D-I-TASSER Q92922-D2

D-I-TASSER results for Q92922-D2

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

Input Sequence in FASTA format

>Q92922 (131 residues)
VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQE
DAFGKHVTNPAFTKLPAKCFMDFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSRMDRNV
EMFMNIEKTLV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCFMDFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSRMDRNVEMFMNIEKTLV
Prediction	CCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHCCCSSSSCCCCHHHHHHHHHHHHHHHHHC
Confidence	97688999886673498899987999999998643312579996478999999999999998565689987564566776137999716689999999987518434324694135569999999999729
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCFMDFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSRMDRNVEMFMNIEKTLV
Prediction	76446734142621436631541550352036415623556424354003002301423364135527544134112310431466210010012024143754034232634643442041034046427
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHCCCSSSSCCCCHHHHHHHHHHHHHHHHHC
VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCFMDFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSRMDRNVEMFMNIEKTLV

6yxoA1

0.99

0.95

26.73

1.33

DEthreader

-YRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCFD-FKAGGALCHILGAAYKYKNEQGWRRFDLQNPSR-DRNVE-F-NIEKTLV

6yxoA1

0.99

0.96

26.94

2.28

SPARKS-K

VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCF-DFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSR-DRNVEF--NIEKTLV

6yxoA

0.98

0.91

25.45

1.50

MapAlign

-----DGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCF-DFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSRD-RNV-EF-NIEKTL-

6yxoA1

0.99

0.96

26.94

1.48

CEthreader

VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCF-DFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSR-DRNVE--FNIEKTLV

3u44B

0.09

0.08

3.21

0.44

MUSTER

TELLFPLNEPKAK--VREQVDQLENYCIAYGIKGDRWTKQEIEMENMLNDTRDWIVPPLFQLQ-KRMKKAKTVQEKAEALYRYLEETDVPLKLDQERQRAEDDG----RIIEAQQHQQAWDAVIQLLEEFV

6yxoA1

0.99

0.96

26.94

4.94

HHsearch

VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCF-DFKAGGALCHILGAAYKYKNEQGWRRFDLQNPSR-DRNVE--FNIEKTLV

5y0eA3

0.09

0.07

2.66

0.72

FFAS-3D

-----------NCQGNPVLKTFINDLQGLLQQRSQQMSQPGRGGSSEMVDFINRHLGQVSHAYHLDHLH------PERLFA------DWLQFATELASFSAQRTLPVYDHDNLA--LCFGKLMLLLRQGL-

6yxoA1

0.92

0.89

24.87

1.70

EigenThreader

VYRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPA-KCFDFKAGGALCHILGAAYKYKNEQGWRRFDLQNP----SRDRNVFNIEKTLV

4c0oA

0.10

0.08

2.80

0.53

CNFpred

-------------------QKVIQEIWPVLSETLNKHR-----ADNRIVERCCRCLRFAVRCVGKGSLLQPLVTQMVNVYHVHQHSCFLYLGSILVDEYGMEE----------GCRQGLLDMLQALCIPTF

6yxoA

0.99

0.95

26.73

1.33

DEthreader

-YRRKDGGPATKFWESPETVSQLDSVRVWLGKHYKKYVHADAPTNKTLAGLVVQLLQFQEDAFGKHVTNPAFTKLPAKCFD-FKAGGALCHILGAAYKYKNEQGWRRFDLQNPSR-DRNVE-F-NIEKTLV

