D-I-TASSER Q13485-D2

D-I-TASSER results for Q13485-D2

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

Input Sequence in FASTA format

>Q13485 (127 residues)
ASTETYSTPALLAPSESNATSTANFPNIPVASTSQPASILGGSHSEGLLQIASGPQPGQQ
QNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMPPHPGHYWPVHNELA
FQPPISN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ASTETYSTPALLAPSESNATSTANFPNIPVASTSQPASILGGSHSEGLLQIASGPQPGQQQNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMPPHPGHYWPVHNELAFQPPISN
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9876567887789888998865557677778877888877787765511136798887666775678765568877666677777789988866677666789999898876654545467899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| ASTETYSTPALLAPSESNATSTANFPNIPVASTSQPASILGGSHSEGLLQIASGPQPGQQQNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMPPHPGHYWPVHNELAFQPPISN
Prediction	8656426434143447454443342442443454444444444444221403444444644542444444444444441444444524452455553434544434544433132346342444378
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
ASTETYSTPALLAPSESNATSTANFPNIPVASTSQPASILGGSHSEGLLQIASGPQPGQQQNGFTGQPATYHHNSTTTWTGSRTAPYTPNLPHHQNGHLQHHPPMPPHPGHYWPVHNELAFQPPISN

6ekvA

0.05

2.28

0.49

CEthreader

NRLQLTKTQAAFGISFPLFIEHFLKQALLSSQFISVDDIVADINTLTITNNKQIIFGKVENSDGKNVDSSLKPGKLKLSLQNNLIVLELFDLTWEQGRGVTGHFDFRQEYELTLESKSEKQIPILKV

5x1yB

0.07

2.87

0.55

EigenThreader

ERVEQSGEIKRVYVTVNGSRDSLNLSAAGVETGKNNEILIFGQTSNEKIYAAGDVTLGPQFVYVAAYEGGII-----TDNAIGGLNKKIDAVPRAIVNRETTGGLTVEDLTETLAPYLTMAEGLKLA

3o2zI

0.12

0.10

3.62

0.43

FFAS-3D

-VFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMT-----------SKPAGFMKKLRAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSYNGKAFNQVEIRHYLGEFSITYTPVRH------

7jjvA

0.11

0.10

3.68

1.23

SPARKS-K

-------MQCDGLDGADGTSNGQAGASGLAGGPN----CNGGKGGKGATAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAGKPGGAPGAGGAGTPAGSAGSPG

1cq0A

0.18

0.04

1.28

0.05

CNFpred

--------------FSGPPGLQGRLQRLLQASGNHAAGILTM-------------------------------------------------------------------------------------

6vinA

0.05

2.18

0.83

DEthreader

LKRVGQALYGCCW-------VSTSGCGEHLGGHTTESMC--VGYMFVL-VHAGAGKAKEYKHVCKRAKAKLLATDAVTALLETNACDASIMD--GKSLNFGAVGLSGIKNPSVALLGPPCLWAGIPS

5isuA

0.07

0.06

2.67

0.71

MapAlign

----EVINPNYASDRVTLTIQQAVYAPLFWEVDGKPALALDISDDNLTYTVKLKDGLTWHDGKPLRGNFVFDDKPVKVEAVDDTTVKFTLPKNPIGSGPYKFVEYKTGEYVSLERFNDYLDKVTFRI

2nbiA2

0.13

0.11

3.80

0.82

MUSTER

---QPSSQPTGPQPSSQPSECADVLELCPYDTCFLPFDDSSRPPD-----CTDPSVNRPDCDKLSTAIDFTCPTCCPTQCRPDNPMFSPSP---DGSPPVCSPTMMPSPL---PSPTE---------

2k49A

0.13

0.09

3.01

0.61

HHsearch

LTSELYTGKSGAMNGIENSPIEARYAKEVAKND-KPYFNLKA------------------ANHQIITSQMYS-STAARDNGISVMENGKTTTIK--DLTLEHHHHH-H-------------------

