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A-NM-T again

ID: 1504639129 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 507 (461)
Sequences: 38548 (26776.1)
Seq/Len: 83.618
Nf(neff/√len): 1247.1

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: 83.618).

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
173_P190_V4.2711.00
375_L414_G3.4861.00
192_S384_E3.0981.00
128_Q178_Y2.9891.00
356_G378_T2.9361.00
69_F105_L2.9111.00
389_D392_L2.8751.00
84_D132_R2.8641.00
65_V105_L2.8431.00
87_A131_V2.8281.00
85_R111_V2.7541.00
415_R423_E2.7481.00
374_E409_R2.7061.00
80_C108_A2.5101.00
214_R239_A2.4761.00
360_L376_Y2.4521.00
448_L472_G2.3381.00
53_F239_A2.3241.00
124_A185_Q2.2871.00
83_Q172_L2.2651.00
46_N49_R2.2621.00
74_K78_L2.2521.00
50_P58_H2.2251.00
40_V65_V2.1991.00
417_T423_E2.1811.00
256_E260_E2.1721.00
372_T413_L2.1341.00
71_V98_T2.1221.00
449_L457_A2.1181.00
42_Q46_N2.1141.00
361_D365_R2.0561.00
417_T421_E2.0341.00
433_K438_R2.0341.00
317_Q335_I2.0311.00
390_P394_Q2.0101.00
169_N172_L2.0031.00
65_V69_F1.9801.00
213_D264_T1.9771.00
130_N388_G1.9421.00
372_T425_L1.9351.00
103_A108_A1.9281.00
192_S195_A1.9171.00
128_Q389_D1.9031.00
82_A172_L1.8971.00
62_E66_K1.8941.00
48_D62_E1.8941.00
445_E459_V1.8931.00
54_D94_A1.8741.00
99_A135_L1.8461.00
376_Y409_R1.8401.00
83_Q384_E1.8301.00
81_K84_D1.7931.00
449_L456_A1.7921.00
68_A105_L1.7771.00
123_Q127_E1.7421.00
85_R109_V1.7411.00
42_Q45_A1.7301.00
176_I387_A1.7051.00
173_P384_E1.7051.00
205_R353_A1.7031.00
213_D292_R1.7011.00
60_T63_E1.6971.00
53_F58_H1.6811.00
53_F261_H1.6801.00
303_L307_D1.6741.00
241_V263_I1.6611.00
204_N236_V1.6541.00
332_N357_F1.6431.00
33_Y41_K1.6431.00
40_V105_L1.6371.00
80_C84_D1.6291.00
41_K45_A1.6241.00
359_V414_G1.6201.00
392_L395_E1.6161.00
34_C37_E1.6131.00
171_D194_R1.6101.00
178_Y188_G1.6001.00
85_R176_I1.5961.00
67_R98_T1.5921.00
459_V472_G1.5821.00
195_A328_S1.5801.00
378_T407_L1.5771.00
368_P371_V1.5691.00
415_R425_L1.5671.00
87_A113_F1.5511.00
104_L174_A1.5461.00
262_G290_A1.5441.00
126_L131_V1.5341.00
414_G424_F1.5201.00
69_F73_N1.5201.00
128_Q185_Q1.5191.00
391_A395_E1.5141.00
244_N247_R1.5091.00
432_V441_L1.5001.00
91_D137_T1.4981.00
357_F377_I1.4921.00
59_M98_T1.4911.00
455_A477_D1.4911.00
413_L428_E1.4851.00
416_Y422_I1.4751.00
50_P239_A1.4741.00
102_G106_A1.4741.00
54_D57_G1.4671.00
463_S468_Q1.4591.00
271_A299_D1.4581.00
71_V102_G1.4281.00
50_P53_F1.4261.00
87_A126_L1.4221.00
96_Q221_L1.4131.00
369_V416_Y1.4060.99
119_E123_Q1.4060.99
257_L261_H1.4040.99
59_M94_A1.4030.99
214_R241_V1.4030.99
190_V387_A1.4020.99
86_V108_A1.4010.99
171_D192_S1.3970.99
194_R380_H1.3920.99
113_F122_R1.3860.99
129_A178_Y1.3850.99
109_V173_P1.3840.99
383_A397_F1.3840.99
350_L421_E1.3650.99
358_R366_D1.3630.99
76_K106_A1.3620.99
334_H421_E1.3600.99
67_R95_H1.3540.99
111_V129_A1.3500.99
214_R263_I1.3490.99
250_D253_H1.3450.99
460_V473_V1.3400.99
