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Lisa N Kinch

ID: 1501792375 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 512 (506)
Sequences: 814 (430.8)
Seq/Len: 1.609
Nf(neff/√len): 19.2

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: 1.609).

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
9_A338_A3.1851.00
105_V110_G3.1601.00
262_I266_F2.6451.00
37_G40_E2.3601.00
446_A450_V2.3161.00
96_F315_G2.3001.00
53_A365_L2.2380.99
198_F202_L2.1890.99
10_V366_L2.1080.99
484_L488_D1.9970.98
438_T441_Q1.9920.98
99_I315_G1.8980.97
480_R483_E1.8880.97
86_E89_V1.8760.97
243_N246_A1.8540.97
53_A364_G1.8270.97
51_L316_V1.7890.96
95_G324_W1.7730.96
95_G318_A1.7510.95
479_F483_E1.7130.95
330_V333_V1.6660.93
318_A324_W1.6110.92
65_F69_L1.5810.91
435_H438_T1.5590.90
145_F172_A1.5570.90
385_P391_G1.5570.90
21_A45_T1.5540.90
106_V110_G1.5400.89
405_Q409_R1.5170.88
185_F214_S1.5120.88
267_A271_P1.4960.87
250_V269_A1.4900.87
6_V363_S1.4860.87
373_L376_L1.4660.86
50_I365_L1.4540.85
421_P435_H1.4510.85
118_S392_I1.4370.84
282_E285_I1.4340.84
433_R483_E1.4310.84
449_W452_K1.4280.84
101_L269_A1.4200.83
430_K483_E1.3960.82
33_R81_E1.3920.82
104_L108_F1.3920.82
283_S291_S1.3880.81
181_G218_M1.3870.81
438_T445_L1.3870.81
449_W453_S1.3820.81
389_L393_F1.3780.81
286_T291_S1.3680.80
278_L282_E1.3670.80
389_L401_L1.3630.80
282_E286_T1.3630.80
133_F139_S1.3590.79
222_D230_T1.3580.79
327_A330_V1.3550.79
96_F100_L1.3490.79
388_V393_F1.3490.79
475_L478_I1.3470.79
49_G57_A1.3440.78
466_L469_P1.3410.78
40_E67_G1.3400.78
328_T332_S1.3400.78
285_I291_S1.3380.78
279_I286_T1.3330.78
501_G504_E1.3300.77
14_Y27_L1.3270.77
385_P393_F1.3210.77
303_F309_L1.3140.76
260_F264_M1.3070.76
79_F83_N1.2960.75
128_L132_I1.2940.75
103_V308_L1.2920.74
183_F186_A1.2910.74
326_S330_V1.2910.74
217_I221_V1.2910.74
410_I442_I1.2900.74
8_A23_T1.2890.74
16_A25_G1.2890.74
312_G316_V1.2870.74
308_L366_L1.2830.74
497_D501_G1.2830.74
222_D232_K1.2800.73
288_L291_S1.2750.73
330_V334_T1.2740.73
299_K306_D1.2730.73
12_F16_A1.2680.72
138_F142_I1.2640.72
133_F136_E1.2630.72
479_F487_L1.2630.72
291_S295_R1.2490.71
30_E34_N1.2440.70
119_R129_I1.2440.70
374_S394_L1.2410.70
441_Q461_P1.2400.70
261_P403_G1.2370.70
68_P389_L1.2370.70
62_V68_P1.2360.70
105_V276_F1.2310.69
412_L425_Y1.2280.69
119_R123_E1.2260.69
433_R480_R1.2190.68
209_F282_E1.2190.68
33_R77_F1.2190.68
322_M357_V1.2190.68
276_F282_E1.2080.67
429_V441_Q1.2030.67
10_V370_L1.2020.67
309_L318_A1.2010.67
185_F218_M1.1990.66
436_L466_L1.1980.66
185_F312_G1.1970.66
53_A56_G1.1910.66
385_P397_G1.1870.65
206_I370_L1.1850.65
51_L54_L1.1820.65
279_I283_S1.1820.65
41_L87_Y1.1810.65
420_H431_T1.1790.64
319_L370_L1.1760.64
55_L184_F1.1750.64
118_S125_F1.1740.64
104_L319_L1.1740.64
263_W279_I1.1660.63
57_A302_G1.1630.63
51_L77_F1.1580.62
76_F90_G1.1540.62
109_E126_S1.1540.62
325_L331_R1.1530.62
194_N200_G1.1520.62
326_S331_R1.1510.62
174_L181_G1.1490.61
282_E291_S1.1480.61
471_R484_L1.1480.61
369_V413_L1.1470.61
385_P396_M1.1440.61
