D-I-TASSER Q53H64-D1

D-I-TASSER results for Q53H64-D1

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

Input Sequence in FASTA format

>Q53H64 (114 residues)
MAEPEQDIGEKPAVRIQNPKENDFIEIELKRQELSYQNLLNVSCCELGIKPERVEKIRKL
PNTLLRKDKDIRRLRDFQEVELILMKNGSSRLTEYVPSLTERPCYDSKAAKMTY

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MAEPEQDIGEKPAVRIQNPKENDFIEIELKRQELSYQNLLNVSCCELGIKPERVEKIRKLPNTLLRKDKDIRRLRDFQEVELILMKNGSSRLTEYVPSLTERPCYDSKAAKMTY
Prediction	CCCCHHHHCCCCSSSSCCCCCCCSSSSSSCHHHCCHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHCCHHHHHHHHCCCSSSSSSSCCCCCCHHHHCCCCCCCCCCHHHHHHCCC
Confidence	986022111264178617999974899726433679999999999969999999999858511201205899870473799999627886234405666778640123443169
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MAEPEQDIGEKPAVRIQNPKENDFIEIELKRQELSYQNLLNVSCCELGIKPERVEKIRKLPNTLLRKDKDIRRLRDFQEVELILMKNGSSRLTEYVPSLTERPCYDSKAAKMTY
Prediction	755366536542413145374421030315456031430041006417144720540351353315446215415615402000233555423532442374431544365357
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHCCCCSSSSCCCCCCCSSSSSSCHHHCCHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHCCHHHHHHHHCCCSSSSSSSCCCCCCHHHHCCCCCCCCCCHHHHHHCCC
MAEPEQDIGEKPAVRIQNPKENDFIEIELKRQELSYQNLLNVSCCELGIKPERVEKIRKLPNTLLRKDKDIRRLRDFQEVELILMKNGSSRLTEYVPSLTERPCYDSKAAKMTY

1v5oA

0.16

0.14

4.66

0.46

CEthreader

--GSSGSSGMLITVYCVRRDLTETFSLQVNP-DFELSNFRVLCELESGVPAEEA-QIVYMEQLLTDDHCSLGGLKDGDMVVLLQKDNVGLRTPGRTPSGPSSG-----------

2dzmA

0.09

0.07

2.72

0.67

EigenThreader

--GSSGSSGRMLDFRVEYR--DRNVDVVLEDT-CTVGEIKQILENELQIPV-SKMLLKGWKTGDVED---STVLKSLHLLYVLTPLPPPSSSSHAGALQESLN-----------

5x0wB

0.13

0.09

3.06

0.48

FFAS-3D

-----GPIRLQVTLEDAASASSAHVALQVHPHC-TVAALQEQVFSELGFPPAVQRWVCLCVPERSLASYGVR--QDGDPAFLYLLSA---------------------------

6b4aA

0.10

0.08

2.94

0.88

SPARKS-K

----IPAPRLMWLYRNGDKHDDG-TPFFVRPYIKSMESLYQQITKEITPIAGPV---RRIFDQNFRVITDLDDIVDGAKYLCTSGEPPAAYDRLEKFLSE--------------

4pyuA

0.10

0.06

2.27

0.62

CNFpred

---------HMIEVVCNDR--GKKVRVKCNT-DDTIGDLKKLIAAQTGTRWNKIVLKK---YTIFKDHVSLGEIHDGMNLELYYQ-----------------------------

4q2jA

0.14

0.11

3.91

1.00

DEthreader

--GP-GSGTMLPVFCVVEHKEEHAEFVLVRKDMLFNQ-LIEMALLLGYSHAAQA-KGLIQVGWYVTDATVADMLQDYVTLKIQLHSC-PKLLPQWSHSAAK-------------

5fwiC2

0.11

3.76

0.66

MapAlign

---FDKDHDVMLFLKMYDPKTRSLNYCHIYTPICKIRDLLPVMCDRAGFIQTSLI-LYEETERIQDYDVSLDKAMDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVD-----

5c1zA

0.16

0.14

4.66

0.56

MUSTER

---------MIVFVRFNSSH---GFPVEVDSD-TSIFQLKEVVAKRQGVPADQLRVI--FAGKELRNDWTVQNCDQQSIVHIVQRPWRKGQEMNATNSFYKGPCQRVQPGKLRV

2l76A

0.17

0.12

4.03

0.58

HHsearch

VEGPETPRLFPLKIRCR---A-DLVRLPLRMSE-PLQSVVDHMATHLGVSPSRILLLF--GETELSPTARTLKLGVADIIDCVVLTSS--------------------------

1t0yA

0.11

0.08

2.88

0.41

CEthreader

-------MTEVYDLEITTNATDFPMEKKYPA-GMSLNDLKKKLELVVGTTVDSMRIQLFDGDELTDGAKSLKDLGVRDGYRIHAVDVTGGNED---------------------

(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	0.6244

(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 AttentionPotential, 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	5fwiC2	0.56	3.14	0.088	0.772	model1_5fwiC2.pdb.gz
2	2ylmA	0.56	3.17	0.096	0.772	model1_2ylmA.pdb.gz
3	2i1kA	0.55	3.84	0.090	0.833	model1_2i1kA.pdb.gz
4	6ts8A	0.55	4.11	0.056	0.860	model1_6ts8A.pdb.gz
5	5lf9A	0.54	3.97	0.067	0.798	model1_5lf9A.pdb.gz
6	4q2jA	0.54	3.94	0.124	0.842	model1_4q2jA.pdb.gz
7	3qa8A	0.54	3.51	0.078	0.781	model1_3qa8A.pdb.gz
8	5b83A	0.54	3.27	0.083	0.746	model1_5b83A.pdb.gz
9	2he7A1	0.49	3.22	0.072	0.711	model1_2he7A1.pdb.gz
10	3tuoA	0.48	3.27	0.100	0.702	model1_3tuoA.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:0051087	0.07	chaperone binding
GO:0019787	0.07	ubiquitin-like protein transferase activity
GO:0003735	0.07	structural constituent of ribosome

