D-I-TASSER Q14164-D4

D-I-TASSER results for Q14164-D4

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

Input Sequence in FASTA format

>Q14164 (98 residues)
RVVVHVFSLSQAVLHHIYIHAHNTIAIFQEAVHKQTSVAPRHQEYLFEGHLCVLEPSVSA
QHIAHTTASSPLTLFSTAIPKGLAFRDPALDVPKFVPK

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| RVVVHVFSLSQAVLHHIYIHAHNTIAIFQEAVHKQTSVAPRHQEYLFEGHLCVLEPSVSAQHIAHTTASSPLTLFSTAIPKGLAFRDPALDVPKFVPK
Prediction	CCSSSSSSCCCCSSSSSSSCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCC
Confidence	91899998277179999977112799999999998399916654331892311389861356788899998799945887654335776678998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| RVVVHVFSLSQAVLHHIYIHAHNTIAIFQEAVHKQTSVAPRHQEYLFEGHLCVLEPSVSAQHIAHTTASSPLTLFSTAIPKGLAFRDPALDVPKFVPK
Prediction	64101002044132020103365314403520263271437302211564304146525056236134631030013445433425454363463458
	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

                   |                   |                   |                   |

SS
Seq

CCSSSSSSCCCCSSSSSSSCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCSSCCCCCCCCCCCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCCCCCCC
RVVVHVFSLSQAVLHHIYIHAHNTIAIFQEAVHKQTSVAPRHQEYLFEGHLCVLEPSVSAQHIAHTTASSPLTLFSTAIPKGLAFRDPALDVPKFVPK

6cq0A

0.42

0.38

11.09

1.17

DEthreader

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHF-PKTTENPIFVVSREP--ILILDAHG-HP------

4iw0A2

0.44

0.38

11.06

2.05

SPARKS-K

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLTIGLI-------------

1v5oA

0.09

0.07

2.71

0.55

MapAlign

GMLITVYCVRREVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLTD-DHCSLGSYG-LKDGDMVVLLQKDN-------------------

1v5oA

0.08

0.07

2.88

0.39

CEthreader

GMLITVYCVRREVTFSLQVNPDFELSNFRVLCELESGVPAEEAQIVYMEQLLT-DDHCSLGSYG-LKDGDMVVLLQKDNVGLRTPGRTPSGPSSG---

4iw0A

0.41

12.02

1.54

MUSTER

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPR

4iw0A2

0.44

0.38

11.06

1.72

HHsearch

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSRELNTIGLI-------------

6cq0A2

0.45

0.38

11.04

1.52

FFAS-3D

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTI---------------

4iw0A

0.41

12.02

0.80

EigenThreader

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPR

4efoA

0.47

0.38

11.00

1.67

CNFpred

RMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSLER-------------------

5ebzA

0.14

0.12

4.19

1.17

DEthreader

LKIVHILNMTSAKIISFLLPPDESLHSLQSRIERETGINTGSQELLSETGISLDP-RKPAS-QCVLGCDYMVYLFDKSKTVY----LKDYSRL-----

(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	0.7504

(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	6cq0A	0.83	1.58	0.388	0.918	model1_6cq0A.pdb.gz
2	4eutA	0.75	1.01	0.474	0.796	model1_4eutA.pdb.gz
3	5ebzA	0.73	2.16	0.156	0.898	model1_5ebzA.pdb.gz
4	2inpE	0.67	2.09	0.134	0.837	model1_2inpE.pdb.gz
5	2kk8A	0.67	1.58	0.093	0.765	model1_2kk8A.pdb.gz
6	2w9nA1	0.61	1.92	0.123	0.735	model1_2w9nA1.pdb.gz
7	3q3fA2	0.60	2.08	0.106	0.755	model1_3q3fA2.pdb.gz
8	2dziA	0.59	2.22	0.160	0.755	model1_2dziA.pdb.gz
9	1we7A	0.59	2.21	0.098	0.755	model1_1we7A.pdb.gz
10	1f0qA	0.44	4.49	0.081	0.796	model1_1f0qA.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:0003824	0.80	catalytic activity
GO:0016740	0.78	transferase activity
GO:0004674	0.77	protein serine/threonine kinase activity
GO:0019899	0.57	enzyme binding
GO:0004871	0.56	signal transducer activity
GO:0031625	0.54	ubiquitin protein ligase binding
GO:0036435	0.53	K48-linked polyubiquitin binding
GO:0004704	0.53	NF-kappaB-inducing 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:0009987	0.92	cellular process
GO:0044260	0.90	cellular macromolecule metabolic process
GO:0044238	0.90	primary metabolic process
GO:0006464	0.89	cellular protein modification process
GO:0006468	0.88	protein phosphorylation
GO:0007165	0.79	signal transduction
GO:0043123	0.76	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0035556	0.76	intracellular signal transduction
GO:0051239	0.75	regulation of multicellular organismal process
GO:0048519	0.75	negative regulation of biological process
GO:0002376	0.74	immune system process
GO:0001817	0.74	regulation of cytokine production
GO:0032479	0.73	regulation of type I interferon production
GO:0002218	0.73	activation of innate immune response
GO:0051704	0.68	multi-organism process
GO:0051707	0.67	response to other organism
GO:0016043	0.62	cellular component organization
GO:0051260	0.61	protein homooligomerization
GO:0035456	0.61	response to interferon-beta
GO:0008630	0.61	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0080090	0.50	regulation of primary metabolic process
GO:0031323	0.50	regulation of cellular metabolic 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:0005737	1.00	cytoplasm
GO:0044444	0.80	cytoplasmic part
GO:0016020	0.64	membrane
GO:0044446	0.63	intracellular organelle part
GO:0043226	0.61	organelle
GO:0043229	0.60	intracellular organelle
GO:0043227	0.60	membrane-bounded organelle
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0031090	0.59	organelle membrane
GO:0005829	0.59	cytosol
GO:0005634	0.56	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	2pnyA	0.496	3.69	0.091	0.765	5.3.3.2	NA
2	0.060	2iw2A	0.439	4.56	0.032	0.786	3.4.13.9	NA
3	0.060	1fo4A	0.513	3.57	0.085	0.796	1.17.1.4	NA
4	0.060	2jrhA	0.536	2.98	0.072	0.765	2.7.11.25	NA
5	0.060	2i6kA	0.502	3.29	0.087	0.745	5.3.3.2	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.03	1nbf1	0.613	1.99	0.120	0.745	0.92	III	complex1.pdb.gz	3,5,7,9,15,35,37,38,39,42,44,46,53,73,74,75
	2	0.02	2c7n1	0.599	2.04	0.137	0.745	0.49	III	complex2.pdb.gz	7,8,9,44,46,47,48,49

	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.