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OPENSEQ.org

stt3a -force run

ID: 1491570148 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 705 (687)
Sequences: 485 (254.4)
Seq/Len: 0.706
Nf(neff/√len): 9.7

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: 0.706).

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
360_Y400_S2.9001.00
54_Y58_R2.4860.98
52_F55_R2.4460.98
667_E671_K2.4060.98
111_D114_N2.3510.97
51_Y534_A2.2030.96
542_V555_V2.1280.94
630_G634_L2.1000.94
96_S166_Y2.0630.93
160_R164_G2.0470.93
630_G670_N2.0150.92
206_V257_V2.0000.92
44_V488_I1.9500.90
679_E693_K1.9470.90
132_Y136_K1.9310.90
503_D506_R1.8860.88
612_I617_Y1.8760.88
82_R87_T1.8720.88
133_H181_Y1.8370.86
176_M215_L1.8310.86
680_E690_R1.7720.83
232_F236_I1.7110.80
642_M675_L1.7040.80
236_I277_C1.6910.79
533_T540_I1.6890.79
218_L395_T1.6880.79
624_F634_L1.6670.78
45_I48_F1.6590.77
95_T204_Y1.6520.77
624_F630_G1.6480.77
183_W222_H1.6190.75
76_A533_T1.6130.75
683_T687_W1.6120.75
516_T538_R1.6100.74
237_Y278_Q1.5940.73
135_T143_A1.5940.73
679_E695_K1.5820.73
186_A198_C1.5770.72
546_T552_I1.5760.72
592_D595_K1.5600.71
99_I103_L1.5220.68
348_S352_H1.5050.67
248_T275_G1.5010.67
216_I243_V1.4960.66
88_I264_S1.4810.65
595_K602_I1.4790.65
668_I673_F1.4770.65
683_T690_R1.4670.64
84_I533_T1.4650.64
183_W261_P1.4640.64
84_I88_I1.4550.63
275_G279_I1.4450.63
631_S646_R1.4330.62
52_F56_T1.4280.61
61_A97_A1.4280.61
53_N56_T1.4240.61
668_I671_K1.4220.61
698_D702_L1.4150.60
373_V421_G1.4110.60
333_L406_L1.4110.60
693_K697_L1.4100.60
350_S535_M1.4030.59
144_G148_A1.4000.59
325_P331_Y1.3950.58
77_W82_R1.3890.58
509_Y531_Q1.3850.58
59_F63_E1.3770.57
559_M599_M1.3730.57
661_D664_R1.3700.56
74_D536_A1.3680.56
196_A246_L1.3610.56
698_D701_G1.3590.56
48_F71_W1.3590.56
130_V178_L1.3560.55
228_L425_V1.3540.55
525_W529_G1.3520.55
75_R134_L1.3450.54
353_Q372_P1.3450.54
148_A163_A1.3440.54
624_F637_C1.3420.54
223_V236_I1.3400.54
659_G671_K1.3350.53
630_G686_H1.3310.53
75_R533_T1.3230.52
264_S395_T1.3190.52
693_K696_D1.3190.52
626_V639_M1.3170.52
88_I395_T1.3160.52
161_S164_G1.3110.51
631_S634_L1.3080.51
526_W529_G1.3040.51
554_R606_T1.3040.51
681_A684_T1.2940.50
505_F631_S1.2920.50
228_L419_G1.2910.50
185_K188_K1.2910.50
646_R649_Q1.2910.50
481_E603_G1.2910.50
681_A694_V1.2900.50
680_E683_T1.2850.49
598_W602_I1.2840.49
346_I401_A1.2830.49
215_L553_S1.2830.49
677_V699_N1.2780.49
667_E677_V1.2750.48
383_S386_R1.2700.48
666_A671_K1.2700.48
77_W90_P1.2670.48
175_C243_V1.2620.47
592_D602_I1.2570.47
