D-I-TASSER Q9H977-D2

D-I-TASSER results for Q9H977-D2

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

Input Sequence in FASTA format

>Q9H977 (152 residues)
AGVSPPLITQVHWCVLPFRVLLVLTSHRGIQMYESNGYTMVYWHALDSGDASPVQAVFAR
GIAASGHFICVGTWSGRVLVFDIPAKGPNIVLSEELAGHQMPITDIATEPAQGQDCVADM
VTADDSGLLCVWRSGPEFTLLTRIPGFGVPCP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AGVSPPLITQVHWCVLPFRVLLVLTSHRGIQMYESNGYTMVYWHALDSGDASPVQAVFARGIAASGHFICVGTWSGRVLVFDIPAKGPNIVLSEELAGHQMPITDIATEPAQGQDCVADMVTADDSGLLCVWRSGPEFTLLTRIPGFGVPCP
Prediction	CCCCCCCSSSSSSSSCCCCSSSSSSCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCSSSSSSSSSCCCSSSSSSCCCCSSSSSSCCCCCCSSSSSSHHHCCCCSSSSSSCCCCCCCCSSSSSSSCCCCCSSSSSCCCCSSSSSSCCCCCCCCC
Confidence	98762013455677427622999963881899936997799998548887887632576345321776999825895899971699981899644120898536787604787763025888539992999827997599987167898799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| AGVSPPLITQVHWCVLPFRVLLVLTSHRGIQMYESNGYTMVYWHALDSGDASPVQAVFARGIAASGHFICVGTWSGRVLVFDIPAKGPNIVLSEELAGHQMPITDIATEPAQGQDCVADMVTADDSGLLCVWRSGPEFTLLTRIPGFGVPCP
Prediction	86443321310210324442000010442030122643320112316456446343200100022232000002312000000357564140353056162301101124455452213002125401000024374042224147473618
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCSSSSSSSSCCCCSSSSSSCCCCSSSSSCCCCSSSSSSSCCCCCCCCCCSSSSSSSSSCCCSSSSSSCCCCSSSSSSCCCCCCSSSSSSHHHCCCCSSSSSSCCCCCCCCSSSSSSSCCCCCSSSSSCCCCSSSSSSCCCCCCCCC
AGVSPPLITQVHWCVLPFRVLLVLTSHRGIQMYESNGYTMVYWHALDSGDASPVQAVFARGIAASGHFICVGTWSGRVLVFDIPAKGPNIVLSEELAGHQMPITDIATEPAQGQDCVADMVTADDSGLLCVWRSGPEFTLLTRIPGFGVPCP

5cxcA

0.09

3.25

1.33

DEthreader

SFEHDDWVSAVDVLSGAVQERVLSASYDLLRIWNA-SGSVIATSPSG-SHG-G-HTASIKAAKFLTDRLASAGMDRTVRVWKYTESTGELKPTLELYGHTGSVDWLDVDGH-----SKHILTASADGAIGFWSASASAPPLGLWSIHAPATS

5oqlL1

0.15

0.13

4.41

1.54

SPARKS-K

-----WPISHISFP--ATNDLFAVTAGPRVEIFSIRKREPLKTIG--------RFDSEAHCGEIRGRVLVAGEDTGRMQVFDV-GQGTRAVILKTWHIHKQPVWVTKWSPTELT----TLMSCSDDKTVRLWDL-PSNDPTRLFTGHTDYVR

5nnzB

0.14

0.12

4.03

0.34

MapAlign

----CAEISSASFN--WDCSLILTGSMKTCKLWDATNGKCVATLTG--------HDDEILDSCFDGKLIATASADGTARIFSA----ATRKCIAKLEGHEGEISKISFNPQ-----GNHLLTGSSDKTARIWDAQ-TGQCLQVLEGHTDEI-

5nnzB

0.14

0.12

4.07

0.26

CEthreader

LIGHCAEISSASFNWD--CSLILTGSMDKCKLWDATNGKCVATLT--------GHDDEILDSCFDGKLIATASADGTARIFSAAT----RKCIAKLEGHEGEISKISFNP-----QGNHLLTGSSDKTARIWDAQ-TGQCLQVLEGHTDEIF

