D-I-TASSER B4DYI2-D1

D-I-TASSER results for B4DYI2-D1

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

Input Sequence in FASTA format

>B4DYI2 (150 residues)
MENLPFPLKLLSASSLNTPSSTPWVLDIFLTLVFALGFFFLLLPYFSYLRCDNPPSPSPK
KRKRHLVSQRPAGRRGRPRGRMKNHSLRACRECPRGLEETWDLLSQLQSLLGPHLEKGDF
GQLSGPDPPGEVGKRTPDGASRSSHEPTED

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MENLPFPLKLLSASSLNTPSSTPWVLDIFLTLVFALGFFFLLLPYFSYLRCDNPPSPSPKKRKRHLVSQRPAGRRGRPRGRMKNHSLRACRECPRGLEETWDLLSQLQSLLGPHLEKGDFGQLSGPDPPGEVGKRTPDGASRSSHEPTED
Prediction	CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	985200145556653169983268999999999999999999999998535799999930113442210012123344555433212355413144788764445788874346677886547889999732466777556778888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MENLPFPLKLLSASSLNTPSSTPWVLDIFLTLVFALGFFFLLLPYFSYLRCDNPPSPSPKKRKRHLVSQRPAGRRGRPRGRMKNHSLRACRECPRGLEETWDLLSQLQSLLGPHLEKGDFGQLSGPDPPGEVGKRTPDGASRSSHEPTED
Prediction	875233304132433143432231203231233133233313211043134653423244657545465554544544454445442542562464155345234304521451377452440436534273254344744444554388
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MENLPFPLKLLSASSLNTPSSTPWVLDIFLTLVFALGFFFLLLPYFSYLRCDNPPSPSPKKRKRHLVSQRPAGRRGRPRGRMKNHSLRACRECPRGLEETWDLLSQLQSLLGPHLEKGDFGQLSGPDPPGEVGKRTPDGASRSSHEPTED

1mhsA3

0.09

3.34

0.39

CEthreader

WVSSFYRSNPIVQILEFTLAITIIGVGLPAVVTTTMAVGAAYLAKKKAIVQKLSAIESLAGVEILCSDKTGTLTKNKLMDPPRHDTYKTVCEAKTLAVGIARETSRQLGLGTNIYNAERLGLGGGGDMPGSEVYDFVEAADGFAEVFPQH

6wlvA

0.04

2.06

0.48

EigenThreader

---GPLLTSAIIFYLAIGAAIFEVLEEPHWKEAKKNYYTQKLHLLKEFNNWNWPNAMIFAATVITPKTPAGRLFCVFYGLFGVPLCLTWISALGKFFGGRAKRLGTAIFIVWGVLVHLVIPPFVFMVTEEWNYIEGLYYSFITISTIGFG

6nbqG

0.10

0.09

3.45

0.44

FFAS-3D

-QTITFFALAAAVIIVLLDNVVYSAFLLGGVFLSIAGLYVNVLILFAIMLVNKRETYTPVPGRWLRQGGASSVPPTPDSITTIGQHFFSDFLLPFELASVLLLMALIGAVLARRELVLE-----PEPILGEEVVPPLELPERP-REP---

7aavA

0.11

3.88

0.96

SPARKS-K

LENMPMPWEQIITGAISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRFPPFDDEEPPLDYADNIEAIQLELDPEEDAPVLDWFYDHQPLQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAALNMAIPGGPKFEPLVRDINLQD

5t0oA

0.08

0.03

1.32

0.59

CNFpred

---------------------RQFALTLAISVTISGFVALTLTPSLCALFLRRNEGEPFKFV------------------------KKFNDFFDWSTSVFSAGVAYIL------------------------------------------

5dfzA

0.05

0.03

1.55

0.83

DEthreader

DDFLSLKNQNHWYMRTVQKSIETLEKEVLQRKKSKKNIEMAQLESNDTINHSKELMSDSINDDYGSI---------------------------------------LLRQAGETSQLSTYF-T------------DQMKHKLAIFNILKQ

1mhsA3

0.11

4.06

0.84

MapAlign

LILVIFTLLIVWVSSFYRSNPIVQILEFTLAITIIGVTTTMAVGAAYLAKKKAIVQKLSAIESLAGVEILCSDKTGTLTKNKLMDPPRHDTYKTVCEAGIARETSRQLGLGTNIYNAERLGLGGGGDMPGSEVYDFVEAADGFAEVFPQH