635_L670_N1.2500.46
59_F693_K1.2450.46
34_R37_A1.2440.46
155_P164_G1.2400.45
180_Y606_T1.2380.45
51_Y336_P1.2370.45
628_R667_E1.2360.45
625_R629_E1.2360.45
175_C669_G1.2350.45
76_A84_I1.2350.45
55_R58_R1.2340.45
348_S598_W1.2340.45
34_R38_V1.2320.45
176_M553_S1.2300.45
54_Y59_F1.2290.45
37_A114_N1.2260.44
531_Q545_N1.2240.44
337_S414_M1.2190.44
130_V177_L1.2170.44
172_A211_G1.2160.43
273_V566_A1.2140.43
180_Y554_R1.2130.43
52_F59_F1.2120.43
379_F390_I1.2060.43
182_M264_S1.2040.42
47_E50_P1.2040.42
307_G311_L1.2020.42
364_L426_L1.2000.42
654_A658_P1.1960.42
678_L681_A1.1950.42
222_H261_P1.1920.41
502_F590_S1.1910.41
554_R607_D1.1900.41
281_A317_L1.1890.41
530_Y543_D1.1890.41
34_R42_E1.1880.41
525_W528_Y1.1870.41
81_G87_T1.1870.41
118_F134_L1.1850.41
235_R384_D1.1850.41
399_F403_M1.1840.41
669_G673_F1.1830.41
186_A304_S1.1830.41
659_G669_G1.1800.41
69_H554_R1.1780.40
227_M277_C1.1740.40
42_E53_N1.1720.40
174_F235_R1.1630.39
324_S609_G1.1620.39
514_H522_V1.1580.39
364_L622_G1.1570.39
393_G417_L1.1550.38
243_V396_S1.1550.38
370_M422_V1.1530.38
653_E656_R1.1530.38
17_L23_L1.1520.38
175_C204_Y1.1490.38
352_H546_T1.1490.38
511_W515_N1.1480.38
336_P534_A1.1440.38
22_I25_M1.1430.38
667_E670_N1.1430.38
137_E185_K1.1410.37
126_F603_G1.1410.37
668_I672_D1.1400.37
168_N576_S1.1390.37
351_E526_W1.1370.37
198_C243_V1.1360.37
156_G163_A1.1350.37
118_F236_I1.1340.37
344_P348_S1.1340.37
340_K347_A1.1320.37
59_F211_G1.1310.37
341_N606_T1.1310.37
157_Y161_S1.1250.36
554_R572_E1.1250.36
115_V392_Y1.1240.36
284_D287_R1.1230.36
488_I642_M1.1210.36
92_L95_T1.1200.36
257_V480_S1.1200.36
510_Y514_H1.1150.35
605_S608_T1.1150.35
126_F129_I1.1130.35
417_L669_G1.1110.35
656_R660_F1.1110.35
457_A682_Y1.1110.35
524_S694_V1.1100.35
523_M558_A1.1100.35
80_L547_W1.1090.35
69_H409_V1.1080.35
375_L397_M1.1060.35
536_A569_I1.1030.34
592_D598_W1.1020.34
78_Y81_G1.1020.34
186_A199_A1.1010.34
502_F534_A1.1000.34
642_M681_A1.1000.34
550_T554_R1.0990.34
224_L540_I1.0980.34
488_I604_G1.0970.34
373_V377_Y1.0960.34
56_T540_I1.0950.34
45_I50_P1.0940.34
474_H484_S1.0940.34
485_S627_D1.0920.34
64_G466_F1.0890.33
145_L150_M1.0890.33
76_A88_I1.0880.33
277_C682_Y1.0880.33
28_V31_F1.0880.33
635_L669_G1.0870.33
419_G568_E1.0860.33
370_M522_V1.0860.33
241_C278_Q1.0850.33
666_A676_D1.0850.33
621_T629_E1.0830.33
373_V560_A1.0830.33
148_A153_V1.0810.33
155_P161_S1.0810.33
262_V395_T1.0800.33
192_I195_A1.0790.33
82_R89_Y1.0770.32
632_P660_F1.0740.32
653_E657_P1.0740.32
613_K616_D1.0730.32
46_H50_P1.0720.32
