D-I-TASSER P06312-D1

D-I-TASSER results for P06312-D1

[Click result.zip to download all results on this page]

Input Sequence in FASTA format

>P06312 (121 residues)
MVLQTQVFISLLLWISGAYGDIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLA
WYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYST
P

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVLQTQVFISLLLWISGAYGDIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP
Prediction	CCCHHHHHHHHHHHCCCCCCCSSSSCCCCCSSSCCCCCSSSSSSCCCCCCCCCCCCCSSSSSCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCHHHCSSSSSCCCCCCC
Confidence	9852799999998548986218873567631118993299988746660357889844675404999997111110222478999882647768864566468894572334231678999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVLQTQVFISLLLWISGAYGDIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP
Prediction	8533122313121023414130201033442403463404040301230344465421000102346532320024014344432332324334332304044233412020000144748
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Contact, Hydrogen and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

Hydrogen bond networks

D-I-TASSER simulation is guided by the consensus contact map (left figure), distance map (middle figure) and Hydrogen bond network (right figure) derived based on confidence scores of DeepPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Top 10 threading templates used by D-I-TASSER

Rank

PDB
hit

ID1

ID2

Cov

Norm.
Zscore

Download
alignment

                  20                  40                  60                  80                 100                 120

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHCCCCCCCSSSSCCCCCSSSCCCCCSSSSSSCCCCCCCCCCCCCSSSSSCCCCCCCCCSSSSCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCHHHCSSSSSCCCCCCC
MVLQTQVFISLLLWISGAYGDIVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP

5yd5A

0.51

0.48

13.88

1.33

DEthreader

----SF-YSNYGGGSGGGGSDIVMTQAAPSVSVTPGESVSISCRSSK-SLLHRNGNTYLFWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCMQHLEY-

7c94A1

0.82

0.69

19.36

1.19

SPARKS-K

--------------------DIVMTQSPSSLAMSVGQKVTMNCKSSQSLLNSSNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSAQAEDLADYFCQQYYSTP

4gftB

0.24

0.19

5.91

0.53

MapAlign

---------------------VQLQESG--GGVQPGGSLKLSCSAAPE---RAFSNYAMGWFRQAPGQEREFVAGIGQYYADSVKGRFTISRDNNAVYLQMNSVKAEDTAVYYCAARVVP-

7c94A

0.82

0.69

19.36

0.28

CEthreader

--------------------DIVMTQSPSSLAMSVGQKVTMNCKSSQSLLNSSNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSAQAEDLADYFCQQYYSTP

5xcsB

0.77

0.64

18.24

1.02

MUSTER

--------------------DIELTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWASTRESGVPDRFTGSGSGRDFTLTISSVQAEDLAVYYCQNDNSHP

2ch8A1

0.19

0.14

4.52

0.45

HHsearch

------------------------------VTAFLGERVTLTSYWRRVSLG---PEIEVSWFKLGPGEEQVLIGRMHHDVEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGET

7jn5L1

0.97

0.81

22.70

1.81

FFAS-3D

--------------------DIQLTQSPDSLAVSLGERATINCKSSQSVLYSSINKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSTP

1lmkA

0.55

0.50

14.30

0.35

EigenThreader

Y---------AYWYVLGGSDIELTQSPL-SLPVSLGDQASISCRSSQSLVHS-NGNTSLHWYLKKPGQSPKLLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVP

5xcsB

0.77

0.64

18.24

1.71

CNFpred

--------------------DIELTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWASTRESGVPDRFTGSGSGRDFTLTISSVQAEDLAVYYCQNDNSHP

4hjjL

0.62

0.55

15.61

1.17

DEthreader

AVKV--EI--KR-TV--AAPEIVMTQSPATLSVSPGERATLSCRASE-S-I----SSNLAWYQQKPGQAPRLFIYTASTRATDIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNW-

(a)	ID1 is the number of template residues identical to query divided by number of aligned residues.
(b)	ID2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment and is highlighted in bold.
(e)	Download alignment lists the threading program used to identify the template, and provide the 3D structure of aligned regions of threading templates (threading[1-10].pdb.gz).
(f)	Template residues identical to query sequence are highlighted in color.

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.894916882030438

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of DeepPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.