D-I-TASSER Q9UBZ9-D1

D-I-TASSER results for Q9UBZ9-D1

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

Input Sequence in FASTA format

>Q9UBZ9 (289 residues)
MRRGGWRKRAENDGWETWGGYMAAKVQKLEEQFRSSNGIFPGREKLKKMKTGRSALVVTD
TGDMSVLNSPRHQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSY
EARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAITEILAETKLTPDEFANAVRMEI
KDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMES
KLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MRRGGWRKRAENDGWETWGGYMAAKVQKLEEQFRSSNGIFPGREKLKKMKTGRSALVVTDTGDMSVLNSPRHQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAITEILAETKLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCSSSSSSCCHHHHHHHHHHCHHHCCCCSSSSCCCCCCCCSSSSSCCHHHHHHCCCCCCHHHHHHHHCCCCSSSCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCSSSSSCCCHHHHHHHHCCCCCCCSSSSCHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHCCCSHHHHHHCCHHHHHHHHCHHHHHHHHHHHCCCCCCCCCCCC
Confidence	9975323444688999989999999999999998612444147888875100355531123554333678778679998167147899975481026996899479998985799967999998299768569999998999299869989999999999999622999999999999999998991899952867999997424799975996887999998618912259957899999999199709999849999999997389999999998198899889999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MRRGGWRKRAENDGWETWGGYMAAKVQKLEEQFRSSNGIFPGREKLKKMKTGRSALVVTDTGDMSVLNSPRHQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAITEILAETKLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK
Prediction	8747411420100000002420452145036315435421423430452544452242464243543645653000000000000000021530614510000011455531000000024024200300110340252026000021316203500330020035110440053016202730500000001311100100153412300120337304510470406401100420151047140500210171336202620144003200310202273604478
	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                 260                 280

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

SS
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCSSSSSSCCHHHHHHHHHHCHHHCCCCSSSSCCCCCCCCSSSSSCCHHHHHHCCCCCCHHHHHHHHCCCCSSSCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCSSSSSCCCHHHHHHHHCCCCCCCSSSSCHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHCCCSHHHHHHCCHHHHHHHHCHHHHHHHHHHHCCCCCCCCCCCC
MRRGGWRKRAENDGWETWGGYMAAKVQKLEEQFRSSNGIFPGREKLKKMKTGRSALVVTDTGDMSVLNSPRHQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAITEILAETKLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3gqcB

0.76

0.66

18.81

1.17

DEthreader

---------SRLHHISMWKCELTEFVNTLQRQ-S-NGIFP-GREKLKKM--------------------Q-S--CIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNR---SRAEIASCSYEARQLGIKNGMFFGHAKQPNLQAVPYDFAYKEVATLYTLASYTHIEILPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTKE

4dezA

0.35

0.26

7.64

2.55

SPARKS-K

------------------------------------------------------------------------TKWVLHVDLDQFLASVELRRRPDLRGQPVIVGGSRK-----VVTCASYEAREFGVHAGMPLRAAARRCPDATFLPSDPAAYDEASEQVMGLLRESDPVEVAERIRTVVAAETGLSCSVGISDNKQRAKVATGFAKPAGIYVLTEANWMTVMGDRPPDALWGVGPKTTKKLAAMGITTVADLAVTDPSVLTTAFGPSTGLWLLLLAKGGGDTEVSS--

3gqcB

0.82

0.74

20.80

1.58

MapAlign

--DCNFISNFYSHSRLHHISMWKCELTEFVNTL--QRQSNGIFPGREKLK--------------------KMQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAQTLILAETKLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPV----

3gqcB

0.81

0.73

20.72

1.00

CEthreader

NFISNFYSHSRLHHISMWKCELTEFVNTLQRQSNGIFPGREKLK--------------------------KMQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGRRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAQTLYETLASLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3gqcB

0.87

0.78

22.02

1.76

MUSTER

IS--NFYSHSRLHHISMWKCELTEFVNTLQRQ---SNGIFPGREKLKKMQ-----------------------SCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAQTLYETLASLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3gqcB

0.88

0.80

22.49

3.52

HHsearch

NFISNFYSHSRLHHISMWKCELTEFVNTLQRQ---SNGIFPGREKL-----------------------KKMQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGRRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAITEILAETKLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3gqcB

0.86

0.77

21.73

2.78

FFAS-3D

----NFYSHSRLHHISMWKCELTEFVNTLQRQ---SNGIFPGREKL-----------------------KKMQSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAQTLYETLASYTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3gqcB

