D-I-TASSER Q9HB65-D2

D-I-TASSER results for Q9HB65-D2

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

Input Sequence in FASTA format

>Q9HB65 (226 residues)
QGQSLPGSSREHMAQWEVRSQTHVPNREPVQALPSSASRKRLDKKRSVPVATVELEEKRF
RTLPLVPSPLQGLTNQDLQEGEDWEQEDEDMDPRLEHSSSVQEDSESPSPEDIPDYLLQY
RAIHSAEQQHAYEQDFETDYAEYRILHARVGTASQRFIELGAEIKRVRRGTPEYKVLEDK
IIQEYKKFRKQYPSYREEKRRCEYLHQKLSHIKGLILEFEEKNRGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| QGQSLPGSSREHMAQWEVRSQTHVPNREPVQALPSSASRKRLDKKRSVPVATVELEEKRFRTLPLVPSPLQGLTNQDLQEGEDWEQEDEDMDPRLEHSSSVQEDSESPSPEDIPDYLLQYRAIHSAEQQHAYEQDFETDYAEYRILHARVGTASQRFIELGAEIKRVRRGTPEYKVLEDKIIQEYKKFRKQYPSYREEKRRCEYLHQKLSHIKGLILEFEEKNRGS
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence	9988999999988876655688999999976789988876667789999988887765555678899976678887766566655556678998777877777888999766862677478889999999999999996999999999999999999999999996899988999999999999999970494899999999999999999999999999873069
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| QGQSLPGSSREHMAQWEVRSQTHVPNREPVQALPSSASRKRLDKKRSVPVATVELEEKRFRTLPLVPSPLQGLTNQDLQEGEDWEQEDEDMDPRLEHSSSVQEDSESPSPEDIPDYLLQYRAIHSAEQQHAYEQDFETDYAEYRILHARVGTASQRFIELGAEIKRVRRGTPEYKVLEDKIIQEYKKFRKQYPSYREEKRRCEYLHQKLSHIKGLILEFEEKNRGS
Prediction	8567445646544464547546544555355533474447436555445556563666444644554545654655545655644564554655454575445454345545234024513404347225403640373163035015305512630450352057256736414512540364046246434604544530530362042035205501655588
	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                 140                 160                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
QGQSLPGSSREHMAQWEVRSQTHVPNREPVQALPSSASRKRLDKKRSVPVATVELEEKRFRTLPLVPSPLQGLTNQDLQEGEDWEQEDEDMDPRLEHSSSVQEDSESPSPEDIPDYLLQYRAIHSAEQQHAYEQDFETDYAEYRILHARVGTASQRFIELGAEIKRVRRGTPEYKVLEDKIIQEYKKFRKQYPSYREEKRRCEYLHQKLSHIKGLILEFEEKNRGS

5jw9B

0.50

0.25

7.19

1.77

FFAS-3D

----------------------------------------------------------------------------------------------------------------LPDYLIKYIAIVSYEQRQNYKDDFNAEYDEYRALHARE-TVARRFIKLDAQRKRLSPGSKEYQNVHEEVLQEYQKIKQSSPNYHEEKYRCEYLHNKLAHIKR-IGEFDQQQAES

5jw9B

0.50

0.25

7.19

2.14

SPARKS-K

----------------------------------------------------------------------------------------------------------------LPDYLIKYIAIVSYEQRQNYKDDFNAEYDEYRALHAR-ETVARRFIKLDAQRKRLSPGSKEYQNVHEEVLQEYQKIKQSSPNYHEEKYRCEYLHNKLAHIKR-IGEFDQQQAES

3g7cA

0.24

0.12

3.59

1.47

MUSTER

-----------------------------------------------------------------------------------------------------------------EEWIREYPPITSDQQRQLYKRNFDTGLQEYKSLQSELDEINKELSRLDKELDDYREESEEYMAAADEYNRLKQVKGD--ADYKSKKNHCKQLKSKLSHIKKMVGDYDRQKT--