195_A382_L1.3320.99
88_I99_A1.3300.99
43_A65_V1.3290.99
331_S377_I1.3240.99
268_S273_M1.3170.99
358_R376_Y1.3130.99
216_L263_I1.2930.99
400_H405_E1.2910.99
430_N442_G1.2870.99
198_N354_N1.2850.99
253_H256_E1.2830.99
168_A172_L1.2710.99
307_D311_K1.2710.99
190_V384_E1.2710.99
247_R253_H1.2660.99
334_H347_P1.2640.99
361_D367_C1.2640.99
434_I439_I1.2540.99
434_I461_L1.2540.99
375_L424_F1.2500.99
170_P194_R1.2470.99
358_R407_L1.2460.98
190_V385_G1.2400.98
210_N213_D1.2340.98
47_P62_E1.2320.98
243_P257_L1.2280.98
49_R212_E1.2280.98
302_P305_L1.2270.98
351_P357_F1.2260.98
431_Q440_E1.2250.98
461_L468_Q1.2230.98
355_Q381_G1.2220.98
101_L234_L1.2060.98
51_A64_L1.2050.98
86_V103_A1.2030.98
65_V163_P1.2000.98
97_V230_I1.1980.98
89_V122_R1.1980.98
39_I43_A1.1950.98
392_L396_R1.1860.98
127_E185_Q1.1850.98
233_P238_G1.1840.98
241_V257_L1.1830.98
176_I188_G1.1780.98
84_D108_A1.1750.98
80_C86_V1.1710.98
137_T140_I1.1680.97
245_A248_Q1.1650.97
64_L101_L1.1650.97
224_D324_A1.1620.97
213_D265_V1.1620.97
372_T415_R1.1610.97
52_V97_V1.1580.97
447_A450_K1.1510.97
64_L98_T1.1500.97
124_A128_Q1.1460.97
189_V383_A1.1460.97
124_A178_Y1.1440.97
456_A475_E1.1440.97
33_Y37_E1.1380.97
213_D238_G1.1360.97
68_A102_G1.1310.97
347_P423_E1.1270.97
266_W291_L1.1260.97
356_G400_H1.1250.97
59_M64_L1.1230.97
65_V68_A1.1060.96
347_P421_E1.1060.96
67_R70_A1.1050.96
273_M294_A1.1050.96
117_Q125_M1.1040.96
348_Y424_F1.1020.96
74_K77_E1.1010.96
200_I235_S1.1000.96
225_L267_N1.0960.96
66_K70_A1.0930.96
296_L301_I1.0920.96
376_Y407_L1.0910.96
198_N380_H1.0900.96
274_Q305_L1.0890.96
267_N330_W1.0850.96
364_M376_Y1.0820.96
219_A225_L1.0810.95
53_F241_V1.0800.95
177_I325_T1.0780.95
78_L149_Q1.0720.95
265_V293_L1.0690.95
367_C371_V1.0660.95
85_R387_A1.0600.95
72_A105_L1.0560.95
71_V135_L1.0550.95
57_G67_R1.0550.95
38_Q201_A1.0540.95
95_H137_T1.0540.95
175_Y191_I1.0540.95
191_I383_A1.0530.95
150_T154_D1.0510.94
199_T329_I1.0500.94
324_A408_Y1.0470.94
462_D471_L1.0450.94
39_I65_V1.0410.94
357_F375_L1.0410.94
63_E66_K1.0410.94
51_A61_Y1.0410.94
215_V233_P1.0390.94
128_Q388_G1.0370.94
57_G94_A1.0330.94
400_H407_L1.0320.94
357_F414_G1.0320.94
52_V94_A1.0290.94
36_H193_H1.0290.94
121_R443_E1.0280.94
179_T189_V1.0260.94
379_G382_L1.0240.93
120_L124_A1.0240.93
295_L321_L1.0190.93
125_M188_G1.0180.93
293_L319_V1.0140.93
241_V261_H1.0100.93
40_V69_F1.0080.93
398_L409_R1.0070.93
321_L330_W1.0050.93
359_V367_C1.0040.93
376_Y398_L1.0010.92
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  
2vsqA10.97831000.18Contact Map
4dg8A10.92311000.203Contact Map
3l8cA20.93291000.221Contact Map
3tsyA10.79291000.222Contact Map
1amuA20.93691000.226Contact Map
3ni2A10.94671000.226Contact Map
3wvnA20.74561000.228Contact Map
4d4iA101000.229Contact Map
3g7sA20.91321000.235Contact Map
2v7bA20.88761000.237Contact 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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