5oqlL1

0.14

0.12

4.25

1.47

MUSTER

-----WPISHISF--PATNDLFAVTAGPRVEIFSIRKREPLKTIG------RFDSEAHCGEIRPDGRVLVAGEDTGRMQVFDVGQGTRA-VILKTWHIHKQPVWVTKWSPTELT----TLMSCSDDKTVRLWDL-PSNDPTRLFTGHTDYVR

3dm0A

0.11

0.09

3.35

0.62

HHsearch

LTGHSHFVEDVVLS--SDGQFALSGSWDGLRLWDLAAGVSTRR--------FVGHTKDVLSVAFDNRQIVSASRDRTIKLWNTL-GE----CKYTIEGHRDWVSCVRFSPNT-----LTIVSASWDKTVKVWNL-SNCKLRSTLAGHTGYVS

5oqlL1

0.14

0.12

4.06

1.59

FFAS-3D

-------ISHISF--PATNDLFAVTAGPRVEIFSIRKREPLKTI------GRFDSEAHCGEIRPDGRVLVAGEDTGRMQVFDVGQGTRAVIL-KTWHIHKQPVWVTKWSPTELT----TLMSCSDDKTVRLWDLPSNDPT-RLFTGHTDYVR

5l56A1

0.07

2.74

0.48

EigenThreader

PAFSDWGLTHLVVH--EQTGEVYVGAVNRIYKLS-GNLTLLRAHVTGPPSVQSCTDNVNKLLLLDANRLLACGSAGICQFLRLDD--LFKLGEPHEHYLSSVSMAGVLIAGPPGQGQAKLFVGTPIDYFSSRRLMAMFGFSQLKIPFDIYYV

3mkqA

0.14

0.12

4.07

1.85

CNFpred

FSNRSDRVKGIDFHP--TEPWVLTTLYGRVEIWNYETQVEVRSIQVT--------ETPVRAGKFIANWIIVGSDDFRIRVFNYNT----GEKVVDFEAHPDYIRSIAVHPT-----KPYVLSGSDDLTVKLWNWENNWALEQTFEGHEHFVM

5a9q7

0.12

4.14

1.33

DEthreader

SWKTSGSVWRVTWAHPEFGQVLASCSDRTAAVWEEIVHWVKRTTLVDS-------RTSVTDVKFAGLMLATCSADGIVRIYEAPVNLSQWSLQHEIS-CKLSCSCISWNPSSSRAHSPMIAVGSDDAKVQIFEYNRKYAKAETLMVTDPVHW

