D-I-TASSER Q9UHD2-D5

D-I-TASSER results for Q9UHD2-D5

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

Input Sequence in FASTA format

>Q9UHD2 (324 residues)
YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVV
ITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTKLLRLSSSQGTIETSLQDIDSR
LSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKF
DKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVS
KYQEYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELA
ENNHILERFGSLTMDGGLRNVDCL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMDGGLRNVDCL
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Confidence	963757999999998899999999999999999999999999999999999999999999999988999999999999987027761445889999999999999999997999999999533007899998632887221429999999999999999999877527999738999999999999999999999999889999999999999999999999999999999999999999999999999999888874101246666777665555435799999999999999999999988999994579998764456779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMDGGLRNVDCL
Prediction	742540142021000000200200310130040023003000210353044014334402430420243243134124312433344542540450253055035305403530440254134673045205546523466422510320042035004303522446704223410030123302520430251047501520440053014003202401410440353034036305513530450255035512636544544444444574443402310440162054005204502410431451334741542506
	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                 300                 320

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

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMDGGLRNVDCL

5ebzA3

0.12

0.09

3.16

1.00

DEthreader

LPIIQLRKVWAEAVHYVSGLKEDYSRLFQGQRAAMLSLLRYNANLTKMKNTLISASQQLKAKLEFFHKSIQLDLERYSEQMTGISSEKMLKAWKEMEEKAIHYA-EVGVI-GYLEDQIMSLH---AEIMELQKS-PY-GRRQ-GDLMESLEQRAIDLYKQLKHRPSDH-S---YS--D---STEMVKIIVHTVQSQD-RVLKELFGHLSKLLGCKQKIIDLLPKVEVALSNIKEADNTVMFMQGKRQKEIWHLLKI-ACT-Q--------------------------------------------------------------

5j1iA

0.10

0.09

3.21

1.00

CNFpred

--QQKAQAEVEGLGKGVARLSAEAEKVL-AAPTLRSELELTLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPATLPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVGERLQQRHGERD--VEVERWRERVAQLLERWQAVLAQVRQRELEQLGRQLRYYRADPLGAWLQDARRRQEQIQ-QAVREQLRQEQALLEEIERHGEKVEECQRFAKQYINAIKDYELQLVTYKAQLE-------------------VQSGSESVIQEYVDLRTHYSELTTLTSQYIKFISET---------------

4iw0A3

1.00

0.75

20.91

1.53

SPARKS-K

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKL----------GEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET------------------------------------------------------------------------

4iw0A3

0.95

0.70

19.56

1.34

MapAlign

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEK----------LGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLDAWAH--QEGTHPDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNEL---------------------------------------------------------------------------

4iw0A3

1.00

0.75

20.91

0.95

CEthreader

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKL----------GEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET------------------------------------------------------------------------

6cq0A3

1.00

0.73

20.48

1.26

MUSTER

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVE--------------LGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET------------------------------------------------------------------------

4iw0A3

0.99

0.74

20.75

5.64

HHsearch

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVY----------EKLGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET------------------------------------------------------------------------

4iw0A3

1.00

0.74

20.83

2.70

FFAS-3D

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEK----------LGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQE-------------------------------------------------------------------------

4iw0A3

1.00

0.74

20.83

1.57

EigenThreader

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLG----------EISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET------------------------------------------------------------------------

4iwoA

1.00

0.75

21.00

1.46

CNFpred

YDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVY---------AAELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET------------------------------------------------------------------------

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6809

(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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	4iw0A	0.73	1.05	0.983	0.747	model1_4iw0A.pdb.gz
2	5ebzA	0.65	2.94	0.103	0.747	model1_5ebzA.pdb.gz
3	4hpqC	0.63	3.68	0.055	0.772	model1_4hpqC.pdb.gz
4	4e40A	0.53	3.64	0.087	0.648	model1_4e40A.pdb.gz
5	6at7B	0.52	5.54	0.069	0.735	model1_6at7B.pdb.gz
6	3nz4A	0.51	5.48	0.069	0.732	model1_3nz4A.pdb.gz
7	6jfkA	0.51	4.52	0.085	0.676	model1_6jfkA.pdb.gz
8	6xj1A	0.51	4.65	0.036	0.688	model1_6xj1A.pdb.gz
9	1w27A	0.51	5.49	0.081	0.722	model1_1w27A.pdb.gz
10	2d4cB	0.50	4.27	0.065	0.654	model1_2d4cB.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:0051219	0.71	phosphoprotein binding
GO:0003824	0.70	catalytic activity
GO:0016740	0.67	transferase activity
GO:0016301	0.65	kinase activity
GO:0004674	0.64	protein serine/threonine kinase activity