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:1901796	0.07	regulation of signal transduction by p53 class mediator
GO:0098792	0.07	xenophagy
GO:0090263	0.07	positive regulation of canonical Wnt signaling pathway
GO:0090090	0.07	negative regulation of canonical Wnt signaling pathway
GO:0075733	0.07	intracellular transport of virus
GO:0071816	0.07	tail-anchored membrane protein insertion into ER membrane
GO:0070987	0.07	error-free translesion synthesis
GO:0070911	0.07	global genome nucleotide-excision repair
GO:0070423	0.07	nucleotide-binding oligomerization domain containing signaling pathway
GO:0061418	0.07	regulation of transcription from RNA polymerase II promoter in response to hypoxia
GO:0060071	0.07	Wnt signaling pathway, planar cell polarity pathway
GO:0051437	0.07	positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
GO:0051436	0.07	negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
GO:0051092	0.07	positive regulation of NF-kappaB transcription factor activity
GO:0050852	0.07	T cell receptor signaling pathway
GO:0045944	0.07	positive regulation of transcription from RNA polymerase II promoter
GO:0045742	0.07	positive regulation of epidermal growth factor receptor signaling pathway
GO:0043488	0.07	regulation of mRNA stability
GO:0043123	0.07	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043066	0.07	negative regulation of apoptotic process
GO:0043065	0.07	positive regulation of apoptotic process
GO:0042769	0.07	DNA damage response, detection of DNA damage
GO:0042276	0.07	error-prone translesion synthesis
GO:0042059	0.07	negative regulation of epidermal growth factor receptor signaling pathway
GO:0038128	0.07	ERBB2 signaling pathway
GO:0038095	0.07	Fc-epsilon receptor signaling pathway
GO:0038061	0.07	NIK/NF-kappaB signaling
GO:0036297	0.07	interstrand cross-link repair
GO:0035666	0.07	TRIF-dependent toll-like receptor signaling pathway
GO:0034220	0.07	ion transmembrane transport
GO:0032480	0.07	negative regulation of type I interferon production
GO:0031145	0.07	anaphase-promoting complex-dependent catabolic process
GO:0030512	0.07	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0019083	0.07	viral transcription
GO:0019068	0.07	virion assembly
GO:0016197	0.07	endosomal transport
GO:0010939	0.07	regulation of necrotic cell death
GO:0010803	0.07	regulation of tumor necrosis factor-mediated signaling pathway
GO:0008543	0.07	fibroblast growth factor receptor signaling pathway
GO:0007254	0.07	JNK cascade
GO:0007219	0.07	Notch signaling pathway
GO:0006977	0.07	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0006614	0.07	SRP-dependent cotranslational protein targeting to membrane
GO:0006413	0.07	translational initiation
GO:0006364	0.07	rRNA processing
GO:0006297	0.07	nucleotide-excision repair, DNA gap filling
GO:0006296	0.07	nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0006294	0.07	nucleotide-excision repair, preincision complex assembly
GO:0006283	0.07	transcription-coupled nucleotide-excision repair
GO:0005978	0.07	glycogen biosynthetic process
GO:0002755	0.07	MyD88-dependent toll-like receptor signaling pathway
GO:0002230	0.07	positive regulation of defense response to virus by host
GO:0002223	0.07	stimulatory C-type lectin receptor signaling pathway
GO:0000717	0.07	nucleotide-excision repair, DNA duplex unwinding
GO:0000715	0.07	nucleotide-excision repair, DNA damage recognition
GO:0000209	0.07	protein polyubiquitination
GO:0000187	0.07	activation of MAPK activity
GO:0000184	0.07	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0000122	0.07	negative regulation of transcription from RNA polymerase II promoter
GO:0000086	0.07	G2/M transition of mitotic cell cycle

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	0.97	intracellular part
GO:0043229	0.94	intracellular organelle
GO:0005737	0.89	cytoplasm
GO:0043227	0.81	membrane-bounded organelle
GO:0044444	0.75	cytoplasmic part
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0016020	0.75	membrane
GO:0044446	0.72	intracellular organelle part
GO:0005634	0.72	nucleus
GO:0005886	0.67	plasma membrane
GO:0044428	0.61	nuclear part
GO:0005829	0.56	cytosol
GO:0043232	0.50	intracellular non-membrane-bounded organelle

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	0.066	2nptD	0.470	2.94	0.066	0.632	2.7.11.25	NA
2	0.060	1yewA	0.465	4.62	0.040	0.833	3.4.21.-	NA
3	0.060	1viuB	0.483	3.47	0.124	0.675	3.6.1.-	58
4	0.060	1q33A	0.497	3.44	0.073	0.763	3.6.1.13	NA
5	0.060	2j0lA	0.316	5.12	0.065	0.667	2.7.10.2	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:

No Binding sites was predicted

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

	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.