D-I-TASSER P28749-D3

D-I-TASSER results for P28749-D3

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

Input Sequence in FASTA format

>P28749 (258 residues)
GNVQGHLPLMPMSPLMHPRVKEVRTDSGSLRRDMQPLSPISVHERYSSPTAGSAKRRLFG
EDPPKEMLMDKIITEGTKLKIAPSSSITAENVSILPGQTLLTMATAPVTGTTGHKVTIPL
HGVANDAGEITLIPLSMNTNQESKVKSPVSLTAHSLIGASPKQTNLTKAQEVHSTGINRP
KRTSGLTPRSALLYKFNGSPSKSLKDINNMIRQGEQRTKKRVIAIDSDAESPAKRVCQEN
DDVLLKRLQDVVSERANH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| GNVQGHLPLMPMSPLMHPRVKEVRTDSGSLRRDMQPLSPISVHERYSSPTAGSAKRRLFGEDPPKEMLMDKIITEGTKLKIAPSSSITAENVSILPGQTLLTMATAPVTGTTGHKVTIPLHGVANDAGEITLIPLSMNTNQESKVKSPVSLTAHSLIGASPKQTNLTKAQEVHSTGINRPKRTSGLTPRSALLYKFNGSPSKSLKDINNMIRQGEQRTKKRVIAIDSDAESPAKRVCQENDDVLLKRLQDVVSERANH
Prediction	CCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCHHHHHHHHHHHHCCCCCCCSSSSCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC
Confidence	986676777778998871233332156777777778999755778889999976555567899877787886799875444666778887788898765444554442357895356526763247775144467616898777678898886656788998767766676655444788889888877533899717951228999888764366444225751689888532335456448999999998875129
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| GNVQGHLPLMPMSPLMHPRVKEVRTDSGSLRRDMQPLSPISVHERYSSPTAGSAKRRLFGEDPPKEMLMDKIITEGTKLKIAPSSSITAENVSILPGQTLLTMATAPVTGTTGHKVTIPLHGVANDAGEITLIPLSMNTNQESKVKSPVSLTAHSLIGASPKQTNLTKAQEVHSTGINRPKRTSGLTPRSALLYKFNGSPSKSLKDINNMIRQGEQRTKKRVIAIDSDAESPAKRVCQENDDVLLKRLQDVVSERANH
Prediction	864422121123333324305403564452447244433443445354245444444114555357554654347444444343544655445344353334434442436454412121402326544122121324365545454344143442445435425446356434432444554432443431202035234540640252164274444320011356564343432565241014204403544678
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCSSSSSSSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSCCCCCHHHHHHHHHHHHCCCCCCCSSSSCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC
GNVQGHLPLMPMSPLMHPRVKEVRTDSGSLRRDMQPLSPISVHERYSSPTAGSAKRRLFGEDPPKEMLMDKIITEGTKLKIAPSSSITAENVSILPGQTLLTMATAPVTGTTGHKVTIPLHGVANDAGEITLIPLSMNTNQESKVKSPVSLTAHSLIGASPKQTNLTKAQEVHSTGINRPKRTSGLTPRSALLYKFNGSPSKSLKDINNMIRQGEQRTKKRVIAIDSDAESPAKRVCQENDDVLLKRLQDVVSERANH

1vt4I

0.06

2.67

1.05

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2azeC

0.29

0.05

1.42

1.01

HHsearch

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRILVSIGESTSEKFQKINQMVCNSD-RVLKRSAE--G--SNPPKPL----------------------

1vt4I

0.06

2.67

0.74

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

7c7lA

0.09

0.08

3.12

0.52

EigenThreader

KEACSKHLKVTTQVERNACLFCKARKLDDKFYQKLRGQFPDAIELYYEIFIKGKGIANASSVEHYLSDVCYTRAAELFKN--AAIASGLRSKIKSNFRIPLVK------QKGGQY----TGFSNHNSDFIIKIPFGFEQVQKSPKP--ISLTQRRKRNKGWSKDEGTEAEIKKVMNGDYQTGVKSPLNAFSRYSI----SDNDLFHFNKKMFARRRILLKKN--RHKRAGHGAKNKLKPITILTEKSERFRKKLIERW

1zboB

0.12

0.09

3.26

0.39

FFAS-3D

-----EIPLFPLSNALFPAGV----------------LRLRVEIRYLDVRRCIADGSEFG--VVVLEQGTEVRRPDGREVLARAGTARIDHWEAPPALLELACT--------GTGRFRLHACTQGKYGLWTGQAEPVPDDAPLEVPPELARSASALGRLIARLQREGVPPHIPAAPFR----------------------LDDCGWVADRWAELSLPPADK------------ARLLLLPPLDRLREIDAVL-AADGH

6zu9p

0.07

0.06

2.62

0.77

SPARKS-K

KSPYLKWPLVRWSYDKYDSLIVHDATKNFMPLEAKALKPSGIRDFSFAPDEPSVLLAYWTPETNNSACTATVPRGRVLKTVNLVQVSNVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPFGWEPISVHEVADMNYAIPTIRFYAPETKEKTDVIKRWSLVKEIPKTFAN---TVSWSPAGRFVVVGAL------------VGPNMRRSDLQFYDMDYPGEKNINASLPTYSAATNITWDPSGRYVTAW

2l82A

0.22

0.05

1.47

0.50

CNFpred

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SQIFVVFSSD-PEILKEIVREIKRQ----GVRVVLLYSD----------QDEKRRRERLEEFEKQGVDV

