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CSD

ID: 1500295252 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 543 (462)
Sequences: 1932 (1262.4)
Seq/Len: 4.182
Nf(neff/√len): 58.7

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: 4.182).

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
48_C276_G3.8211.00
135_S174_F2.9701.00
109_T172_T2.9611.00
117_I128_L2.7681.00
110_D449_K2.7471.00
369_K421_D2.7451.00
128_L184_F2.6241.00
511_R514_Q2.3391.00
106_D449_K2.1261.00
105_W169_T2.1051.00
110_D172_T2.0351.00
118_S438_P1.9921.00
427_H435_G1.9531.00
94_S157_T1.9491.00
72_L330_L1.8911.00
109_T169_T1.8811.00
256_L260_G1.8601.00
120_S131_W1.8551.00
107_A446_F1.8371.00
117_I184_F1.8321.00
120_S123_T1.7951.00
316_F497_L1.7941.00
103_R106_D1.7650.99
485_M489_M1.7460.99
113_V172_T1.7330.99
515_N519_L1.7300.99
367_F375_V1.7240.99
338_F341_E1.6910.99
516_K520_Q1.6820.99
106_D172_T1.6500.99
307_Y440_F1.6310.99
428_L518_A1.6160.99
97_I101_V1.6020.99
186_S195_A1.5970.99
319_L494_L1.5850.99
335_T480_K1.5720.98
157_T161_L1.5630.98
192_R421_D1.5600.98
113_V116_C1.5540.98
133_I274_I1.5460.98
381_V492_I1.5450.98
362_W365_T1.5420.98
525_E530_G1.5170.98
53_G199_R1.5040.98
179_S441_F1.4960.98
142_A170_M1.4940.98
293_A296_R1.4910.98
172_T449_K1.4760.97
73_D468_Y1.4680.97
387_V489_M1.4560.97
126_G130_P1.4540.97
176_V180_A1.4540.97
268_I272_I1.4530.97
506_P511_R1.4510.97
52_G178_Y1.4500.97
142_A166_L1.4470.97
368_G371_T1.4380.97
96_S100_F1.4370.97
395_I399_A1.4320.97
475_Q479_V1.4130.96
521_A524_D1.4120.96
106_D110_D1.4090.96
512_R516_K1.4040.96
500_L504_M1.4010.96
334_Y468_Y1.3970.96
192_R424_D1.3920.96
120_S130_P1.3900.96
363_F372_A1.3900.96
100_F457_G1.3880.96
427_H523_R1.3870.96
381_V499_L1.3780.96
428_L515_N1.3710.96
71_L103_R1.3670.96
330_L483_L1.3600.95
380_A495_I1.3590.95
520_Q523_R1.3580.95
310_L444_Y1.3580.95
68_Q95_A1.3520.95
144_F260_G1.3440.95
418_M505_Y1.3430.95
295_F302_M1.3410.95
374_Y503_K1.3320.95
382_P407_S1.3260.94
517_K521_A1.3240.94
363_F367_F1.3240.94
517_K520_Q1.3050.94
71_L163_F1.3010.94
458_I462_S1.3000.94
379_S407_S1.2960.94
313_G502_F1.2830.93
369_K417_S1.2780.93
54_A209_L1.2690.93
521_A526_A1.2670.93
299_R303_S1.2610.92
185_I468_Y1.2580.92
73_D334_Y1.2550.92
514_Q517_K1.2520.92
188_E191_E1.2450.92
518_A522_L1.2440.92
315_L455_S1.2380.91
370_K374_Y1.2360.91
305_G506_P1.2320.91
158_Y162_L1.2320.91
417_S421_D1.2300.91
261_V458_I1.2280.91
496_L500_L1.2280.91
48_C486_L1.2170.90
117_I127_R1.2150.90
257_L260_G1.2150.90
485_M493_V1.2130.90
46_K194_S1.2120.90
426_F436_T1.2120.90
113_V173_C1.2080.90
143_Y147_W1.2020.90
352_S402_V1.2010.90
