OPENSEQ.org
Lisa N Kinch

ID: 1517540806 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 487 (481)
Sequences: 2294 (1347.9)
Seq/Len: 4.769
Nf(neff/√len): 61.5

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: 4.769).

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
241_A334_L4.6051.00
182_V206_V4.5911.00
354_Q401_A4.2281.00
296_A323_F3.9201.00
148_I242_Y3.9191.00
459_T462_T3.5791.00
236_I296_A3.5331.00
355_L369_F3.3951.00
359_M369_F3.2831.00
348_D405_R3.2701.00
203_A221_Y3.2061.00
364_V369_F3.1981.00
133_S156_V2.9411.00
213_H227_E2.8431.00
35_V447_Y2.7911.00
302_A305_Q2.7411.00
143_L263_F2.6961.00
101_Y107_H2.6861.00
441_A449_E2.5491.00
204_E221_Y2.5201.00
428_Y456_V2.4881.00
436_Q440_A2.4351.00
57_F61_F2.3811.00
41_A177_L2.3081.00
289_F366_Y2.3001.00
254_M296_A2.2701.00
30_D161_T2.2461.00
226_R322_L2.2381.00
355_L359_M2.1591.00
428_Y464_Q2.1401.00
297_Q324_L2.1231.00
249_M296_A2.1211.00
395_F399_A2.0901.00
187_L256_I2.0781.00
206_V256_I2.0611.00
38_S137_F2.0261.00
234_E330_H2.0211.00
427_L463_E2.0161.00
141_E152_R2.0111.00
95_L115_A2.0051.00
155_C175_L2.0051.00
34_L58_A1.9961.00
374_G422_H1.9871.00
420_R424_V1.9821.00
73_R96_L1.9601.00
75_M186_S1.9291.00
345_Q408_L1.8931.00
22_T120_Y1.8901.00
206_V224_M1.8861.00
203_A310_F1.8711.00
245_C269_L1.8691.00
224_M228_I1.8681.00
330_H333_D1.8671.00
229_V319_A1.8641.00
41_A44_L1.8481.00
184_F232_N1.8291.00
138_L450_V1.8291.00
438_A453_L1.8281.00
138_L430_L1.8271.00
227_E231_R1.8241.00
438_A449_E1.7961.00
233_A237_A1.7951.00
211_Y227_E1.7891.00
58_A61_F1.7871.00
33_Q158_S1.7631.00
236_I249_M1.7561.00
76_V189_Y1.7501.00
242_Y338_R1.7471.00
184_F254_M1.7291.00
222_L319_A1.7130.99
434_L437_N1.6940.99
331_Y335_M1.6850.99
339_L355_L1.6840.99
29_I64_H1.6780.99
142_A146_L1.6650.99
44_L108_W1.6630.99
40_S458_C1.6620.99
441_A446_D1.6400.99
227_E230_E1.6380.99
129_V169_E1.6360.99
179_Q259_I1.6330.99
157_V175_L1.6100.99
207_L221_Y1.6030.99
200_K204_E1.5660.99
238_K334_L1.5560.99
150_S263_F1.5220.99
330_H334_L1.5210.99
386_R396_D1.5100.98
274_E360_Q1.5060.98
236_I323_F1.5020.98
368_L372_R1.4910.98
245_C276_F1.4820.98
303_L306_A1.4740.98
375_D463_E1.4690.98
371_R463_E1.4620.98
237_A334_L1.4530.98
230_E326_L1.4250.97
164_W168_Q1.4230.97
158_S447_Y1.4140.97
207_L224_M1.4110.97
128_A172_A1.4070.97
454_H457_L1.4040.97
335_M366_Y1.4030.97
182_V187_L1.4020.97
225_F229_V1.4000.97
332_L336_R1.3990.97
108_W177_L1.3980.97
62_S157_V1.3980.97
371_R374_G1.3930.97
405_R409_E1.3810.97
230_E330_H1.3770.97
225_F320_I1.3760.97
208_T215_Q1.3570.96
225_F304_A1.3520.96
36_V450_V1.3500.96
449_E470_Y1.3390.96
456_V464_Q1.3260.96
484_S487_S1.3240.96
199_L309_P1.3230.96
226_R319_A1.3200.96