(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	0.8137

(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	5cxcA	0.83	1.84	0.098	0.941	model1_5cxcA.pdb.gz
2	3bg1D	0.83	1.94	0.119	0.941	model1_3bg1D.pdb.gz
3	4l9oA	0.82	2.03	0.141	0.934	model1_4l9oA.pdb.gz
4	4jxmA	0.82	1.67	0.117	0.901	model1_4jxmA.pdb.gz
5	3f3fA	0.82	2.14	0.140	0.941	model1_3f3fA.pdb.gz
6	5a9q7	0.82	1.94	0.112	0.941	model1_5a9q7.pdb.gz
7	4xfvA	0.82	2.10	0.121	0.928	model1_4xfvA.pdb.gz
8	6tblE	0.82	1.73	0.124	0.901	model1_6tblE.pdb.gz
9	5ganH	0.82	1.63	0.146	0.901	model1_5ganH.pdb.gz
10	5vh9B	0.82	1.74	0.087	0.908	model1_5vh9B.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	0.69	heterocyclic compound binding
GO:0097159	0.69	organic cyclic compound binding
GO:0042802	0.58	identical protein binding
GO:0003824	0.57	catalytic activity
GO:0016787	0.52	hydrolase activity
GO:0000166	0.52	nucleotide binding
GO:0097367	0.51	carbohydrate derivative binding
GO:0035639	0.50	purine ribonucleoside triphosphate binding
GO:0032555	0.50	purine ribonucleotide binding
GO:0032550	0.50	purine ribonucleoside 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	0.90	cellular process
GO:0044237	0.79	cellular metabolic process
GO:0071704	0.78	organic substance metabolic process
GO:0044260	0.77	cellular macromolecule metabolic process
GO:0044238	0.77	primary metabolic process
GO:0065007	0.71	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:0034641	0.69	cellular nitrogen compound metabolic process
GO:0044699	0.68	single-organism process
GO:0071840	0.66	cellular component organization or biogenesis
GO:0090304	0.64	nucleic acid metabolic process
GO:0016043	0.64	cellular component organization
GO:0044763	0.63	single-organism cellular process
GO:0019538	0.61	protein metabolic process
GO:0006996	0.60	organelle organization
GO:0048518	0.57	positive regulation of biological process
GO:0080090	0.56	regulation of primary metabolic process
GO:0060255	0.56	regulation of macromolecule metabolic process
GO:0044267	0.56	cellular protein metabolic process
GO:0031323	0.56	regulation of cellular metabolic process
GO:0048522	0.55	positive regulation of cellular process
GO:2000112	0.54	regulation of cellular macromolecule biosynthetic process
GO:0051179	0.54	localization
GO:0051171	0.54	regulation of nitrogen compound metabolic process
GO:0050896	0.54	response to stimulus
GO:0032502	0.54	developmental process
GO:0010468	0.54	regulation of gene expression
GO:0051716	0.53	cellular response to stimulus
GO:0051641	0.53	cellular localization
GO:0048583	0.53	regulation of response to stimulus
GO:0044767	0.53	single-organism developmental process
GO:0042221	0.53	response to chemical
GO:0008104	0.53	protein localization
GO:0006810	0.53	transport
GO:0006508	0.53	proteolysis
GO:0071702	0.52	organic substance transport
GO:0050790	0.52	regulation of catalytic activity
GO:0048584	0.52	positive regulation of response to stimulus
GO:0046907	0.52	intracellular transport
GO:0045184	0.52	establishment of protein localization
GO:0044710	0.52	single-organism metabolic process
GO:0044265	0.52	cellular macromolecule catabolic process
GO:0034613	0.52	cellular protein localization
GO:0030163	0.52	protein catabolic process
GO:0016192	0.52	vesicle-mediated transport
GO:0010033	0.52	response to organic substance
GO:0009966	0.52	regulation of signal transduction
GO:0006950	0.52	response to stress
GO:0006355	0.52	regulation of transcription, DNA-templated
GO:1903432	0.51	regulation of TORC1 signaling
GO:0051664	0.51	nuclear pore localization
GO:0050658	0.51	RNA transport
GO:0048856	0.51	anatomical structure development
GO:0043161	0.51	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043087	0.51	regulation of GTPase activity
GO:0036503	0.51	ERAD pathway
GO:0032008	0.51	positive regulation of TOR signaling
GO:0006997	0.51	nucleus organization
GO:0006900	0.51	membrane budding
GO:0006888	0.51	ER to Golgi vesicle-mediated transport
GO:0022607	0.50	cellular component assembly
GO:0006464	0.50	cellular protein modification process
GO:0006357	0.50	regulation of transcription from RNA polymerase II promoter

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:0032991	0.93	macromolecular complex
GO:0044446	0.92	intracellular organelle part
GO:0043226	0.92	organelle
GO:0043229	0.91	intracellular organelle
GO:0043227	0.90	membrane-bounded organelle
GO:0043231	0.88	intracellular membrane-bounded organelle
GO:0005634	0.85	nucleus
GO:0043234	0.84	protein complex
GO:0044444	0.78	cytoplasmic part
GO:0044428	0.78	nuclear part
GO:0016020	0.53	membrane
GO:0005829	0.50	cytosol

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	0.066	1rwlA	0.721	2.28	0.069	0.855	2.7.11.1	NA
2	0.066	2iwaA	0.674	2.73	0.084	0.862	2.3.2.5	69
3	0.066	1uv4A	0.734	2.96	0.069	0.947	3.2.1.99	NA
4	0.060	2vk6A	0.717	3.31	0.092	0.987	3.2.1.18	NA
5	0.060	2madH	0.725	2.82	0.136	0.921	1.4.99.3	66

	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	0.05	3sbpB	0.778	2.35	0.102	0.901	0.64	CUA	complex1.pdb.gz	59,71,75,79
2	0.05	1cvmA	0.805	1.95	0.086	0.921	0.63	CA	complex2.pdb.gz	71,72,73,77
3	0.03	3cfvB	0.793	1.96	0.088	0.895	0.89	III	complex3.pdb.gz	75,78,98
4	0.03	3sbpA	0.776	2.36	0.102	0.901	0.69	CUA	complex4.pdb.gz	96,98,100,103
5	0.03	3sbrF	0.777	2.36	0.102	0.901	0.63	IMD	complex5.pdb.gz	61,62,78,79

	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.