7d5cA

0.03

0.02

1.41

0.83

DEthreader

----SLCVNAFYILLTGIVHNADACLKESVLPNAIGYVKDADKLIIKLTGNLLLASQ---------------L-RSVPAWFVR--------------GTPIPLW-VSDD----FEEVVCVGSI-TD--LHRIDLTIPSQGKGDLKRIE-EV-F-DCWFESSMPYAFDERVPAN-HEMGQKLTVVPKLLNFIDEL----WYIFNRRLKALNSL-FD-A--LFTFVAMAPFTPFLSESYGSVFLSYPV-VKKEYFDEA--

2pffB

0.07

2.88

1.03

MapAlign

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGATQFTQPALTLMEKAAFEDLKS

5az4A

0.11

0.10

3.77

0.66

MUSTER

AKGQG-LNLRDGQGIWVSYADATYSTNKVGVNAFDPNLQQNQTAAFWGTANQKVNLDI-IQNADIQSIDDAIAYINTFTAPTDTRDGTGVKAVKNKDGSGIDFVNDNADGTTDNMKNINLVVANTNTAGELWNAVWNNNNQTNNGNGQAGTPTINKNGSSLWTATNITFTPQPPQAATNVQLTGGLNAQIITAHKYIYSSN------------PVDIGPMYNPDGGPAFQPGANATTRPTEPGSAAYWDAVNGGLLNT

(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	0.4236

(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	4el8A	0.44	6.05	0.044	0.740	model1_4el8A.pdb.gz
2	3wkyA	0.44	6.00	0.030	0.740	model1_3wkyA.pdb.gz
3	3hhsB	0.44	5.90	0.032	0.736	model1_3hhsB.pdb.gz
4	4yzwA	0.44	5.94	0.044	0.733	model1_4yzwA.pdb.gz
5	5yy2A	0.44	6.00	0.049	0.736	model1_5yy2A.pdb.gz
6	7c6oA	0.44	6.09	0.056	0.744	model1_7c6oA.pdb.gz
7	3hhsA	0.43	6.21	0.053	0.748	model1_3hhsA.pdb.gz
8	3ixvM	0.43	5.77	0.032	0.713	model1_3ixvM.pdb.gz
9	6ebnA	0.43	6.14	0.061	0.740	model1_6ebnA.pdb.gz
10	3cmuA	0.43	5.91	0.053	0.705	model1_3cmuA.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:1990841	0.74	promoter-specific chromatin binding
GO:0008134	0.54	transcription factor 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	0.94	regulation of cellular process
GO:0080090	0.89	regulation of primary metabolic process
GO:0060255	0.89	regulation of macromolecule metabolic process
GO:0031323	0.89	regulation of cellular metabolic process
GO:0065009	0.88	regulation of molecular function
GO:0010605	0.88	negative regulation of macromolecule metabolic process
GO:0050790	0.87	regulation of catalytic activity
GO:0010468	0.87	regulation of gene expression
GO:0043549	0.86	regulation of kinase activity
GO:0010629	0.86	negative regulation of gene expression
GO:0043550	0.85	regulation of lipid kinase activity
GO:2000112	0.63	regulation of cellular macromolecule biosynthetic process
GO:0051252	0.63	regulation of RNA metabolic process
GO:0006357	0.62	regulation of transcription from RNA polymerase II promoter
GO:0048522	0.50	positive regulation of cellular 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:0044464	1.00	cell part
GO:0044424	0.98	intracellular part
GO:0044422	0.92	organelle part
GO:0044446	0.90	intracellular organelle part
GO:0044428	0.80	nuclear part
GO:0005654	0.64	nucleoplasm
GO:0043229	0.51	intracellular organelle
GO:0043227	0.51	membrane-bounded organelle
GO:0032991	0.51	macromolecular complex
GO:0043231	0.50	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	2aw5B	0.399	5.64	0.042	0.636	1.1.1.40	NA
2	0.060	3hhsB	0.439	5.90	0.032	0.736	1.14.18.1	NA
3	0.060	1gd9A	0.398	6.21	0.065	0.682	2.6.1.-	NA
4	0.060	1xc6A	0.404	6.24	0.050	0.709	3.2.1.23	NA
5	0.060	2j5wA	0.426	6.08	0.053	0.725	1.16.3.1	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:

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	3cmvC	0.387	6.10	0.040	0.655	0.21	ANP	complex1.pdb.gz	75,79,80,113
2	0.01	3cmvB	0.380	6.29	0.020	0.651	0.13	ANP	complex2.pdb.gz	74,75,79
3	0.01	3cmtD	0.419	5.86	0.045	0.690	0.13	ALF	complex3.pdb.gz	76,80,113
4	0.01	3cmvB	0.380	6.29	0.020	0.651	0.23	ANP	complex4.pdb.gz	76,77,110
5	0.01	1xmvA	0.278	6.09	0.053	0.473	0.12	ADP	complex5.pdb.gz	75,78,112
6	0.01	3cmvG	0.370	6.60	0.056	0.702	0.22	ANP	complex6.pdb.gz	76,77,78,110
7	0.01	3cmvC	0.387	6.10	0.040	0.655	0.16	ANP	complex7.pdb.gz	77,79,80,116
8	0.01	3cmtA	0.410	6.31	0.041	0.713	0.13	ALF	complex8.pdb.gz	76,80,113

	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.