404_V566_A1.0720.32
334_L337_S1.0710.32
398_Y546_T1.0680.32
624_F643_C1.0670.32
77_W81_G1.0660.32
156_G161_S1.0660.32
52_F58_R1.0650.32
155_P162_V1.0640.32
160_R163_A1.0640.32
653_E658_P1.0630.31
553_S557_Q1.0630.31
263_L590_S1.0630.31
44_V505_F1.0630.31
562_T565_K1.0610.31
261_P325_P1.0600.31
543_D546_T1.0580.31
266_E566_A1.0570.31
76_A83_I1.0570.31
352_H406_L1.0550.31
139_K248_T1.0550.31
666_A670_N1.0550.31
660_F669_G1.0540.31
354_P372_P1.0540.31
559_M627_D1.0530.31
93_M113_R1.0530.31
534_A590_S1.0520.31
180_Y553_S1.0520.31
389_I400_S1.0510.31
632_P635_L1.0510.31
595_K598_W1.0500.30
413_V416_I1.0500.30
400_S482_A1.0490.30
530_Y546_T1.0480.30
655_K660_F1.0480.30
68_F71_W1.0470.30
400_S411_A1.0470.30
570_M678_L1.0450.30
80_L123_F1.0450.30
159_S163_A1.0450.30
660_F671_K1.0450.30
593_I599_M1.0440.30
470_T688_L1.0440.30
174_F178_L1.0440.30
682_Y688_L1.0440.30
652_T655_K1.0430.30
335_D338_Y1.0430.30
274_F573_L1.0430.30
134_L177_L1.0420.30
343_I346_I1.0420.30
245_C660_F1.0410.30
176_M605_S1.0400.30
42_E52_F1.0400.30
677_V700_R1.0390.30
634_L637_C1.0390.30
52_F57_T1.0360.29
356_T499_R1.0360.29
213_V217_N1.0350.29
624_F648_G1.0350.29
393_G396_S1.0330.29
603_G618_Y1.0330.29
51_Y56_T1.0320.29
251_S557_Q1.0320.29
508_A520_A1.0310.29
30_S34_R1.0310.29
570_M573_L1.0310.29
107_H678_L1.0300.29
77_W546_T1.0290.29
336_P488_I1.0290.29
344_P352_H1.0280.29
576_S637_C1.0270.29
592_D599_M1.0250.29
666_A682_Y1.0250.29
666_A672_D1.0250.29
186_A201_A1.0230.29
116_C167_D1.0200.28
669_G672_D1.0160.28
348_S351_E1.0160.28
525_W543_D1.0160.28
527_D543_D1.0160.28
330_F340_K1.0150.28
525_W530_Y1.0150.28
527_D530_Y1.0150.28
431_K666_A1.0130.28
185_K189_T1.0130.28
145_L148_A1.0110.28
310_L682_Y1.0100.28
307_G310_L1.0100.28
181_Y475_S1.0090.28
356_T382_L1.0080.28
161_S551_H1.0080.28
334_L471_Y1.0070.27
642_M678_L1.0050.27
651_Y654_A1.0050.27
63_E171_I1.0040.27
73_D405_R1.0040.27
84_I467_F1.0020.27
557_Q611_H1.0020.27
47_E352_H1.0010.27
564_E684_T1.0010.27
59_F462_L1.0010.27
55_R73_D1.0000.27
693_K699_N1.0000.27
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  
3wajA10.83691000.549Contact Map
3rceA10.82551000.553Contact Map
2lgzA10.35041000.676Contact Map
3vgpA10.2171000.805Contact Map
3vu0A30.21421000.815Contact Map
3vu1A20.21281000.821Contact Map
2zaiA40.24261000.837Contact Map
3aagA20.23121000.86Contact Map
3waiA10.672399.90.898Contact Map
4c2mA20.082315.30.988Contact 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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