5fvmC

0.02

1.64

0.48

CEthreader

IRSNNPNPVSSFEGHKGSIAFQQENRWMVSSSEDGTIKVWDVRSPSVQRNYKHNAPVNEVAIHPNQGELISCDQDGNIRIWDLGENQCTNQLTPEDNTPLQSLSVASDGSMLVAGNNKGNCYVWRMP

(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	0.4988

(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	2xr9A2	0.53	4.70	0.080	0.945	model1_2xr9A2.pdb.gz
2	6c01A3	0.53	4.59	0.024	0.937	model1_6c01A3.pdb.gz
3	6y5mA	0.53	4.76	0.072	0.937	model1_6y5mA.pdb.gz
4	4b56A	0.53	4.72	0.040	0.945	model1_4b56A.pdb.gz
5	5gz4A	0.53	4.77	0.056	0.937	model1_5gz4A.pdb.gz
6	1ei6A	0.39	5.57	0.050	0.819	model1_1ei6A.pdb.gz
7	3szyA	0.38	5.76	0.050	0.843	model1_3szyA.pdb.gz
8	1p49A	0.38	4.96	0.058	0.701	model1_1p49A.pdb.gz
9	1ujmA	0.37	5.91	0.048	0.803	model1_1ujmA.pdb.gz
10	1n2lA1	0.35	5.46	0.046	0.701	model1_1n2lA1.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:0003677	1.00	DNA binding
GO:0046332	0.91	SMAD binding
GO:0046983	0.71	protein dimerization activity
GO:0043565	0.71	sequence-specific DNA binding
GO:0000975	0.71	regulatory region DNA binding
GO:0003700	0.64	transcription factor activity, sequence-specific DNA binding
GO:0044212	0.63	transcription regulatory region DNA binding
GO:0004871	0.63	signal transducer activity
GO:0042803	0.62	protein homodimerization activity
GO:0005057	0.62	receptor signaling protein activity
GO:0000981	0.62	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000977	0.62	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0070412	0.61	R-SMAD binding
GO:0070411	0.61	I-SMAD binding
GO:0030616	0.61	transforming growth factor beta receptor, common-partner cytoplasmic mediator activity
GO:0001077	0.61	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0000988	0.61	transcription factor activity, protein binding
GO:0000978	0.61	RNA polymerase II core promoter proximal region sequence-specific DNA 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:0065007	0.95	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0080090	0.93	regulation of primary metabolic process
GO:0060255	0.93	regulation of macromolecule metabolic process
GO:0051246	0.92	regulation of protein metabolic process
GO:0048519	0.92	negative regulation of biological process
GO:0051248	0.91	negative regulation of protein metabolic process
GO:0009987	0.80	cellular process
GO:0044699	0.78	single-organism process
GO:0050794	0.74	regulation of cellular process
GO:0044707	0.71	single-multicellular organism process
GO:0016043	0.71	cellular component organization
GO:0006461	0.70	protein complex assembly
GO:0048518	0.68	positive regulation of biological process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0048522	0.66	positive regulation of cellular process
GO:0044763	0.66	single-organism cellular process
GO:0032502	0.66	developmental process
GO:2000112	0.65	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.65	regulation of nitrogen compound metabolic process
GO:0044767	0.65	single-organism developmental process
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0010468	0.65	regulation of gene expression
GO:0051173	0.64	positive regulation of nitrogen compound metabolic process
GO:0050896	0.64	response to stimulus
GO:0048856	0.64	anatomical structure development
GO:0048583	0.64	regulation of response to stimulus
GO:0048523	0.64	negative regulation of cellular process
GO:0007165	0.64	signal transduction
GO:0006355	0.64	regulation of transcription, DNA-templated
GO:0051239	0.63	regulation of multicellular organismal process
GO:0045893	0.63	positive regulation of transcription, DNA-templated
GO:0031399	0.63	regulation of protein modification process
GO:0023051	0.63	regulation of signaling
GO:0019220	0.63	regulation of phosphate metabolic process
