D-I-TASSER Q9HAZ2-D7

D-I-TASSER results for Q9HAZ2-D7

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

Input Sequence in FASTA format

>Q9HAZ2 (95 residues)
GLLALEPMPTFGKGLDLRRAAEEAFEVKDVLNSTLDSEALKHTLCRQAKNQAYAMMLSLS
EDTPLHTPSQGSLDAWLKVTGATSESGAFHPINHL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| GLLALEPMPTFGKGLDLRRAAEEAFEVKDVLNSTLDSEALKHTLCRQAKNQAYAMMLSLSEDTPLHTPSQGSLDAWLKVTGATSESGAFHPINHL
Prediction	CCCCCCCCCCCCCHHHHHHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
Confidence	95533367787740567775540454444216655737776689999988999999841258988887889767898741577766665656679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| GLLALEPMPTFGKGLDLRRAAEEAFEVKDVLNSTLDSEALKHTLCRQAKNQAYAMMLSLSEDTPLHTPSQGSLDAWLKVTGATSESGAFHPINHL
Prediction	84452542441564251452565515345224453347414540344354422321231356442444454334112423534444433443557
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCHHHHHHHHHCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCC
GLLALEPMPTFGKGLDLRRAAEEAFEVKDVLNSTLDSEALKHTLCRQAKNQAYAMMLSLSEDTPLHTPSQGSLDAWLKVTGATSESGAFHPINHL