0.75

0.69

19.51

1.72

EigenThreader

-SDCNFISNFYSHSRLHHISMWKCELTEFVNTLQRQSNGIFPGREKLK---------------------KMQSCIMHVDMD-CFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAQTLYETLASYTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3gqcA

0.91

0.79

22.27

2.22

CNFpred

----NFYSHSRLHHISMWKCELTEFVNTLQR--------FPGREKLKK------------------------QSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGSRAEIASCSYEARQLGIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAITEILAETKLTPDEFANAVRMEIKDQTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKLASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEK

3bq1A

0.29

0.21

6.54

1.00

DEthreader

------------------------------------------------------------------------M-IVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVMRIYAFSNRIMLLNKHADVKVNGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQNKYSEPVENKI

(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	0.7907

(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	3gqcB	0.88	1.15	0.856	0.910	model1_3gqcB.pdb.gz
2	2aq4A	0.77	2.79	0.251	0.875	model1_2aq4A.pdb.gz
3	2oh2B	0.69	1.60	0.244	0.730	model1_2oh2B.pdb.gz
4	4dezA	0.68	1.74	0.357	0.727	model1_4dezA.pdb.gz
5	3mr2A	0.68	2.32	0.304	0.751	model1_3mr2A.pdb.gz
6	3bq1A	0.67	2.19	0.292	0.737	model1_3bq1A.pdb.gz
7	1t3nA1	0.65	2.39	0.322	0.730	model1_1t3nA1.pdb.gz
8	3fdsA3	0.52	1.94	0.270	0.564	model1_3fdsA3.pdb.gz
9	1lwwA	0.30	6.12	0.033	0.498	model1_1lwwA.pdb.gz
10	4xsoB	0.30	6.20	0.033	0.491	model1_4xsoB.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:0016740	0.98	transferase activity
GO:0016779	0.97	nucleotidyltransferase activity
GO:0034061	0.89	DNA polymerase activity
GO:0003887	0.87	DNA-directed DNA polymerase activity
GO:0003684	0.77	damaged DNA binding
GO:0000287	0.63	magnesium ion 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:0050896	1.00	response to stimulus
GO:0009987	0.98	cellular process
GO:0006974	0.96	cellular response to DNA damage stimulus
GO:0006259	0.96	DNA metabolic process
GO:0006281	0.91	DNA repair
GO:0034645	0.90	cellular macromolecule biosynthetic process
GO:0006260	0.71	DNA replication
GO:0006301	0.70	postreplication repair
GO:0000731	0.70	DNA synthesis involved in DNA repair
GO:0019985	0.69	translesion synthesis
GO:0006261	0.63	DNA-dependent DNA replication
GO:0009411	0.51	response to UV
GO:0042276	0.50	error-prone translesion synthesis

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	1.00	intracellular part
GO:0044446	0.78	intracellular organelle part
GO:0044428	0.73	nuclear part
GO:0043231	0.66	intracellular membrane-bounded organelle
GO:0005634	0.63	nucleus
GO:0005654	0.62	nucleoplasm
GO:0005737	0.50	cytoplasm

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	0.215	3bq1A	0.670	2.19	0.292	0.737	2.7.7.7	85,120,123,128,130,207
2	0.060	2imwP	0.679	2.26	0.301	0.747	2.7.7.7	121,126,128,130,207
3	0.060	2r8jA	0.640	3.16	0.203	0.758	2.7.7.7	279
4	0.060	2gv9B	0.373	5.14	0.059	0.533	2.7.7.7	197,204
5	0.060	3b9jJ	0.323	6.08	0.057	0.526	1.17.1.4 1.17.3.2	243

	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	0.43	3gqcB	0.885	1.15	0.856	0.910	1.32	MG	complex1.pdb.gz	229,230,231,232,234
2	0.20	2asdA	0.680	2.25	0.301	0.747	1.10	CA	complex2.pdb.gz	80,200,207
3	0.20	1jxlA	0.678	2.28	0.301	0.747	1.08	DG3	complex3.pdb.gz	80,81,83,84,116,117,123,129,207
4	0.14	3gqcB	0.885	1.15	0.856	0.910	1.15	UUU	complex4.pdb.gz	200,231,232,233,234,235,236,237,238
5	0.13	3gqcD	0.875	1.15	0.854	0.900	1.02	QNA	complex5.pdb.gz	6,7,9,10,11,12,13,15,16,20,105,111,112,113,114,265,266,267,268,269

	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.