1jvrA

0.12

0.11

3.77

0.60

MUSTER

MGQIHGLSPTPIPK---APRGLS--THHWLNFLQAAYRL------------QPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTT

2pffB

0.16

0.15

4.89

0.76

HHsearch

AEKVFT-QGLNILEWLENPSNTPDKDYLSIPISCPLIGVIQLAHYVVTAKLLG--FTPGELKGATAIAETDSWESF-FVSVRKAPMLSISNLTQEQ---VQDYVNKTNSHL---PAGKQVESLVNGAPPQSRKAKAPSGLDQS-RIPFSE

6rohA3

0.03

1.90

0.39

CEthreader

GDRQETAINIGMSCRLLSEDMNLLIINEETRDDTERNLLEKINALNEHQLSTHDMNTLALVIDGKFALEPELEDYLLTVAKLCKAVICCRVSPLQKALVVKMVKRKSSSLLLAIGDAAHVGVGISGMEGMQAARSADIAVGQFKFLKKLL

(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	0.37

(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.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	6wjvA	0.58	4.10	0.065	0.887	model1_6wjvA.pdb.gz
2	3cfrA2	0.57	4.10	0.100	0.867	model1_3cfrA2.pdb.gz
3	4q5vA	0.56	4.23	0.046	0.867	model1_4q5vA.pdb.gz
4	6v8pA	0.56	4.18	0.068	0.867	model1_6v8pA.pdb.gz
5	3iayA2	0.56	4.24	0.053	0.880	model1_3iayA2.pdb.gz
6	3k5nA2	0.56	4.22	0.046	0.860	model1_3k5nA2.pdb.gz
7	5n2eA	0.55	4.11	0.070	0.853	model1_5n2eA.pdb.gz
8	4m8oA	0.55	4.52	0.065	0.920	model1_4m8oA.pdb.gz
9	1s5jA2	0.54	4.25	0.078	0.840	model1_1s5jA2.pdb.gz
10	2gv9B2	0.54	4.23	0.087	0.833	model1_2gv9B2.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:1901265	0.50	nucleoside phosphate binding
GO:0036094	0.50	small molecule binding
GO:0034061	0.50	DNA polymerase activity
GO:0004527	0.50	exonuclease activity
GO:0003676	0.50	nucleic acid binding
GO:0003779	0.40	actin binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0034654	0.58	nucleobase-containing compound biosynthetic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	0.92	intracellular part
GO:0043231	0.89	intracellular membrane-bounded organelle
GO:0044444	0.81	cytoplasmic part
GO:0001669	0.79	acrosomal vesicle

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	1yrlA	0.479	4.86	0.043	0.813	1.1.1.86	NA
2	0.060	1b3bE	0.517	4.72	0.031	0.833	1.4.1.3	9,143
3	0.060	2ajqA	0.506	4.89	0.094	0.833	2.7.7.7	NA
4	0.060	1y2mB	0.463	4.71	0.079	0.727	4.3.1.24	NA
5	0.060	1gz3A	0.500	4.68	0.015	0.833	1.1.1.38	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.01	3tafD	0.559	4.35	0.098	0.880	0.23	QNA	complex1.pdb.gz	118,125,138,139,143,144
2	0.01	3suoA	0.557	4.20	0.091	0.873	0.28	TTP	complex2.pdb.gz	40,41,42,106,110
3	0.01	2oyqA	0.558	4.30	0.075	0.873	0.30	N5P	complex3.pdb.gz	121,130,133,134
4	0.01	2p5oB	0.552	4.41	0.092	0.867	0.14	QNA	complex4.pdb.gz	39,108,109,111
5	0.01	3rmcD	0.552	4.36	0.091	0.873	0.13	QNA	complex5.pdb.gz	103,104,108,109,110,124,125,127,128
6	0.01	1q9xA	0.557	4.36	0.076	0.860	0.26	QNA	complex6.pdb.gz	32,110,111,125,139
7	0.01	3k5mA	0.570	4.09	0.061	0.880	0.34	DG3	complex7.pdb.gz	35,36,80,84,87
8	0.01	1ih7A	0.548	4.41	0.076	0.860	0.27	GMP	complex8.pdb.gz	32,40,110,111,125
9	0.01	1ig9A	0.560	4.26	0.083	0.880	0.15	TTP	complex9.pdb.gz	31,32,33,34
10	0.01	3kd5E	0.541	4.28	0.061	0.873	0.15	PPF	complex10.pdb.gz	33,35,36

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[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.