GO:0010646	0.63	regulation of cell communication
GO:0010033	0.63	response to organic substance
GO:2000113	0.62	negative regulation of cellular macromolecule biosynthetic process
GO:2000026	0.62	regulation of multicellular organismal development
GO:1902531	0.62	regulation of intracellular signal transduction
GO:0070848	0.62	response to growth factor
GO:0065008	0.62	regulation of biological quality
GO:0051241	0.62	negative regulation of multicellular organismal process
GO:0051240	0.62	positive regulation of multicellular organismal process
GO:0051172	0.62	negative regulation of nitrogen compound metabolic process
GO:0045944	0.62	positive regulation of transcription from RNA polymerase II promoter
GO:0045595	0.62	regulation of cell differentiation
GO:0035556	0.62	intracellular signal transduction
GO:0032269	0.62	negative regulation of cellular protein metabolic process
GO:0022603	0.62	regulation of anatomical structure morphogenesis
GO:0010629	0.62	negative regulation of gene expression
GO:0009968	0.62	negative regulation of signal transduction
GO:0009967	0.62	positive regulation of signal transduction
GO:0009719	0.62	response to endogenous stimulus
GO:0009653	0.62	anatomical structure morphogenesis
GO:0007179	0.62	transforming growth factor beta receptor signaling pathway
GO:0006950	0.62	response to stress
GO:0001934	0.62	positive regulation of protein phosphorylation
GO:0001817	0.62	regulation of cytokine production
GO:2000617	0.61	positive regulation of histone H3-K9 acetylation
GO:0071559	0.61	response to transforming growth factor beta
GO:0070373	0.61	negative regulation of ERK1 and ERK2 cascade
GO:0070102	0.61	interleukin-6-mediated signaling pathway
GO:0060412	0.61	ventricular septum morphogenesis
GO:0060395	0.61	SMAD protein signal transduction
GO:0060391	0.61	positive regulation of SMAD protein import into nucleus
GO:0060021	0.61	palate development
GO:0051571	0.61	positive regulation of histone H3-K4 methylation
GO:0032909	0.61	regulation of transforming growth factor beta2 production
GO:0030513	0.61	positive regulation of BMP signaling pathway
GO:0030511	0.61	positive regulation of transforming growth factor beta receptor signaling pathway
GO:0030509	0.61	BMP signaling pathway
GO:0030308	0.61	negative regulation of cell growth
GO:0010862	0.61	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0010718	0.61	positive regulation of epithelial to mesenchymal transition
GO:0010614	0.61	negative regulation of cardiac muscle hypertrophy
GO:0007183	0.61	SMAD protein complex assembly
GO:0006879	0.61	cellular iron ion homeostasis
GO:0003220	0.61	left ventricular cardiac muscle tissue morphogenesis
GO:0001666	0.61	response to hypoxia
GO:0000122	0.61	negative regulation of transcription from RNA polymerase II promoter

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:0043234	1.00	protein complex
GO:0005634	1.00	nucleus
GO:0005737	0.91	cytoplasm
GO:0071141	0.70	SMAD protein complex
GO:0044446	0.68	intracellular organelle part
GO:0044428	0.65	nuclear part
GO:0005667	0.64	transcription factor complex
GO:0000790	0.62	nuclear chromatin
GO:0032444	0.61	activin responsive factor complex

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	1g8tA	0.481	4.66	0.078	0.858	3.1.30.2	NA
2	0.060	1f1sA	0.474	4.73	0.033	0.890	4.2.2.1	NA
3	0.060	1i8qA	0.470	4.86	0.024	0.905	4.2.2.1	NA
4	0.060	1y9mA	0.477	4.92	0.066	0.913	3.2.1.80	NA
5	0.060	3c75J	0.463	5.05	0.059	0.890	1.4.99.3	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	2xl3B	0.497	4.83	0.033	0.898	0.13	III	complex1.pdb.gz	53,54,55,67
	2	0.01	1by5A	0.448	5.15	0.076	0.866	0.11	III	complex2.pdb.gz	57,67,79

	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.