5jw9B

0.50

0.25

7.19

4.91

HHsearch

----------------------------------------------------------------------------------------------------------------LPDYLIKYIAIVSYEQRQNYKDDFNAEYDEYRALHAR-ETVARRFIKLDAQRKRLSPGSKEYQNVHEEVLQEYQKIKQSSPNYHEEKYRCEYLHNKLAHIKR-IGEFDQQQAES

3g7cA

0.24

0.12

3.59

0.61

CEthreader

-----------------------------------------------------------------------------------------------------------------EEWIREYPPITSDQQRQLYKRNFDTGLQEYKSLQSELDEINKELSRLDKELDDYREESEEYMAAADEYNRLKQVKGD--ADYKSKKNHCKQLKSKLSHIKKMVGDYDRQKT--

3s84A

0.08

3.09

0.78

EigenThreader

----DSEKLKEEIGKELEELRARLLPHANEVSQKIGDNLRELQQRLEPYADQLRTQVNTQAEQLRRQLTPYAQRMERVLRENADSLQASLRPHADELKAKIDQNVEELKGRLTPYADEFKVKIQLEGLTFQMKKNAEELKARISASAEELRQRLAPLAEDVRGN---LRGN---TEGLQKSLAELGGHLD---QQVEEFRRRVEGENFNKALVQQMEQLRQKLGPH

3g7cA

0.25

0.12

3.70

1.69

FFAS-3D

------------------------------------------------------------------------------------------------------------------EWIREYPPITSDQQRQLYKRNFDTGLQEYKSLQSELDEINKELSRLDKELDDYREESEEYMAAADEY-NRLKQVKG-DADYKSKKNHCKQLKSKLSHIKKMVGDYDRQKT--

3g7cA

0.23

0.11

3.46

2.12

SPARKS-K

-----------------------------------------------------------------------------------------------------------------EEWIREYPPITSDQQRQLYKRNFDTGLQEYKSLQSELDEINKELSRLDKELDDYREESE----EYMAAADEYNRLKQVKADYKSKKNHCKQLKSKLSHIKKMVGDYDRQKT--

5jw9B

0.49

0.25

7.19

0.99

CNFpred

----------------------------------------------------------------------------------------------------------------LPDYLIKYIAIVSYEQRQNYKDDFNAEYDEYRALHARMETVARRFIKLDAQRKRLSPGSKEYQNVHEEVLQEYQKIKQSSPNYHEEKYRCEYLHNKLAHIKRMIGEFDQQQAES

6rw8A

0.07

0.06

2.39

0.67

DEthreader

-SLDLILLWINQITPTTALQ-DPT-R------LIKLKYVTPMPTFD----AAAYYIKAPQIYVEGKVS-TKNKASFTGNIPFLLKNGSEGYDIIKLKSKDTSNVISLHKMPSGTTLFSRKLARANIGIDNVSMETQNLPE-PQ----FYATFKLFKIEGVGY--KKI------I--YDKSW-ESA-FF-YFDQFI--M--NTEPMDGANAYFWELFYYTPMMVFRL