6djlB

0.08

0.07

2.89

1.17

DEthreader

--QAEAQKTQDFQRATEVLAKETATQRMEAEQTKTRSELVHKETAARYNAAMGRMRQLEKKLAISKFELKYYVQLEQLK-KTVDDLAKL------

3c9vN4

0.02

1.49

1.03

MapAlign

------AVKVTLGPKGRNVVLDKSFGAPTITKDNPMDLKRGIDKAVTAAVEELKALSVPCVEEGVVPSVVANTVKGGDGNYGYNAATEEYGNMI-

7c0qA

0.12

4.13

0.46

CEthreader

RNPDPQSRADFYCGYVLYLAALKESSYYDYLNLSFTTFNCFYAAQEILTFLIGACKNDTKRENIDLLYNFVTANAYFYLAGFYLSLDLKAESIEC

5h9dA

0.02

1.57

0.52

EigenThreader

TSEQTYQVAVALELIHMATLVHDDVIDLTGNFLLALGLEHLMLIQISTEVGAITSQSDKETVRKLKMIGHYIGMSFQIIDDVLDFTSTLPILLEM

6n7pJ

0.12

0.11

3.71

0.45

FFAS-3D

-----DRKFDKVDKEDISLIVDG--LIKQRNEKIQQKLQNERRILEQKKHYFWLLLQRTYTKTGKPKPST-----WDLASKELGESLEYKALGD-

5u0pI

0.07

0.05

2.21

0.79

SPARKS-K

-----------------TLLRQGIRQLKEKVSKMEPEEMTVKEKKSIIEILKARIALKKAFLKMALSESNDTVVKKEDVRESPVDTFMENAT---

5k3iA

0.08

0.05

2.08

0.44

CNFpred

--------------NKFFGLMENGEKREIAWN------KSSVELNRASRLHTRLFIVEAFARRVNEIGDITIKEALSDLLHLH------------

6r9tA

0.10

0.09

3.48

1.00

DEthreader

KVLASFLGGKMVAAAKASVP-TIQ-DQASAMQLSQCAKNLGTALAELRTAAQKAQEAC----GPLEMSALVVQNLRLAQ-AARGVAALTSCLPGQ

4b3hA

0.05

2.41

0.74

MapAlign

SRGFFTSRVIGTFVNEALAMLGEGVEPASIEQAGPPLQLSDELLELMHKIAVATRKGVEDAGGTYQPHPAEAVVEKMIELGRSGRLKGAGFYEY-

6fw7B

0.11

3.83

0.53

MUSTER

SQSEVYPFTQLKFKSHVQQKLKRAMNELSPRLKEHGKESFLQFVSRYQGHDSAVGMIRSMGYDALFLPD-ISAEMAYDIVGKHPEIQSVTDNDAN

(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	0.4732

(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	2wtgA	0.54	3.80	0.079	0.884	model1_2wtgA.pdb.gz
2	6cc2A	0.52	4.25	0.116	0.937	model1_6cc2A.pdb.gz
3	3p9dD2	0.51	3.84	0.087	0.863	model1_3p9dD2.pdb.gz
4	6aayA1	0.50	3.61	0.060	0.853	model1_6aayA1.pdb.gz
5	1kfrA	0.50	4.20	0.101	0.884	model1_1kfrA.pdb.gz
6	6o3vA	0.50	4.50	0.054	0.937	model1_6o3vA.pdb.gz
7	3p9dC	0.50	4.09	0.066	0.863	model1_3p9dC.pdb.gz
8	1a6eA2	0.50	3.95	0.065	0.895	model1_1a6eA2.pdb.gz
9	6qp6A2	0.50	3.96	0.045	0.863	model1_6qp6A2.pdb.gz
10	1q3rA	0.50	3.97	0.076	0.874	model1_1q3rA.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:0003677	1.00	DNA binding
GO:0043565	0.72	sequence-specific DNA binding
GO:0033613	0.72	activating transcription factor binding
GO:0003713	0.72	transcription coactivator activity
GO:0003824	0.59	catalytic activity
GO:0016740	0.55	transferase activity
GO:0018024	0.52	histone-lysine N-methyltransferase 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:0044699	1.00	single-organism process
GO:0050794	0.93	regulation of cellular process
GO:0031323	0.91	regulation of cellular metabolic process
GO:0048523	0.90	negative regulation of cellular process
GO:0006355	0.90	regulation of transcription, DNA-templated
GO:0045892	0.89	negative regulation of transcription, DNA-templated
GO:0048518	0.82	positive regulation of biological process
GO:0048522	0.81	positive regulation of cellular process
GO:0048583	0.80	regulation of response to stimulus
GO:0045893	0.80	positive regulation of transcription, DNA-templated
GO:0009968	0.79	negative regulation of signal transduction
GO:0006357	0.79	regulation of transcription from RNA polymerase II promoter
GO:0009987	0.74	cellular process
GO:0045595	0.68	regulation of cell differentiation
GO:0030512	0.67	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0000122	0.67	negative regulation of transcription from RNA polymerase II promoter
GO:0044763	0.64	single-organism cellular process
GO:0032502	0.64	developmental process
GO:0044767	0.63	single-organism developmental process
GO:0048856	0.62	anatomical structure development
GO:0044707	0.61	single-multicellular organism process
GO:0048869	0.58	cellular developmental process
GO:2000026	0.57	regulation of multicellular organismal development
GO:0051241	0.57	negative regulation of multicellular organismal process
GO:0030154	0.57	cell differentiation
GO:0002682	0.57	regulation of immune system process
GO:0050873	0.56	brown fat cell differentiation
GO:0043457	0.56	regulation of cellular respiration
GO:0030853	0.56	negative regulation of granulocyte differentiation

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:0043231	1.00	intracellular membrane-bounded organelle
GO:0032991	0.82	macromolecular complex
GO:0005634	0.82	nucleus
GO:0044444	0.81	cytoplasmic part
GO:0043234	0.81	protein complex
GO:0044446	0.57	intracellular organelle part
GO:0017053	0.56	transcriptional repressor complex
GO:0044428	0.50	nuclear 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

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	1cqxA	0.455	4.17	0.084	0.810	1.14.12.17	NA
2	0.060	1r1jA	0.464	4.36	0.056	0.842	3.4.24.11	NA
3	0.060	1uiqD	0.469	4.18	0.046	0.810	4.2.3.1	NA
4	0.060	1cqxB	0.456	3.98	0.061	0.800	1.14.12.17	NA
5	0.060	1q2vA	0.494	4.17	0.075	0.884	3.6.4.9	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	2ekuA	0.490	4.44	0.110	0.916	0.17	7HE	complex1.pdb.gz	55,72,73,76
2	0.01	1h97A	0.492	4.24	0.112	0.884	0.22	HEM	complex2.pdb.gz	42,43,47,50
3	0.01	1m6cA	0.482	4.52	0.109	0.926	0.13	UUU	complex3.pdb.gz	55,76,91
4	0.01	1q3qA	0.493	4.13	0.075	0.884	0.15	ANP	complex4.pdb.gz	50,51,52,72,74,75,76,77
5	0.01	1iopA	0.479	4.53	0.109	0.926	0.12	UUU	complex5.pdb.gz	66,68,73
6	0.01	2wthA	0.461	4.44	0.022	0.874	0.16	UUU	complex6.pdb.gz	6,17,51,54
7	0.01	2nx0A	0.495	4.51	0.054	0.916	0.19	HEM	complex7.pdb.gz	54,72,76
8	0.01	1vxbA	0.490	4.53	0.108	0.926	0.15	HEM	complex8.pdb.gz	68,72,73
9	0.01	1mcyA	0.483	4.64	0.076	0.916	0.13	UUU	complex9.pdb.gz	55,58,70,75
10	0.01	1q3qD	0.493	4.30	0.074	0.905	0.14	ANP	complex10.pdb.gz	18,48,71,77

	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.