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Hsp104

ID: 1513269922 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 908 (825)
Sequences: 7859 (3755.5)
Seq/Len: 9.526
Nf(neff/√len): 130.7

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: 9.526).

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 > 50% 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
173_D242_K5.5861.00
176_E180_Q5.5821.00
785_D811_K5.2931.00
171_A244_F4.5111.00
781_H812_D4.2461.00
348_T376_A4.1771.00
777_R816_K4.0701.00
707_R715_T3.9071.00
843_R848_E3.8571.00
577_S584_M3.5451.00
807_T858_V3.4481.00
575_D578_S3.4421.00
571_H574_R3.3461.00
273_E309_Q3.2381.00
345_V376_A3.1951.00
609_S703_L3.1851.00
725_M766_I3.0631.00
344_S347_Q3.0121.00
172_I177_Q2.9601.00
349_V372_L2.8341.00
542_D545_T2.7551.00
421_L452_E2.6691.00
776_S779_A2.6541.00
573_E588_K2.6511.00
367_I400_C2.6121.00
249_A300_I2.6121.00
512_D516_Q2.5811.00
789_K792_E2.5571.00
788_L806_L2.5461.00
579_E629_G2.5321.00
572_M630_F2.5281.00
199_V338_I2.4861.00
592_N838_N2.4701.00
196_T338_I2.4321.00
165_E168_S2.4221.00
592_N842_L2.3931.00
256_K260_D2.3581.00
345_V380_K2.2571.00
251_L268_V2.2471.00
624_A724_I2.2441.00
729_L757_H2.2101.00
814_L831_L2.2051.00
817_Y835_E2.2021.00
501_T504_D2.2001.00
777_R812_D2.1991.00
486_L505_L2.1941.00
164_L168_S2.1911.00
173_D176_E2.1851.00
414_L459_L2.1721.00
494_E506_R2.1701.00
500_A504_D2.1571.00
236_T239_Q2.1551.00
270_K274_E2.1441.00
650_Y659_T2.1411.00
611_L766_I2.1381.00
177_Q182_K2.1341.00
573_E595_R2.1131.00
612_F724_I2.1041.00
639_I681_S2.0731.00
492_D496_R2.0591.00
428_I449_R2.0551.00
649_K694_D2.0541.00
483_L510_I2.0531.00
813_F817_Y2.0471.00
209_C286_I2.0441.00
429_K432_E2.0251.00
587_I623_L1.9791.00
176_E179_R1.9731.00
425_Q456_Q1.9701.00
345_V377_Q1.9641.00
395_L550_A1.9631.00
831_L835_E1.9561.00
702_M723_V1.9401.00
575_D630_F1.9371.00
581_V786_I1.9291.00
286_I325_V1.9281.00
373_V377_Q1.9251.00
350_A353_R1.9081.00
375_A396_V1.8901.00
95_V119_A1.8631.00
791_I832_I1.8601.00
353_R369_D1.8551.00
585_D773_N1.8551.00
579_E622_E1.8431.00
475_E516_Q1.8411.00
729_L754_V1.8291.00
613_L727_S1.8091.00
637_M678_K1.8031.00
563_E571_H1.8021.00
702_M708_I1.7811.00
183_L227_Q1.7801.00
787_R829_N1.7791.00
787_R790_E1.7691.00
166_Y267_G1.7591.00
374_T543_S1.7551.00
349_V373_V1.7551.00
55_I60_Y1.7371.00
579_E626_K1.7201.00
650_Y653_S1.7141.00
809_E858_V1.7141.00
345_V349_V1.7131.00
782_K785_D1.7111.00
579_E635_E1.7111.00
290_M331_F1.7111.00
270_K273_E1.7101.00
675_L718_C1.7091.00
450_Q454_S1.7071.00
781_H808_Q1.7041.00
604_P794_R1.7021.00
807_T856_N1.6941.00
481_K485_E1.6861.00
806_L810_A1.6841.00
754_V763_L1.6821.00
780_I815_A1.6741.00
348_T388_L1.6661.00
571_H575_D1.6651.00
570_I845_L1.6591.00
228_R233_D1.6401.00
486_L510_I1.6361.00
323_S667_E1.6351.00
647_S651_A1.6321.00