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:0048584	1.00	positive regulation of response to stimulus
GO:0048522	1.00	positive regulation of cellular process
GO:0006950	1.00	response to stress
GO:0048519	0.93	negative regulation of biological process
GO:0032479	0.93	regulation of type I interferon production
GO:0002218	0.93	activation of innate immune response
GO:0051707	0.92	response to other organism
GO:0080090	0.86	regulation of primary metabolic process
GO:0060255	0.86	regulation of macromolecule metabolic process
GO:0031323	0.86	regulation of cellular metabolic process
GO:0051247	0.85	positive regulation of protein metabolic process
GO:0031328	0.85	positive regulation of cellular biosynthetic process
GO:0010557	0.85	positive regulation of macromolecule biosynthetic process
GO:0010468	0.85	regulation of gene expression
GO:0006952	0.85	defense response
GO:0001819	0.85	positive regulation of cytokine production
GO:0032728	0.84	positive regulation of interferon-beta production
GO:0009987	0.83	cellular process
GO:0071704	0.79	organic substance metabolic process
GO:0044238	0.79	primary metabolic process
GO:0044237	0.79	cellular metabolic process
GO:0044260	0.78	cellular macromolecule metabolic process
GO:0019538	0.77	protein metabolic process
GO:0006464	0.76	cellular protein modification process
GO:0006468	0.75	protein phosphorylation
GO:0044699	0.68	single-organism process
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0045935	0.61	positive regulation of nucleobase-containing compound metabolic process
GO:0045944	0.60	positive regulation of transcription from RNA polymerase II promoter
GO:0032727	0.59	positive regulation of interferon-alpha production
GO:0018105	0.59	peptidyl-serine phosphorylation
GO:0010605	0.55	negative regulation of macromolecule metabolic process
GO:0098542	0.54	defense response to other organism
GO:0010629	0.54	negative regulation of gene expression
GO:0007165	0.54	signal transduction
GO:0050830	0.53	defense response to Gram-positive bacterium
GO:0045359	0.53	positive regulation of interferon-beta biosynthetic process
GO:0035556	0.50	intracellular signal transduction
GO:0023051	0.50	regulation of signaling
GO:0010646	0.50	regulation of cell communication

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:0005737	1.00	cytoplasm
GO:0044444	0.84	cytoplasmic part
GO:0005829	0.72	cytosol
GO:0016020	0.57	membrane
GO:0044446	0.55	intracellular organelle part

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

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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	1q5nA	0.397	5.12	0.051	0.568	5.5.1.2	NA
2	0.060	2fonB	0.408	3.88	0.043	0.503	1.3.3.6	301
3	0.060	2iukB	0.378	6.19	0.038	0.599	1.13.11.12	NA
4	0.060	1c3cA	0.406	5.00	0.051	0.574	4.3.2.2	NA
5	0.060	1u8vA	0.384	4.82	0.045	0.512	5.3.3.3	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

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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	1i4d0	0.378	4.67	0.069	0.522	0.69	III	complex1.pdb.gz	16,17,23,27,30,33,37,40,41,189,193,194,197,198,200
2	0.01	2j68A	0.460	4.31	0.063	0.583	0.45	GDP	complex2.pdb.gz	12,14,15,16,17,183,189,190
3	0.01	1wdz0	0.487	4.28	0.058	0.636	0.49	III	complex3.pdb.gz	1,12,13,16,20,23,27,30,31,34,37,38,40,41,44,108,111,114,117,128,186,190,193,194,195,197,198
4	0.01	2g381	0.421	3.41	0.052	0.518	0.54	III	complex4.pdb.gz	37,38,40,49,52,55,56,58,59,62,63,65,66,69,70,73,76,80,89,96,99,107,218
5	0.01	1zww0	0.431	4.68	0.083	0.593	0.62	III	complex5.pdb.gz	8,9,12,13,15,16,19,20,24,27,37,38,41,44,45,48,51,52,192,196,198,200,201,204
6	0.01	1i490	0.420	4.57	0.053	0.571	0.73	III	complex6.pdb.gz	16,20,23,27,30,33,34,37,40,41,45,47,51,189,190,193,194,197,198,200,201,204

	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.