264_C375_V1.2000.90
57_Q203_E1.1990.90
428_L519_L1.1990.90
466_A482_T1.1970.89
126_G279_E1.1960.89
360_W410_A1.1920.89
457_G461_L1.1910.89
462_S482_T1.1890.89
138_L170_M1.1870.89
312_T501_L1.1800.89
478_R481_F1.1750.88
184_F426_F1.1730.88
40_Q191_E1.1720.88
137_P141_I1.1670.88
351_L355_L1.1650.88
512_R515_N1.1630.88
186_S191_E1.1620.88
275_L331_F1.1590.87
145_L159_W1.1590.87
167_F452_S1.1580.87
326_G453_G1.1430.86
144_F263_V1.1420.86
109_T449_K1.1410.86
111_P195_A1.1350.86
295_F301_V1.1340.86
210_G214_Q1.1330.86
518_A521_A1.1270.85
508_D511_R1.1260.85
192_R320_A1.1250.85
264_C267_I1.1230.85
353_A409_A1.1230.85
128_L426_F1.1190.85
69_I333_T1.1160.85
178_Y181_L1.1140.84
416_W441_F1.1120.84
309_K504_M1.1090.84
45_N280_Q1.1060.84
264_C385_I1.1060.84
58_V262_I1.1010.83
280_Q354_T1.1000.83
469_Q475_Q1.0980.83
489_M493_V1.0960.83
356_T409_A1.0930.83
78_D94_S1.0920.83
42_S45_N1.0870.82
316_F494_L1.0860.82
98_I161_L1.0830.82
103_R111_P1.0810.82
141_I145_L1.0800.82
52_G206_G1.0800.82
135_S170_M1.0800.82
514_Q518_A1.0720.81
351_L399_A1.0710.81
511_R515_N1.0700.81
477_E481_F1.0690.81
295_F299_R1.0680.81
331_F363_F1.0670.81
71_L95_A1.0620.80
41_L45_N1.0600.80
352_S409_A1.0600.80
367_F372_A1.0580.80
329_V343_Q1.0570.80
54_A205_L1.0550.80
229_L236_S1.0540.80
117_I180_A1.0500.79
492_I496_L1.0490.79
142_A163_F1.0490.79
330_L360_W1.0470.79
378_S499_L1.0470.79
305_G485_M1.0460.79
198_Y202_V1.0460.79
520_Q524_D1.0460.79
162_L378_S1.0420.78
353_A487_V1.0400.78
129_M133_I1.0390.78
136_T174_F1.0390.78
105_W110_D1.0390.78
47_L272_I1.0350.78
135_S443_F1.0350.78
501_L504_M1.0330.78
66_F210_G1.0320.78
527_S530_G1.0290.77
428_L522_L1.0290.77
317_T498_G1.0290.77
123_T130_P1.0280.77
493_V497_L1.0280.77
140_V291_P1.0240.77
132_I337_G1.0230.77
54_A206_G1.0210.76
267_I270_A1.0200.76
162_L493_V1.0200.76
301_V439_I1.0180.76
403_A478_R1.0170.76
105_W316_F1.0150.76
383_F389_L1.0150.76
141_I458_I1.0120.76
358_P362_W1.0110.75
106_D113_V1.0090.75
130_P279_E1.0080.75
103_R110_D1.0080.75
271_V275_L1.0080.75
374_Y499_L1.0070.75
516_K519_L1.0070.75
481_F485_M1.0060.75
314_F444_Y1.0050.75
182_T420_P1.0040.75
131_W177_P1.0010.74
68_Q460_T1.0000.74
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  
4m64A40.81221000.549Contact Map
3wdoA10.77721000.735Contact Map
1pw4A10.76431000.741Contact Map
2cfqA10.74591000.741Contact Map
4tphA20.71271000.745Contact Map
4u4vA101000.748Contact Map
4j05A20.7331000.753Contact Map
3o7qA10.75511000.757Contact Map
4w6vA101000.763Contact Map
4pypA10.71641000.763Contact 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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