D-I-TASSER P49763-D1

D-I-TASSER results for P49763-D1

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

Input Sequence in FASTA format

>P49763 (221 residues)
MPVMRLFPCFLQLLAGLALPAVPPQQWALSAGNGSSEVEVVPFQEVWGRSYCRALERLVD
VVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVEL
TFSQHVRCECRHSPGRQSPDMPGDFRADAPSFLPPRRSLPMLFRMEWGCALTGSQSAVWP
SSPVPEEIPRMHPGRNGKKQQRKPLREKMKPERCGDAVPRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPVMRLFPCFLQLLAGLALPAVPPQQWALSAGNGSSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRHSPGRQSPDMPGDFRADAPSFLPPRRSLPMLFRMEWGCALTGSQSAVWPSSPVPEEIPRMHPGRNGKKQQRKPLREKMKPERCGDAVPRR
Prediction	CCCCHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCSSSHHHHHHCCCCSSSSSSSSCCCCCCCCCCCSSCCCSSSSSSCCCCCCCCCSSSSSCCSSSSSSSSSSSSSCCCCCSSSSSSSSCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCCHHHHHCHHHHCCCCCCC
Confidence	97414799999999873378887122244555677552202113332125213665899753237988762234871786530367799861787111389999999986168872699996203431015168866655556555578852588766765453221235678998731787654775765689887653255213201366536787899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPVMRLFPCFLQLLAGLALPAVPPQQWALSAGNGSSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRHSPGRQSPDMPGDFRADAPSFLPPRRSLPMLFRMEWGCALTGSQSAVWPSSPVPEEIPRMHPGRNGKKQQRKPLREKMKPERCGDAVPRR
Prediction	64314123010312120213234354442447546253423424531551304225220503553475352222032040320000044642414435444243422414366554314030430450525135655657446645573362426764152336364545461564330266404031574454653554645536551446406544678
	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                 120                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCSSSHHHHHHCCCCSSSSSSSSCCCCCCCCCCCSSCCCSSSSSSCCCCCCCCCSSSSSCCSSSSSSSSSSSSSCCCCCSSSSSSSSCCCCCCSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCCSSSCCCCCCCCCCCCCCCCCHHHHHCHHHHCCCCCCC
MPVMRLFPCFLQLLAGLALPAVPPQQWALSAGNGSSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRHSPGRQSPDMPGDFRADAPSFLPPRRSLPMLFRMEWGCALTGSQSAVWPSSPVPEEIPRMHPGRNGKKQQRKPLREKMKPERCGDAVPRR

1fzvA

0.97

0.44

12.30

1.40

FFAS-3D

----------------------------------SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLR---------------------------------------------------------------------------------------

1bj1V

0.51

0.22

6.29

2.29

SPARKS-K

---------------------------------------VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK----------------------------------------------------------------------------------------

4epaA

0.07

0.06

2.46

0.80

EigenThreader

DQPW---------------EGQDAYVGWNDIKGRKLSTFPSGSLIVNRTVDVFGLYRQNTRAYDPTPYLSSTGYTTAETLAAYSDLTTDRFDIGGGVRFSHDKSSTQYHGSLGN--PGKSNDDQVLGQLSAGYLTDDGYSGYNIVPTAGLDAKPFVAQLQTLSN-------AGFAPGWNDSELYHGNRVPFVVIDTRYGALPPHY----FDGDNQLRQGTY

1fzvA

0.97

0.44

12.30

2.44

CNFpred

----------------------------------SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLR---------------------------------------------------------------------------------------

4o9xA

0.04

0.03

1.61

0.67

DEthreader

-------------------GPDGMASGAGAPKSSDGQPFPIYARGFGYVEQALTKNWYATGLPPFLTPEDSRYNRLKGQLLRSELYGKHV-PYTVT--EFRSQVRR-QHT-DSRYPVLWSSVVESRNYHYEIDRRPINLYPDTLLSTWFTVNE----TAAEV--QTPTVIDFDP------------V---SLYQYDRGGNLVSNATEDPAQV---------

1fzvA

0.97

0.44

12.30

1.67

MUSTER

----------------------------------SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLR---------------------------------------------------------------------------------------

3j0fI

0.07

0.06

2.49

0.76

MapAlign

---------------------SPYLGTCSYCHHTVPCFSPVKIEQVWDEADDNTIRIQAQFGYDQSGAASANKYRKGYFLLAKCFVGPPVHGKKIPCTPRPHAYGKVYAVSTRTEITGCTYKSDIPSTCMVPVISLQLDTDHLTLLEPTTEWIVGKTVRVDRDGLEYIWGNHEPVRVYAQESAPGDPHGWPHEIVQHYYHRHPVYTILAVASATVAMMIG-

1fzvA

0.97

0.44

12.30

3.52

HHsearch

----------------------------------SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLR---------------------------------------------------------------------------------------

1bj1V

0.51

0.22

6.29

1.38

FFAS-3D

---------------------------------------VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK----------------------------------------------------------------------------------------

1fzvA

0.97

0.44

12.30

2.28

SPARKS-K

----------------------------------SSEVEVVPFQEVWGRSYCRALERLVDVVSEYPSEVEHMFSPSCVSLLRCTGCCGDENLHCVPVETANVTMQLLKIRSGDRPSYVELTFSQHVRCECRPLR---------------------------------------------------------------------------------------