139_A266_F1.3130.95
435_A457_L1.2970.95
16_L20_F1.2920.95
343_V409_E1.2810.94
235_L249_M1.2770.94
75_M109_D1.2670.94
249_M254_M1.2660.94
143_L260_T1.2590.94
76_V120_Y1.2580.94
366_Y370_F1.2560.94
36_V137_F1.2540.94
133_S174_V1.2530.94
96_L109_D1.2480.93
110_L175_L1.2380.93
35_V130_L1.2370.93
220_P223_A1.2360.93
452_R470_Y1.2350.93
335_M352_V1.2330.93
437_N449_E1.2270.93
418_Q422_H1.2220.92
153_A174_V1.2200.92
228_I303_L1.2140.92
78_S189_Y1.2090.92
75_M111_H1.2090.92
148_I238_K1.2070.92
234_E326_L1.2040.92
342_T409_E1.2030.92
38_S41_A1.2020.92
78_S85_Y1.1970.91
288_S291_N1.1960.91
442_A447_Y1.1940.91
336_R344_A1.1930.91
99_E107_H1.1900.91
371_R422_H1.1860.91
43_A49_P1.1860.91
456_V470_Y1.1840.91
291_N294_P1.1840.91
107_H205_H1.1790.91
25_L127_R1.1770.91
139_A143_L1.1740.90
23_S71_E1.1650.90
269_L276_F1.1630.90
76_V88_R1.1620.90
297_Q301_S1.1610.90
203_A224_M1.1580.90
187_L203_A1.1420.89
438_A450_V1.1420.89
417_R420_R1.1410.89
336_R345_Q1.1410.89
61_F155_C1.1400.89
245_C278_C1.1390.89
36_V451_R1.1380.88
190_F198_Q1.1350.88
430_L435_A1.1280.88
94_G111_H1.1260.88
275_H288_S1.1250.88
46_D102_N1.1230.88
37_A57_F1.1220.88
203_A207_L1.1220.88
200_K221_Y1.1200.87
232_N296_A1.1170.87
328_Q349_E1.1100.87
149_P238_K1.1090.87
254_M300_L1.1040.86
211_Y231_R1.1040.86
281_S483_I1.1000.86
459_T464_Q1.0970.86
449_E452_R1.0950.86
215_Q220_P1.0920.86
195_Q198_Q1.0910.85
237_A241_A1.0900.85
35_V158_S1.0880.85
322_L326_L1.0850.85
204_E207_L1.0820.85
151_S259_I1.0800.85
204_E220_P1.0800.85
338_R367_T1.0790.85
220_P224_M1.0770.84
109_D181_H1.0670.84
254_M299_N1.0660.84
393_K397_G1.0640.83
419_T423_A1.0580.83
35_V450_V1.0540.83
222_L311_I1.0530.83
36_V454_H1.0520.83
187_L202_L1.0510.82
162_P168_Q1.0460.82
129_V132_S1.0450.82
134_I442_A1.0380.81
478_G481_L1.0370.81
336_R405_R1.0370.81
127_R161_T1.0340.81
267_A483_I1.0320.81
128_A133_S1.0290.81
464_Q467_M1.0290.81
214_C220_P1.0290.81
199_L306_A1.0260.80
358_L362_S1.0240.80
76_V86_N1.0230.80
111_H175_L1.0230.80
72_P97_L1.0200.80
237_A330_H1.0190.80
240_Q327_Y1.0180.80
88_R189_Y1.0180.80
59_E65_K1.0160.79
275_H290_S1.0070.79
228_I256_I1.0060.78
30_D127_R1.0060.78
273_D360_Q1.0050.78
219_E224_M1.0000.78
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  
2ppqA10.57743.20.981Contact Map
3tm0A10.369632.70.983Contact Map
3c57A20.102717.20.985Contact Map
4ocvA10.624217.20.985Contact Map
4gmuA10.392215.30.985Contact Map
2pywA20.714615.20.985Contact Map
2v1nA10.223811.10.986Contact Map
3atsA10.50729.60.986Contact Map
1ny9A10.18899.40.986Contact Map
2olcA20.527790.987Contact 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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