(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	0.5319

(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	4a01A	0.49	5.37	0.046	0.774	model1_4a01A.pdb.gz
2	6uebA	0.48	5.56	0.051	0.792	model1_6uebA.pdb.gz
3	6v85A3	0.46	5.94	0.038	0.823	model1_6v85A3.pdb.gz
4	6ijcA	0.46	5.21	0.042	0.708	model1_6ijcA.pdb.gz
5	5y9dA	0.46	5.31	0.065	0.726	model1_5y9dA.pdb.gz
6	5x0mA	0.45	5.38	0.019	0.739	model1_5x0mA.pdb.gz
7	2ww9A	0.45	6.09	0.041	0.801	model1_2ww9A.pdb.gz
8	7jpkA	0.44	5.60	0.027	0.743	model1_7jpkA.pdb.gz
9	5fj8O	0.44	4.96	0.042	0.659	model1_5fj8O.pdb.gz
10	3kcrA	0.43	6.06	0.047	0.761	model1_3kcrA.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:1901363	0.79	heterocyclic compound binding
GO:0097159	0.79	organic cyclic compound binding
GO:0003676	0.76	nucleic acid binding
GO:0003677	0.73	DNA binding
GO:0044212	0.70	transcription regulatory region DNA binding
GO:0035326	0.69	enhancer 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:0009987	1.00	cellular process
GO:0044699	0.90	single-organism process
GO:0071704	0.83	organic substance metabolic process
GO:0044763	0.83	single-organism cellular process
GO:0044238	0.83	primary metabolic process
GO:0044260	0.82	cellular macromolecule metabolic process
GO:0065007	0.81	biological regulation
GO:0090304	0.80	nucleic acid metabolic process
GO:0050789	0.80	regulation of biological process
GO:0050794	0.79	regulation of cellular process
GO:0016070	0.79	RNA metabolic process
GO:0080090	0.78	regulation of primary metabolic process
GO:0032774	0.78	RNA biosynthetic process
GO:0031326	0.77	regulation of cellular biosynthetic process
GO:0019219	0.77	regulation of nucleobase-containing compound metabolic process
GO:0010556	0.77	regulation of macromolecule biosynthetic process
GO:2001141	0.76	regulation of RNA biosynthetic process
GO:0031325	0.76	positive regulation of cellular metabolic process
GO:0010604	0.76	positive regulation of macromolecule metabolic process
GO:0010468	0.76	regulation of gene expression
GO:1902680	0.75	positive regulation of RNA biosynthetic process
GO:0010628	0.75	positive regulation of gene expression
GO:0006351	0.75	transcription, DNA-templated
GO:2000112	0.74	regulation of cellular macromolecule biosynthetic process
GO:0034660	0.74	ncRNA metabolic process
GO:0042795	0.73	snRNA transcription from RNA polymerase II promoter
GO:0006355	0.73	regulation of transcription, DNA-templated
GO:0045893	0.72	positive regulation of transcription, DNA-templated
GO:0006357	0.72	regulation of transcription from RNA polymerase II promoter
GO:0045944	0.71	positive regulation of transcription from RNA polymerase II promoter
GO:0048869	0.66	cellular developmental process
GO:0030154	0.60	cell differentiation
GO:2000026	0.55	regulation of multicellular organismal development
GO:0048863	0.54	stem cell differentiation
GO:0010717	0.54	regulation of epithelial to mesenchymal transition

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	0.98	cell part
GO:0044424	0.97	intracellular part
GO:0043226	0.85	organelle
GO:0044446	0.84	intracellular organelle part
GO:0044428	0.81	nuclear part
GO:0043229	0.80	intracellular organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0032991	0.76	macromolecular complex
GO:0044451	0.75	nucleoplasm part
GO:0043234	0.75	protein complex
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0008023	0.70	transcription elongation factor complex
GO:0005634	0.70	nucleus

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	2vz9B	0.298	6.12	0.036	0.544	2.3.1.85	NA
2	0.060	1fo4A	0.412	5.74	0.037	0.704	1.17.1.4	NA
3	0.060	3g61A	0.402	5.59	0.042	0.655	3.6.3.44	NA
4	0.060	3g4dA	0.402	5.41	0.042	0.646	4.2.3.13	NA
5	0.060	2e1qA	0.433	5.97	0.038	0.757	1.17.3.2 1.17.1.4	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	2ckjD	0.405	6.25	0.058	0.726	0.48	FES	complex1.pdb.gz	161,162,165,167
2	0.01	2ckjC	0.418	5.95	0.064	0.717	0.54	FES	complex2.pdb.gz	144,149,150,151
3	0.01	3eubS	0.200	5.62	0.040	0.327	0.55	FES	complex3.pdb.gz	147,148,151,153
4	0.01	1v97A	0.425	5.78	0.037	0.726	0.44	FES	complex4.pdb.gz	160,161,164,175,177,178
5	0.01	2ckjA	0.393	6.32	0.035	0.712	0.43	FES	complex5.pdb.gz	160,161,184
6	0.01	1fo4A	0.412	5.74	0.037	0.704	0.40	FES	complex6.pdb.gz	214,215,216,218,220

	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.