331_R334_T1.1430.61
15_F20_P1.1400.61
497_D500_E1.1400.61
496_F501_G1.1360.60
127_F338_A1.1340.60
479_F484_L1.1340.60
302_G306_D1.1330.60
387_A398_V1.1330.60
359_E363_S1.1320.60
96_F107_A1.1300.60
131_L446_A1.1290.59
130_S400_S1.1270.59
56_G61_L1.1270.59
42_L322_M1.1250.59
7_L48_Q1.1230.59
409_R412_L1.1220.59
384_I389_L1.1210.59
436_L439_G1.1210.59
377_M380_I1.1160.58
288_L303_F1.1160.58
409_R441_Q1.1140.58
55_L63_V1.1100.58
36_M244_S1.1090.57
471_R479_F1.1080.57
42_L48_Q1.1080.57
199_P202_L1.1050.57
309_L314_G1.1040.57
120_Y457_S1.1020.57
366_L439_G1.0990.56
327_A336_A1.0980.56
20_P32_T1.0960.56
466_L486_C1.0960.56
467_T471_R1.0960.56
73_E91_R1.0950.56
87_Y401_L1.0930.56
35_Q243_N1.0910.56
129_I280_F1.0910.56
122_Q137_T1.0900.55
360_Q363_S1.0890.55
272_A279_I1.0880.55
385_P388_V1.0860.55
5_Q13_I1.0830.55
85_L261_P1.0830.55
94_I273_L1.0820.55
254_L270_L1.0800.54
93_W175_S1.0790.54
123_E489_A1.0770.54
197_Y217_I1.0760.54
306_D309_L1.0730.54
440_I478_I1.0730.54
123_E137_T1.0720.54
437_F441_Q1.0720.54
202_L353_Q1.0710.53
361_R370_L1.0680.53
451_V459_A1.0680.53
306_D323_P1.0680.53
87_Y273_L1.0660.53
248_G252_H1.0660.53
284_Q287_T1.0650.53
272_A277_I1.0640.53
500_E510_M1.0620.53
284_Q291_S1.0590.52
299_K323_P1.0590.52
503_D511_P1.0590.52
152_K156_Y1.0550.52
272_A282_E1.0550.52
114_V120_Y1.0540.52
376_L382_S1.0530.52
80_C136_E1.0520.51
303_F306_D1.0520.51
454_T468_V1.0510.51
86_E255_G1.0490.51
78_S108_F1.0490.51
202_L417_P1.0460.51
12_F22_I1.0460.51
111_S304_H1.0460.51
214_S218_M1.0460.51
464_L469_P1.0460.51
57_A68_P1.0450.51
136_E193_K1.0450.51
299_K304_H1.0450.51
303_F450_V1.0440.51
427_K435_H1.0430.51
136_E139_S1.0400.50
233_L381_L1.0360.50
327_A331_R1.0360.50
37_G67_G1.0350.50
307_L332_S1.0320.49
93_W97_W1.0310.49
464_L467_T1.0300.49
272_A278_L1.0280.49
356_E418_K1.0280.49
104_L216_L1.0270.49
250_V253_P1.0270.49
174_L225_I1.0270.49
389_L396_M1.0260.49
70_L73_E1.0260.49
305_L308_L1.0250.49
289_I464_L1.0240.49
437_F460_L1.0240.49
48_Q102_V1.0230.48
14_Y26_G1.0230.48
12_F15_F1.0210.48
215_I233_L1.0210.48
400_S403_G1.0200.48
131_L219_V1.0200.48
214_S377_M1.0190.48
5_Q23_T1.0180.48
283_S286_T1.0180.48
305_L440_I1.0180.48
127_F406_L1.0160.48
308_L341_V1.0120.47
392_I399_T1.0120.47
17_A27_L1.0110.47
183_F187_M1.0110.47
22_I63_V1.0100.47
285_I290_V1.0080.47
74_E219_V1.0050.47
416_P419_Y1.0050.47
420_H423_V1.0050.47
430_K433_R1.0040.46
182_T185_F1.0030.46
324_W327_A1.0030.46
284_Q290_V1.0020.46
286_T290_V1.0020.46
90_G268_S1.0010.46
101_L365_L1.0010.46
67_G132_I1.0000.46
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  
3qe7A10.7383990.929Contact Map
1bh7A10.060598.70.937Contact Map
1bzkA10.060598.50.94Contact Map
1btqA10.039197.40.954Contact Map
1bnxA10.0508970.957Contact Map
1btsA10.04196.90.958Contact Map
2l8sA10.07427.30.986Contact Map
3k3fA10.24860.986Contact Map
2m3eA10.0824.30.987Contact Map
4ezcA30.24613.90.987Contact 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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