227_Q231_D1.6151.00
773_N779_A1.6121.00
485_E489_K1.6091.00
734_I746_T1.6081.00
784_V811_K1.6071.00
399_S549_T1.6041.00
482_K509_A1.6041.00
379_A388_L1.6021.00
675_L721_C1.6021.00
489_K501_T1.5971.00
509_A512_D1.5951.00
418_E463_R1.5881.00
403_V541_V1.5821.00
232_D239_Q1.5781.00
498_D501_T1.5641.00
463_R467_N1.5591.00
813_F835_E1.5571.00
817_Y831_L1.5521.00
585_D747_K1.5411.00
565_E598_R1.5401.00
850_K853_E1.5301.00
27_H73_L1.5271.00
283_I312_V1.5221.00
356_Q369_D1.5211.00
818_G828_L1.5131.00
572_M591_S1.5091.00
341_A678_K1.5021.00
184_D203_R1.4981.00
788_L832_I1.4901.00
504_D509_A1.4881.00
807_T810_A1.4881.00
570_I846_K1.4801.00
213_E318_N1.4731.00
388_L392_A1.4721.00
781_H811_K1.4721.00
11_A116_I1.4671.00
478_Q482_K1.4661.00
357_P361_I1.4601.00
479_A513_I1.4591.00
785_D808_Q1.4521.00
751_M754_V1.4461.00
402_G548_E1.4451.00
482_K485_E1.4441.00
424_I448_A1.4361.00
366_R540_V1.4341.00
487_E514_K1.4341.00
195_S398_I1.4331.00
835_E839_K1.4301.00
166_Y271_E1.4271.00
178_A183_L1.4260.99
410_K418_E1.4220.99
792_E804_L1.4220.99
368_L371_A1.4210.99
843_R846_K1.4200.99
229_I243_L1.4190.99
122_N137_I1.4170.99
175_T230_I1.4170.99
37_A66_K1.4140.99
168_S176_E1.4100.99
577_S587_I1.4080.99
753_A756_Q1.4060.99
595_R842_L1.4040.99
806_L811_K1.4030.99
486_L513_I1.4010.99
503_A506_R1.3990.99
347_Q350_A1.3970.99
467_N471_H1.3960.99
779_A782_K1.3910.99
813_F859_L1.3910.99
733_F753_A1.3900.99
704_D829_N1.3900.99
784_V815_A1.3860.99
35_I92_L1.3810.99
631_L722_I1.3800.99
186_V193_I1.3790.99
211_I337_K1.3750.99
339_E678_K1.3730.99
780_I819_Y1.3630.99
457_E461_P1.3610.99
165_E271_E1.3600.99
428_I445_L1.3600.99
420_Q451_K1.3580.99
453_A457_E1.3530.99
137_I141_K1.3500.99
810_A859_L1.3390.99
843_R849_I1.3380.99
836_I857_V1.3350.99
589_A770_V1.3350.99
370_S543_S1.3330.99
95_V120_L1.3330.99
374_T377_Q1.3310.99
818_G831_L1.3290.99
248_L251_L1.3250.99
576_L580_V1.3240.99
349_V376_A1.3180.99
21_L38_A1.3140.99
802_Y849_I1.3130.99
732_E736_S1.3130.99
590_V623_L1.3120.99
25_H74_V1.3090.99
269_L304_A1.3020.99
612_F772_F1.2980.99
457_E460_E1.2940.99
641_V655_L1.2910.99
21_L24_D1.2910.99
805_N854_T1.2880.99
342_E380_K1.2850.99
486_L509_A1.2770.99
173_D244_F1.2700.99
747_K751_M1.2680.99
639_I675_L1.2680.99
685_F702_M1.2650.99
699_M702_M1.2650.99
801_H851_D1.2590.98
573_E591_S1.2580.98
179_R242_K1.2450.98
849_I855_V1.2450.98
809_E812_D1.2440.98
31_Q89_S1.2430.98
839_K843_R1.2420.98
576_L626_K1.2370.98
577_S588_K1.2340.98
803_K854_T1.2330.98
490_A510_I1.2320.98
372_L396_V1.2320.98
545_T548_E1.2320.98
840_L855_V1.2300.98
240_G278_L1.2300.98
482_K516_Q1.2290.98
805_N856_N1.2280.98
14_I39_F1.2280.98
32_P95_V1.2200.98
597_S602_A1.2190.98
611_L754_V1.2100.98
743_Q746_T1.2090.98
500_A503_A1.2080.98
794_R837_L1.2080.98
790_E793_E1.2070.98
648_E659_T1.2050.98
812_D816_K1.2050.98
286_I314_G1.2050.98
