L1.0410.16
218_I231_E1.0400.16
38_I102_Q1.0380.16
27_R110_G1.0370.16
108_G113_E1.0370.16
143_V303_L1.0360.16
45_L196_I1.0360.16
146_G196_I1.0360.16
145_L234_N1.0350.16
209_P234_N1.0350.16
189_N195_R1.0340.16
13_G41_I1.0340.16
270_T294_T1.0290.16
171_H257_M1.0280.16
166_E174_Y1.0260.16
221_L270_T1.0250.15
140_G261_P1.0240.15
101_L204_F1.0210.15
190_S194_R1.0210.15
27_R214_D1.0190.15
141_P303_L1.0190.15
218_I234_N1.0160.15
209_P212_I1.0150.15
14_Y295_W1.0120.15
7_V211_E1.0120.15
175_M290_P1.0120.15
172_S218_I1.0110.15
202_S283_L1.0080.15
28_G194_R1.0070.15
6_V116_Q1.0070.15
9_V151_E1.0050.15
145_L176_A1.0050.15
54_S268_T1.0020.15
145_L184_F1.0020.15
215_D218_I1.0010.15
175_M197_L1.0010.15
26_Q60_H1.0000.15
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: (12Jul14)
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  
2bgoA10.346292.40.957Contact Map
2vzsA20.028886.10.962Contact Map
4kmqA10.365484.60.963Contact Map
2w87A20.394279.70.965Contact Map
2vzpA20.352677.50.966Contact Map
2w47A10.3846570.97Contact Map
2y8kA10.371854.60.971Contact Map
2xwxA20.3878520.971Contact Map
2w3jA10.394248.90.972Contact Map
2wz8A10.368645.20.972Contact 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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