GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
dpbp

ID: 1501847237 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 507 (495)
Sequences: 14685 (9424.2)
Seq/Len: 29.667
Nf(neff/√len): 423.6

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: 29.667).

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
188_Q199_K4.5371.00
130_V136_Q4.1531.00
131_D134_T4.0121.00
330_K333_A3.9811.00
128_K136_Q3.9261.00
292_D296_K3.8101.00
280_K337_E3.7501.00
91_V95_D3.4711.00
69_K133_N3.4311.00
441_D445_P3.4251.00
186_Q199_K3.2861.00
91_V129_K3.2241.00
333_A337_E2.9761.00
290_N293_A2.9601.00
449_T454_K2.8461.00
62_T136_Q2.8401.00
85_L182_T2.8371.00
287_Y330_K2.8091.00
280_K283_Q2.7731.00
53_K66_H2.7271.00
438_P441_D2.6941.00
285_L372_W2.6891.00
62_T138_V2.6751.00
445_P458_L2.6281.00
37_V54_W2.6041.00
57_S61_K2.5611.00
280_K334_L2.5511.00
128_K138_V2.5091.00
56_V63_Y2.4871.00
88_D129_K2.4741.00
88_D160_K2.4721.00
77_K161_E2.4671.00
454_K457_E2.4391.00
197_R213_T2.4341.00
279_V283_Q2.4211.00
66_H134_T2.4061.00
347_D380_K2.3991.00
451_D454_K2.3921.00
160_K164_D2.3761.00
71_V85_L2.3751.00
64_T136_Q2.3511.00
436_Y465_V2.3431.00
434_W469_Q2.3411.00
72_K203_G2.3361.00
186_Q202_D2.3291.00
55_E66_H2.3041.00
2_T213_T2.3021.00
274_K277_D2.2991.00
72_K78_E2.2671.00
74_H201_F2.2631.00
345_S378_Q2.2241.00
94_F137_F2.1841.00
422_C435_C2.1771.00
269_Y473_L2.1691.00
457_E461_Q2.1411.00
185_F211_I2.0871.00
442_L461_Q2.0821.00
422_C440_E2.0561.00
228_K233_E2.0471.00
373_A378_Q2.0291.00
75_D159_S2.0151.00
458_L461_Q2.0091.00
289_V368_I2.0081.00
438_P461_Q2.0001.00
283_Q330_K1.9941.00
327_D330_K1.9901.00
90_V135_V1.9891.00
88_D91_V1.9781.00
4_V215_V1.9751.00
6_C234_C1.9581.00
15_N96_R1.9471.00
52_E66_H1.9361.00
442_L458_L1.9191.00
439_F462_A1.9001.00
436_Y469_Q1.8901.00
332_K336_K1.8871.00
189_Q197_R1.8801.00
77_K159_S1.8661.00
438_P465_V1.8621.00
2_T215_V1.8621.00
288_A375_V1.8581.00
34_N49_G1.8531.00
87_A129_K1.8321.00
88_D132_D1.8301.00
269_Y400_T1.8231.00
125_S140_T1.8231.00
199_K213_T1.8191.00
273_K399_Q1.8181.00
37_V65_F1.8111.00
197_R215_V1.8081.00
57_S62_T1.7981.00
64_T134_T1.7981.00
219_T228_K1.7971.00
89_D160_K1.7911.00
435_C440_E1.7891.00
200_A212_D1.7871.00
195_R215_V1.7831.00
40_K47_I1.7651.00
369_Q373_A1.7621.00
446_A459_Y1.7471.00
86_N89_D1.7461.00
191_Q194_S1.7391.00
306_A477_H1.7311.00
385_E388_E1.7221.00
464_V468_D1.7121.00
52_E69_K1.7111.00
71_V182_T1.7101.00
392_R397_E1.6981.00
281_V338_A1.6951.00
54_W65_F1.6731.00
126_E138_V1.6591.00
188_Q213_T1.6251.00
40_K45_E1.6171.00
446_A458_L1.6161.00
347_D382_V1.5971.00
75_D161_E1.5871.00
461_Q464_V1.5581.00
456_V460_K1.5541.00
70_G78_E1.5521.00
437_K441_D1.5511.00
130_V134_T1.5421.00
159_S162_Y1.5371.00
334_L337_E1.5361.00
292_D305_S1.5301.00
362_R366_E1.5281.00
66_H133_N1.5261.00
279_V468_D1.5241.00
198_Y216_F1.5071.00
279_V469_Q1.5071.00
57_S64_T1.5051.00
191_Q195_R1.4981.00
