D-I-TASSER Q13489-D1

D-I-TASSER results for Q13489-D1

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

Input Sequence in FASTA format

>Q13489 (192 residues)
MNIVENSIFLSNLMKSANTFELKYDLSCELYRMSTYSTFPAGVPVSERSLARAGFYYTGV
NDKVKCFCCGLMLDNWKRGDSPTEKHKKLYPSCRFVQSLNSVNNLEASSIIHFEPGEDHS
EDAIMMNTPVINAAVEMGFSRSLVKQTVQRKILATGENYRLVNDLVLDLLNAEDEIREEE
RERATEEKESND

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNIVENSIFLSNLMKSANTFELKYDLSCELYRMSTYSTFPAGVPVSERSLARAGFYYTGVNDKVKCFCCGLMLDNWKRGDSPTEKHKKLYPSCRFVQSLNSVNNLEASSIIHFEPGEDHSEDAIMMNTPVINAAVEMGFSRSLVKQTVQRKILATGENYRLVNDLVLDLLNAEDEIREEERERATEEKESND
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCHCHHHHHHHHHCCCCCCCCCHHHHHHCCCSSCCCCCSSSSSCCCCSSCCCCCCCCHHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCC
Confidence	986558864223467899998895500599999988337898888999998718666389973897006867248899999999999974678128761454446754433468777776543212674566789848987888888999999958987987688999862267520222214642223469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNIVENSIFLSNLMKSANTFELKYDLSCELYRMSTYSTFPAGVPVSERSLARAGFYYTGVNDKVKCFCCGLMLDNWKRGDSPTEKHKKLYPSCRFVQSLNSVNNLEASSIIHFEPGEDHSEDAIMMNTPVINAAVEMGFSRSLVKQTVQRKILATGENYRLVNDLVLDLLNAEDEIREEERERATEEKESND
Prediction	774363352055336646444442403326302503651344241325300500002235723020010422054045734014203422530310222434641644633445453445434433644324413624154630351145204612441442431040015366625547566455566488
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCHCHHHHHHHHHCCCCCCCCCHHHHHHCCCSSCCCCCSSSSSCCCCSSCCCCCCCCHHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCC
MNIVENSIFLSNLMKSANTFELKYDLSCELYRMSTYSTFPAGVPVSERSLARAGFYYTGVNDKVKCFCCGLMLDNWKRGDSPTEKHKKLYPSCRFVQSLNSVNNLEASSIIHFEPGEDHSEDAIMMNTPVINAAVEMGFSRSLVKQTVQRKILATGENYRLVNDLVLDLLNAEDEIREEERERATEEKESND

5amqA

0.06

0.05

2.25

0.83

DEthreader

ELVVQRISLFDNMYLALTMMEQSKKILSITGYWQCISDFSTVSSPGFLTTCMIMNFS------IYT----SLSIT----------LTEPARIIWFPGSVTEYLTQIYL-F-TKDREI-FVG-YAKCMYAVERIAKE-RCKEMIS-----MSKWSAQDVFYKYWLSYVHSCAMSNSLVNQTSIKNLYGEPFMG

3t6pA

0.49

0.43

12.55

2.36

SPARKS-K

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQYPHLLEQLLSTEDAVMMNTPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAEEMASDD

3t6pA

0.48

0.42

12.11

1.71

MapAlign

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVEIQGRYPHLLEQLLSTEAVMMNTPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAEEM----

3t6pA

0.49

0.43

12.55

1.64

CEthreader

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQYPHLLEQLLSTEDAVMMNTPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAEEMASDD

3t6pA

0.49

0.43

12.41

1.81

MUSTER

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQLLSDAVMMNTPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAEEMASDD

3t6pA

0.49

0.43

12.41

4.68

HHsearch

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLQLLSTEDAVMMNTPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAEEMASDD

1jd5A

0.32

0.17

5.18

1.64

FFAS-3D

-----------------NYFPQYPEYAIETARLRTFEAWPRNLKQKPHQLAEAGFFYTGVGDRVRCFSCGGGLMDWNDNDEPWEQHALWLSQCRFVKLMKG-------------------------------------------------------------QLYIDTVAAKPVLAEEKEES----------

3t6pA

0.47

0.39

11.23

1.20

EigenThreader

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPEDAVMMN-------TPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAE---EMA

3t6pA

0.49

0.43

12.55

2.28

CNFpred

-----------------------GSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFSCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVDEIQGRYPHLLEQL-EDAVMMNTPVVKSALEMGFNRDLVKQTVQSKILTTGENYKTVNDIVSALLNAEDEKREEEKEKQAEEMASDD