486_L490_A1.2030.98
606_Q829_N1.2010.98
490_A506_R1.2000.98
784_V832_I1.2000.98
282_F315_A1.1940.98
778_K781_H1.1900.98
418_E459_L1.1850.97
27_H34_H1.1810.97
177_Q180_Q1.1800.97
647_S694_D1.1780.97
88_P92_L1.1760.97
379_A391_S1.1750.97
489_K492_D1.1740.97
768_S834_N1.1690.97
548_E559_K1.1680.97
820_S827_P1.1640.97
399_S546_I1.1630.97
781_H785_D1.1600.97
732_E753_A1.1590.97
751_M755_R1.1560.97
641_V685_F1.1550.97
564_S567_E1.1540.97
588_K592_N1.1520.97
68_V71_R1.1490.97
483_L513_I1.1420.97
136_D139_A1.1400.97
652_V698_V1.1380.97
100_A111_I1.1370.97
210_L340_V1.1360.97
14_I42_T1.1330.96
751_M771_I1.1320.96
791_I837_L1.1320.96
102_I106_Q1.1310.96
748_N752_G1.1300.96
777_R815_A1.1280.96
28_P79_Q1.1270.96
646_L670_F1.1240.96
265_F268_V1.1230.96
432_E449_R1.1200.96
611_L688_V1.1200.96
427_E444_R1.1190.96
806_L836_I1.1180.96
201_A237_I1.1170.96
478_Q481_K1.1140.96
810_A836_I1.1140.96
58_G135_V1.1120.96
488_N492_D1.1120.96
15_L96_L1.1120.96
10_R13_T1.1110.96
813_F816_K1.1070.96
33_I37_A1.1050.96
117_L140_I1.1040.96
353_R372_L1.1040.96
102_I137_I1.0990.96
98_D101_K1.0990.96
175_T178_A1.0990.96
685_F725_M1.0980.96
596_L837_L1.0960.95
626_K629_G1.0960.95
849_I853_E1.0930.95
688_V725_M1.0930.95
272_I281_L1.0870.95
291_G296_D1.0830.95
221_I340_V1.0820.95
513_I516_Q1.0810.95
21_L25_H1.0780.95
676_Q714_K1.0780.95
638_M682_V1.0750.95
420_Q423_L1.0740.95
103_Q111_I1.0730.95
102_I119_A1.0710.95
32_P92_L1.0700.95
90_Y94_K1.0700.95
596_L838_N1.0690.95
514_K518_E1.0690.95
842_L846_K1.0680.95
404_A408_D1.0680.95
652_V695_V1.0680.95
254_G264_R1.0660.95
580_V626_K1.0660.95
21_L66_K1.0640.94
355_L358_K1.0630.94
703_L723_V1.0540.94
375_A399_S1.0520.94
586_A770_V1.0510.94
261_F297_A1.0510.94
641_V654_K1.0480.94
379_A395_L1.0480.94
7_F11_A1.0450.94
569_L598_R1.0450.94
193_I224_G1.0440.94
353_R373_V1.0430.94
459_L463_R1.0420.94
752_G755_R1.0420.94
569_L595_R1.0420.94
428_I432_E1.0420.94
51_L117_L1.0370.93
512_D515_K1.0370.93
225_V229_I1.0340.93
421_L455_L1.0310.93
792_E806_L1.0310.93
802_Y844_I1.0300.93
574_R577_S1.0280.93
361_I364_G1.0250.93
788_L792_E1.0250.93
454_S458_E1.0210.93
603_N790_E1.0200.93
762_F766_I1.0200.93
289_L298_A1.0190.93
37_A41_E1.0160.92
413_E458_E1.0140.92
654_K711_G1.0100.92
422_Q425_Q1.0080.92
368_L540_V1.0080.92
22_A34_H1.0070.92
764_N830_R1.0060.92
349_V377_Q1.0040.92
785_D789_K1.0010.92
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  
4d2uA60.86671000.378Contact Map
1qvrA30.88221000.378Contact Map
1r6bX10.7611000.412Contact Map
3pxiA30.78411000.436Contact Map
4ciuA10.72251000.516Contact Map
3pxgA60.49121000.714Contact Map
3vkgA20.80951000.752Contact Map
4lj9A10.36341000.778Contact Map
4hseA10.40641000.779Contact Map
3j94A60.47471000.823Contact 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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