(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	0.5784

(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	2uvcG	0.46	5.43	0.062	0.778	model1_2uvcG.pdb.gz
2	3hmjG	0.46	5.70	0.070	0.792	model1_3hmjG.pdb.gz
3	6n8eA	0.43	6.05	0.069	0.760	model1_6n8eA.pdb.gz
4	6ysgA	0.43	5.93	0.036	0.778	model1_6ysgA.pdb.gz
5	4ecnA	0.42	5.57	0.037	0.715	model1_4ecnA.pdb.gz
6	4bedB	0.42	6.20	0.046	0.756	model1_4bedB.pdb.gz
7	5uowB	0.42	5.77	0.084	0.729	model1_5uowB.pdb.gz
8	4xqkA	0.42	5.86	0.024	0.747	model1_4xqkA.pdb.gz
9	6um1A	0.42	6.09	0.041	0.765	model1_6um1A.pdb.gz
10	5a22A	0.41	5.77	0.034	0.679	model1_5a22A.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:0004871	0.99	signal transducer activity
GO:0005102	0.94	receptor binding
GO:0070851	0.76	growth factor receptor binding
GO:0008083	0.71	growth factor activity
GO:0005008	0.68	hepatocyte growth factor-activated receptor activity
GO:0005172	0.55	vascular endothelial growth factor receptor 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:0050794	0.96	regulation of cellular process
GO:0044699	0.84	single-organism process
GO:0048518	0.82	positive regulation of biological process
GO:0048523	0.81	negative regulation of cellular process
GO:0048522	0.81	positive regulation of cellular process
GO:0008284	0.80	positive regulation of cell proliferation
GO:0048583	0.79	regulation of response to stimulus
GO:0032502	0.76	developmental process
GO:0080090	0.70	regulation of primary metabolic process
GO:0060255	0.70	regulation of macromolecule metabolic process
GO:0043069	0.70	negative regulation of programmed cell death
GO:0031323	0.70	regulation of cellular metabolic process
GO:0032268	0.68	regulation of cellular protein metabolic process
GO:0044767	0.67	single-organism developmental process
GO:0001934	0.64	positive regulation of protein phosphorylation
GO:0080134	0.63	regulation of response to stress
GO:0048585	0.61	negative regulation of response to stimulus
GO:0080135	0.60	regulation of cellular response to stress
GO:1901299	0.59	negative regulation of hydrogen peroxide-mediated programmed cell death
GO:0048646	0.57	anatomical structure formation involved in morphogenesis
GO:0007169	0.57	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0030334	0.55	regulation of cell migration
GO:0009987	0.55	cellular process
GO:0051239	0.53	regulation of multicellular organismal process
GO:0030335	0.53	positive regulation of cell migration
GO:0050793	0.51	regulation of developmental process
GO:0050679	0.51	positive regulation of epithelial cell proliferation
GO:0051240	0.50	positive regulation of multicellular organismal process
GO:0001938	0.50	positive regulation of endothelial cell proliferation

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:0044464	0.94	cell part
GO:0005615	0.80	extracellular space
GO:0044424	0.62	intracellular part
GO:0016020	0.61	membrane
GO:0098590	0.60	plasma membrane region
GO:0009925	0.59	basal plasma membrane
GO:0043227	0.55	membrane-bounded organelle
GO:0043231	0.53	intracellular 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	0.060	2pffD	0.357	6.78	0.034	0.733	2.3.1.86	NA
2	0.060	1rw9A	0.405	5.84	0.024	0.701	4.2.2.5	NA
3	0.060	2g25A	0.347	6.12	0.037	0.629	1.2.4.1	NA
4	0.060	1ordA	0.364	5.61	0.032	0.602	4.1.1.17	NA
5	0.060	1j0mA	0.364	6.48	0.035	0.724	4.2.2.12	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	3cmvG	0.378	5.82	0.029	0.665	0.20	ANP	complex1.pdb.gz	84,85,86
2	0.01	3cmvA	0.354	6.26	0.039	0.656	0.12	ANP	complex2.pdb.gz	48,49,53,54
3	0.01	3cmvF	0.372	5.93	0.033	0.661	0.14	ANP	complex3.pdb.gz	47,48,49,85
4	0.01	2vkzI	0.459	5.72	0.070	0.792	0.13	FMN	complex4.pdb.gz	44,48,56,84,88
5	0.01	1fw6A	0.396	5.67	0.056	0.674	0.20	QNA	complex5.pdb.gz	82,83,84,88,89,129,130
6	0.01	3cmvE	0.336	5.91	0.052	0.597	0.20	ANP	complex6.pdb.gz	85,86,87
7	0.01	1ewqB	0.331	6.25	0.022	0.624	0.19	QNA	complex7.pdb.gz	53,88,90,133
8	0.01	3cmvD	0.381	5.84	0.034	0.674	0.13	ANP	complex8.pdb.gz	49,50,51,52,53
9	0.01	2uvaI	0.411	5.79	0.077	0.720	0.15	FMN	complex9.pdb.gz	85,88,89,130
10	0.01	3cmvA	0.354	6.26	0.039	0.656	0.11	ANP	complex10.pdb.gz	86,87,88

	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.