7abiU

0.07

0.05

2.20

0.83

DEthreader

---ENVP-AWEIFKKPFPFISQVQQLISMGRLSQLIQKFVLKCEFIELMILEATRF-------------------LFSQLMLYICLALPKLNLQ--FLTHDYLLRNFNFESYEIR--QDIEDSVSPVFQPIVAFTVVEA---FLITYVRGC--EI----ESRTF--RV--FLDPNQQKALETIRNLMNTDCV

(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	0.6688

(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	3t6pA	0.82	1.98	0.479	0.875	model1_3t6pA.pdb.gz
2	6mzbB	0.49	5.01	0.038	0.781	model1_6mzbB.pdb.gz
3	1jd5A	0.48	1.77	0.297	0.521	model1_1jd5A.pdb.gz
4	7jsnA	0.48	4.95	0.034	0.776	model1_7jsnA.pdb.gz
5	1oxqB	0.47	1.70	0.307	0.505	model1_1oxqB.pdb.gz
6	1tftA	0.40	2.79	0.257	0.464	model1_1tftA.pdb.gz
7	2vm5A	0.40	1.95	0.294	0.427	model1_2vm5A.pdb.gz
8	1c9qA	0.39	2.11	0.302	0.432	model1_1c9qA.pdb.gz
9	1qbhA	0.37	3.09	0.274	0.469	model1_1qbhA.pdb.gz
10	2knaA	0.27	1.82	0.221	0.292	model1_2knaA.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:0003824	0.98	catalytic activity
GO:0004869	0.95	cysteine-type endopeptidase inhibitor activity
GO:0004842	0.95	ubiquitin-protein transferase activity
GO:0043027	0.87	cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0008270	0.74	zinc ion binding
GO:0016874	0.72	ligase activity

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:0050794	1.00	regulation of cellular process
GO:0009987	0.97	cellular process
GO:0009966	0.97	regulation of signal transduction
GO:0044699	0.96	single-organism process
GO:0043066	0.96	negative regulation of apoptotic process
GO:0044763	0.95	single-organism cellular process
GO:0022607	0.95	cellular component assembly
GO:0090307	0.94	mitotic spindle assembly
GO:0043154	0.94	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:1990001	0.93	inhibition of cysteine-type endopeptidase activity involved in apoptotic process
GO:0050776	0.73	regulation of immune response
GO:0031347	0.73	regulation of defense response
GO:0045088	0.72	regulation of innate immune response
GO:1902531	0.67	regulation of intracellular signal transduction
GO:0048518	0.67	positive regulation of biological process
GO:0032101	0.67	regulation of response to external stimulus
GO:0070424	0.66	regulation of nucleotide-binding oligomerization domain containing signaling pathway
GO:0050727	0.66	regulation of inflammatory response
GO:0048522	0.66	positive regulation of cellular process
GO:0034121	0.64	regulation of toll-like receptor signaling pathway
GO:0009967	0.63	positive regulation of signal transduction
GO:0051291	0.59	protein heterooligomerization
GO:0051239	0.59	regulation of multicellular organismal process
GO:0043900	0.58	regulation of multi-organism process
GO:0043123	0.57	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0039535	0.57	regulation of RIG-I signaling pathway
GO:0038061	0.57	NIK/NF-kappaB signaling
GO:0035666	0.57	TRIF-dependent toll-like receptor signaling pathway
GO:0010803	0.57	regulation of tumor necrosis factor-mediated signaling pathway
GO:0042127	0.55	regulation of cell proliferation
GO:0060546	0.52	negative regulation of necroptotic 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:0043227	1.00	membrane-bounded organelle
GO:0005737	1.00	cytoplasm
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0005634	0.94	nucleus
GO:0044446	0.93	intracellular organelle part
GO:0044430	0.92	cytoskeletal part
GO:0005876	0.91	spindle microtubule
GO:0044444	0.57	cytoplasmic part

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	1ut9A	0.430	5.07	0.054	0.693	3.2.1.4	NA
2	0.060	1kl7A	0.429	5.95	0.067	0.828	4.2.3.1	NA
3	0.060	2occN	0.415	5.40	0.035	0.698	1.9.3.1	26
4	0.060	1mhyD	0.369	5.00	0.029	0.599	1.14.13.25	58
5	0.060	1gw6A	0.395	5.43	0.065	0.667	3.3.2.6	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	0.55	3f7gE	0.466	1.28	0.330	0.490	1.48	389	complex1.pdb.gz	63,64,65,72,73,74,75,76,80,85,89
	2	0.14	1jd4A	0.466	1.67	0.302	0.500	1.43	ZN	complex2.pdb.gz	66,69,86,93

	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.