(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	0.7799

(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	6yxoA	0.94	1.14	0.992	0.962	model1_6yxoA.pdb.gz
2	2qfzA	0.58	3.83	0.043	0.870	model1_2qfzA.pdb.gz
3	3qyeA	0.57	3.94	0.026	0.863	model1_3qyeA.pdb.gz
4	2g77A	0.57	3.99	0.026	0.885	model1_2g77A.pdb.gz
5	2qq8A	0.56	3.84	0.069	0.863	model1_2qq8A.pdb.gz
6	3hzjC	0.56	3.94	0.062	0.855	model1_3hzjC.pdb.gz
7	3qwlA	0.54	3.91	0.046	0.832	model1_3qwlA.pdb.gz
8	4p17A2	0.47	3.56	0.053	0.695	model1_4p17A2.pdb.gz
9	3l2nA2	0.38	4.60	0.069	0.626	model1_3l2nA2.pdb.gz
10	1hg4A	0.37	4.71	0.028	0.649	model1_1hg4A.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	0.77	heterocyclic compound binding
GO:0097159	0.77	organic cyclic compound binding
GO:0003676	0.74	nucleic acid binding
GO:0003677	0.71	DNA binding
GO:0044877	0.68	macromolecular complex binding
GO:0003682	0.67	chromatin binding
GO:0000975	0.66	regulatory region DNA binding
GO:0044212	0.65	transcription regulatory region DNA binding
GO:0003690	0.65	double-stranded DNA binding
GO:0031492	0.64	nucleosomal DNA binding
GO:0000980	0.64	RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000978	0.64	RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0003713	0.56	transcription coactivator 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	0.89	single-organism process
GO:0009987	0.84	cellular process
GO:0065007	0.79	biological regulation
GO:0050794	0.78	regulation of cellular process
GO:0080090	0.75	regulation of primary metabolic process
GO:0060255	0.75	regulation of macromolecule metabolic process
GO:0031323	0.75	regulation of cellular metabolic process
GO:2000112	0.74	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.74	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.74	regulation of gene expression
GO:0006355	0.73	regulation of transcription, DNA-templated
GO:0016043	0.70	cellular component organization
GO:0006325	0.69	chromatin organization
GO:0048518	0.66	positive regulation of biological process
GO:0048522	0.65	positive regulation of cellular process
GO:0044763	0.65	single-organism cellular process
GO:0006338	0.65	chromatin remodeling
GO:1902680	0.64	positive regulation of RNA biosynthetic process
GO:0010628	0.64	positive regulation of gene expression
GO:0045893	0.63	positive regulation of transcription, DNA-templated
GO:0006357	0.62	regulation of transcription from RNA polymerase II promoter
GO:0043044	0.61	ATP-dependent chromatin remodeling
GO:0048523	0.59	negative regulation of cellular process
GO:0044767	0.58	single-organism developmental process

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:0044428	1.00	nuclear part
GO:0032991	0.86	macromolecular complex
GO:0043234	0.84	protein complex
GO:0090544	0.79	BAF-type complex
GO:0005654	0.77	nucleoplasm
GO:0016514	0.59	SWI/SNF complex
GO:0044427	0.58	chromosomal part
GO:0043226	0.57	organelle
GO:0000790	0.56	nuclear chromatin
GO:0043229	0.55	intracellular organelle
GO:0071565	0.54	nBAF complex
GO:0071564	0.54	npBAF complex
GO:0043227	0.52	membrane-bounded organelle
GO:0043231	0.51	intracellular membrane-bounded organelle

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	2axqA	0.511	3.92	0.060	0.794	1.5.1.10	NA
2	0.060	1qo9A	0.469	4.35	0.072	0.771	3.1.1.7	NA
3	0.060	2wybB	0.480	3.29	0.067	0.672	3.5.1.97	NA
4	0.060	3etdA	0.488	4.43	0.045	0.779	1.4.1.3	NA
5	0.060	1zj8A	0.466	3.67	0.085	0.702	1.8.7.1	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	2cmoA	0.317	4.23	0.130	0.511	0.13	M1L	complex1.pdb.gz	60,63,110
2	0.01	3abiA	0.523	3.93	0.044	0.809	0.12	NAD	complex2.pdb.gz	56,116,119
3	0.01	1ftjA	0.317	4.22	0.130	0.511	0.18	GLU	complex3.pdb.gz	58,116,120
4	0.01	1m5cA	0.319	4.28	0.130	0.519	0.15	BRH	complex4.pdb.gz	51,52,93
5	0.01	1ftl0	0.298	5.31	0.065	0.557	0.20	III	complex5.pdb.gz	88,89,92,93,95,96
6	0.01	3dlnA	0.318	4.29	0.117	0.519	0.21	GLU	complex6.pdb.gz	49,54,86,89
7	0.01	3rtwF	0.302	4.99	0.051	0.550	0.17	NWD	complex7.pdb.gz	53,92,93,94
8	0.01	3keiA	0.302	4.22	0.030	0.473	0.18	GLU	complex8.pdb.gz	64,123,124
9	0.01	3b6tA	0.318	4.29	0.130	0.519	0.16	QUS	complex9.pdb.gz	52,92,93,94
10	0.01	3fatA	0.320	5.43	0.040	0.641	0.17	AMQ	complex10.pdb.gz	99,127,130

	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.