454_K458_L1.4881.00
189_Q195_R1.4841.00
68_R71_V1.4771.00
52_E68_R1.4731.00
276_L346_I1.4541.00
457_E460_K1.4541.00
441_D444_Q1.4471.00
86_N132_D1.4411.00
465_V469_Q1.4391.00
281_V335_L1.4351.00
329_E332_K1.4291.00
286_T470_A1.4271.00
74_H186_Q1.4211.00
336_K341_E1.4201.00
442_L465_V1.4161.00
371_D374_K1.4020.99
34_N182_T1.3850.99
276_L285_L1.3780.99
367_M371_D1.3750.99
328_P332_K1.3740.99
438_P442_L1.3740.99
65_F137_F1.3620.99
78_E133_N1.3610.99
288_A372_W1.3610.99
295_I305_S1.3580.99
50_L90_V1.3570.99
230_Q247_R1.3540.99
283_Q470_A1.3540.99
50_L182_T1.3450.99
445_P454_K1.3360.99
442_L445_P1.3180.99
283_Q334_L1.2900.99
162_Y180_I1.2850.99
52_E133_N1.2850.99
34_N205_W1.2730.99
72_K201_F1.2720.99
95_D99_N1.2700.99
285_L377_V1.2650.99
91_V127_V1.2580.99
195_R217_S1.2570.99
129_K132_D1.2460.98
396_G433_K1.2430.98
50_L71_V1.2410.98
386_W390_L1.2390.98
445_P461_Q1.2380.98
293_A371_D1.2360.98
295_I303_G1.2340.98
421_S444_Q1.2330.98
40_K43_T1.2270.98
449_T458_L1.2230.98
186_Q201_F1.2230.98
92_F160_K1.2190.98
21_S25_Y1.2100.98
228_K234_C1.2100.98
188_Q197_R1.2090.98
3_L488_V1.2050.98
382_V392_R1.1930.98
74_H203_G1.1900.98
90_V157_I1.1900.98
55_E64_T1.1820.98
74_H180_I1.1800.98
370_A373_A1.1800.98
372_W379_A1.1720.98
445_P449_T1.1680.97
74_H181_G1.1680.97
286_T473_L1.1650.97
299_Y303_G1.1650.97
330_K334_L1.1630.97
369_Q379_A1.1600.97
125_S138_V1.1570.97
296_K301_G1.1570.97
333_A336_K1.1530.97
293_A297_A1.1520.97
329_E333_A1.1480.97
87_A130_V1.1450.97
141_R448_A1.1420.97
370_A374_K1.1400.97
312_P477_H1.1310.97
116_E138_V1.1290.97
411_D455_R1.1270.97
34_N204_Y1.1210.97
369_Q381_I1.1200.96
349_W382_V1.1190.96
127_V135_V1.1180.96
442_L462_A1.1140.96
421_S435_C1.1110.96
93_S157_I1.1100.96
294_I364_M1.1010.96
224_V228_K1.1000.96
246_A249_K1.0990.96
453_N456_V1.0960.96
4_V217_S1.0840.96
68_R205_W1.0830.96
3_L236_V1.0830.96
453_N457_E1.0820.96
51_A65_F1.0810.95
280_K338_A1.0800.95
368_I372_W1.0790.95
465_V468_D1.0770.95
87_A135_V1.0690.95
66_H69_K1.0690.95
258_E479_T1.0660.95
255_N486_K1.0560.95
328_P375_V1.0500.94
66_H131_D1.0490.94
227_A230_Q1.0480.94
57_S60_G1.0460.94
365_A381_I1.0450.94
91_V135_V1.0390.94
235_Q485_R1.0330.94
63_Y139_L1.0320.94
28_S198_Y1.0320.94
446_A462_A1.0300.94
85_L157_I1.0260.94
299_Y476_A1.0240.93
269_Y285_L1.0240.93
289_V294_I1.0240.93
38_E47_I1.0230.93
284_A335_L1.0190.93
64_T130_V1.0180.93
78_E86_N1.0140.93
88_D92_F1.0040.93
347_D378_Q1.0030.93
200_A209_P1.0020.92
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  
1dpeA10.98621000.064Contact Map
3m8uA10.98421000.065Contact Map
4qflA20.98621000.067Contact Map
3tpaA10.98421000.071Contact Map
3zs6A10.95861000.095Contact Map
1uqwA20.94081000.097Contact Map
4tozA201000.099Contact Map
1xocA10.94871000.105Contact Map
1jetA10.95861000.111Contact Map
4gl8A20.95461000.115Contact 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 0.0364 seconds.