D-I-TASSER Q9H6E5-D3

D-I-TASSER results for Q9H6E5-D3

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

Input Sequence in FASTA format

>Q9H6E5 (214 residues)
LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGDLEEPQP
VPKAPESPSLDSALASPLDPQALACTPASPPDSQPPASPQDSEALDFETPSSSLAPQTPD
SALASETLASPQSLPPASPLLEDREEGDLGKASELAETPKEEKAEGAAMLELVGSILRGC
VPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGDLEEPQPVPKAPESPSLDSALASPLDPQALACTPASPPDSQPPASPQDSEALDFETPSSSLAPQTPDSALASETLASPQSLPPASPLLEDREEGDLGKASELAETPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLS
Prediction	CCHHHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCSSSCCCCCCCSSSSSSCCCCCSSSSSCC
Confidence	9788999999999999999999789958984476544445357640379843777766655678888788878789999866777899988889999999888888999998889999998777778899888899777778889898887756444777774014568999999999719883230553335773478651345852554339
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGDLEEPQPVPKAPESPSLDSALASPLDPQALACTPASPPDSQPPASPQDSEALDFETPSSSLAPQTPDSALASETLASPQSLPPASPLLEDREEGDLGKASELAETPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLS
Prediction	7556524003200420250045102503132222210323444030201021454544543454654364664444445354554446445755545437556436372465644253375544674465564445655366755655355435355446464543341042015105513130440341240321002022541404130348
	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                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCSSSCCCCCCCSSSSSSCCCCCSSSSSCC
LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLGDLEEPQPVPKAPESPSLDSALASPLDPQALACTPASPPDSQPPASPQDSEALDFETPSSSLAPQTPDSALASETLASPQSLPPASPLLEDREEGDLGKASELAETPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFCHRPSGLHGDVSLS

5a2vA3

0.38

0.22

6.51

1.85

SPARKS-K

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHD-------------------------------IMKKGPFEMEYQ---------------------------------MKRLPS-------------------------ERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5a2vA

0.37

0.21

6.39

2.08

HHsearch

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHDIMKKGPFE------------------------------------------MEY---------QMKR--------------------------------------LPSERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5a2vA3

0.38

0.22

6.51

1.55

FFAS-3D

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHDIMKKGPFEMEYQMKRLPS-----------------------------------------------------------------------------------------ERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5wu1A

0.99

0.50

14.14

1.94

CNFpred

LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDL---------------------------------------------------------------------------------------------------------TPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFAHRPSGLHGDVSLS

5wu1A1

0.99

0.50

14.14

0.83

DEthreader

LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDL---------------------------------------------------------------------------------------------------------TPKEEKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFAHRPSGLHGDVSLS

5a2vA

0.38

0.22

6.51

1.69

SPARKS-K

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHD-------------------------------IMKKGPFEMEYQ---------------------------------MKRLPS-------------------------ERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5a2vA

0.35

0.21

6.14

0.79

MapAlign

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHDI-----------------------------------------------------------------------------------------MKKGPFEMEYQMKRLPSERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5a2vA

0.36

0.21

6.26

0.85

CEthreader

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHDIMKKGPFEMEYQMKR-----------------------------------------------------------------------------------------LPSERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5a2vA3

0.38

0.22

6.51

0.93

MUSTER

LTEENIKLRYLACSLVRDFARAYFPDSTVKPFGSSVNTFGKLGCDVDMFLDFHDIMKKGPFEMEYQMKRLPS-----------------------------------------------------------------------------------------ERLATQKILSIIGDCLDNFGPGYSSVQKILNARCPLVKFSHQPTGFQCDLSVS

5wu1A

0.96

0.49

13.76

2.06

HHsearch

LSEAERQLRSLVVALMQEVFTEFFPGCVVHPFGSSINSFDVHGCDLDLFLDLTPKE---------------------------------------------------------------------------------------------------------EKAEGAAMLELVGSILRGCVPGVYRVQTVPSARRPVVKFAHRPSGLHGDVSLS

(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	0.6416

(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	6es9A	0.52	5.02	0.067	0.808	model1_6es9A.pdb.gz
2	5wu1A1	0.49	1.26	0.954	0.509	model1_5wu1A1.pdb.gz
3	3pq1A	0.48	2.22	0.353	0.523	model1_3pq1A.pdb.gz
4	5a2vA	0.48	2.63	0.360	0.542	model1_5a2vA.pdb.gz
5	4m5dA	0.47	2.98	0.084	0.556	model1_4m5dA.pdb.gz
6	2b51A1	0.46	2.49	0.218	0.514	model1_2b51A1.pdb.gz
7	3nybA1	0.45	2.05	0.283	0.495	model1_3nybA1.pdb.gz
8	1bj4A	0.35	5.70	0.038	0.603	model1_1bj4A.pdb.gz
9	1ktcA1	0.32	6.34	0.011	0.608	model1_1ktcA1.pdb.gz
10	4l3tA	0.31	6.23	0.023	0.561	model1_4l3tA.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:0044822	1.00	poly(A) RNA binding
GO:0016740	0.97	transferase activity
GO:0016779	0.96	nucleotidyltransferase activity
GO:0050265	0.92	RNA uridylyltransferase activity
GO:0004652	0.92	polynucleotide adenylyltransferase activity
GO:0003730	0.88	mRNA 3'-UTR 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:0031123	1.00	RNA 3'-end processing
GO:0016071	1.00	mRNA metabolic process
GO:0006378	0.96	mRNA polyadenylation
GO:0034470	0.92	ncRNA processing
GO:0098789	0.88	pre-mRNA cleavage required for polyadenylation
GO:0016180	0.88	snRNA processing
GO:0006402	0.75	mRNA catabolic process
GO:0071044	0.74	histone mRNA catabolic 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:0043229	1.00	intracellular organelle
GO:0044422	0.95	organelle part
GO:0044446	0.94	intracellular organelle part
GO:0044428	0.93	nuclear part
GO:0005730	0.92	nucleolus
GO:0032991	0.79	macromolecular complex
GO:0043234	0.75	protein complex
GO:0016607	0.73	nuclear speck
GO:0005847	0.73	mRNA cleavage and polyadenylation specificity factor complex
GO:0043227	0.67	membrane-bounded organelle
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0005634	0.56	nucleus

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	3kzwA	0.441	4.84	0.021	0.673	3.4.11.1	149
2	0.060	1pb3A	0.410	5.89	0.046	0.710	1.1.1.42	NA
3	0.060	2hb6B	0.429	5.36	0.055	0.696	3.4.11.1	137,144
4	0.060	2d1cA	0.408	5.82	0.089	0.701	1.1.1.42	NA
5	0.060	1gytA	0.434	5.16	0.052	0.692	3.4.11.1	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:

Click to view	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	3cf4A	0.442	6.35	0.039	0.813	0.53	SF4	complex1.pdb.gz	137,138,143,144,146,147,152,155
	2	0.01	3kr5I	0.450	4.96	0.059	0.692	0.41	CO3	complex2.pdb.gz	144,145,146,147,151

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.