D-I-TASSER Q13099-D4

D-I-TASSER results for Q13099-D4

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

Input Sequence in FASTA format

>Q13099 (51 residues)
FAQASSYADIAVNSDRYNPAALTNKGNTVFANGDYEKAAEFYKEALRNDSS

Predicted Secondary Structure

Sequence	20 40 \| \| FAQASSYADIAVNSDRYNPAALTNKGNTVFANGDYEKAAEFYKEALRNDSS
Prediction	CCHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHCCHHHHHHHHHHHHHHCCC
Confidence	505999999999828878567641010113208699999999999971059
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 \| \| FAQASSYADIAVNSDRYNPAALTNKGNTVFANGDYEKAAEFYKEALRNDSS
Prediction	675155105203733432040101321031245426403620450274558
	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

                   |                   |

SS
Seq

CCHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHCCHHHHHHHHHHHHHHCCC
FAQASSYADIAVNSDRYNPAALTNKGNTVFANGDYEKAAEFYKEALRNDSS

5dseA

0.22

6.82

1.50

DEthreader

YSLAEKILRDAVQVNSTAHEVWNGLGEVLQAQGNDAAATECFLTALELEAS

6tntJ5

0.16

5.24

1.53

SPARKS-K

NEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKG

3fp3A4

0.20

6.27

1.27

FFAS-3D

SQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLNP-

5dseA5

0.22

6.82

1.50

DEthreader

YSLAEKILRDAVQVNSTAHEVWNGLGEVLQAQGNDAAATECFLTALELEAS

2xpiA5

0.18

5.76

1.45

SPARKS-K

ISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQG

4abnA

0.20

6.29

0.66

MapAlign

VMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYISQQALSAYAQAEKVDRK

4abnA2

0.20

6.29

0.36

CEthreader

VMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYISQQALSAYAQAEKVDRK

6b85J

0.24

7.35

0.94

MUSTER

LDEAAEAYKKAIELKPNDASAWKELGKVLEKLGRLDEAAEAYKKAIELDPE

5nnpA

0.14

4.71

0.47

HHsearch

LGDAMKFLNYILQFSPKNIDGQIAGFEVYIRKKKYLLALRCLKAASAIDKN

1ihgA3

0.20

6.29

1.21

FFAS-3D

WQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPE

(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	0.7423

(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	4kvmA	0.94	0.60	0.196	1.000	model1_4kvmA.pdb.gz
2	5lynA	0.94	0.61	0.275	1.000	model1_5lynA.pdb.gz
3	5nnpA	0.93	0.62	0.275	1.000	model1_5nnpA.pdb.gz
4	5dseA5	0.93	0.92	0.216	1.000	model1_5dseA5.pdb.gz
5	1w3bA	0.93	0.79	0.196	1.000	model1_1w3bA.pdb.gz
6	2c0mC	0.93	0.67	0.196	1.000	model1_2c0mC.pdb.gz
7	2hyzA2	0.90	1.04	0.333	1.000	model1_2hyzA2.pdb.gz
8	2q7fA2	0.88	0.96	0.235	1.000	model1_2q7fA2.pdb.gz
9	1elrA	0.85	1.05	0.294	1.000	model1_1elrA.pdb.gz
10	3fp3A1	0.81	1.16	0.100	0.980	model1_3fp3A1.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:0008092	0.44	cytoskeletal protein binding
GO:0019894	0.41	kinesin binding
GO:0097159	0.34	organic cyclic compound binding
GO:1901363	0.33	heterocyclic compound 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:0044767	1.00	single-organism developmental process
GO:0030030	1.00	cell projection organization
GO:0065007	0.94	biological regulation
GO:0050789	0.89	regulation of biological process
GO:0050794	0.88	regulation of cellular process
GO:0060271	0.85	cilium morphogenesis
GO:1902589	0.84	single-organism organelle organization
GO:0042384	0.83	cilium assembly
GO:0007017	0.77	microtubule-based process
GO:0051179	0.76	localization
GO:0035058	0.76	nonmotile primary cilium assembly
GO:0008104	0.75	protein localization
GO:0048856	0.70	anatomical structure development
GO:0048522	0.70	positive regulation of cellular process
GO:0032501	0.70	multicellular organismal process
GO:0050896	0.69	response to stimulus
GO:0044707	0.69	single-multicellular organism process
GO:0048584	0.68	positive regulation of response to stimulus
GO:0009966	0.68	regulation of signal transduction
GO:0007368	0.68	determination of left/right symmetry
GO:0000226	0.68	microtubule cytoskeleton organization
GO:0060122	0.67	inner ear receptor stereocilium organization
GO:0048598	0.67	embryonic morphogenesis
GO:0009967	0.67	positive regulation of signal transduction
GO:0009888	0.67	tissue development
GO:0008589	0.67	regulation of smoothened signaling pathway
GO:0006928	0.61	movement of cell or subcellular component
GO:0007018	0.60	microtubule-based movement
GO:0006810	0.60	transport
GO:0051649	0.59	establishment of localization in cell
GO:0051641	0.59	cellular localization
GO:0044765	0.59	single-organism transport
GO:0015031	0.59	protein transport
GO:1902582	0.58	single-organism intracellular transport
GO:0042073	0.58	intraciliary transport
GO:0030705	0.58	cytoskeleton-dependent intracellular transport
GO:0098840	0.57	protein transport along microtubule
GO:0022402	0.53	cell cycle process
GO:1903047	0.52	mitotic cell cycle process
GO:0045494	0.52	photoreceptor cell maintenance
GO:0072019	0.51	proximal convoluted tubule development
GO:0071482	0.51	cellular response to light stimulus
GO:0060785	0.51	regulation of apoptosis involved in tissue homeostasis
GO:0045880	0.51	positive regulation of smoothened signaling pathway
GO:0042462	0.51	eye photoreceptor cell development
GO:0007369	0.51	gastrulation
GO:0003351	0.51	epithelial cilium movement
GO:0000132	0.51	establishment of mitotic spindle orientation

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	1.00	cell part
GO:0044424	0.95	intracellular part
GO:0044422	0.93	organelle part
GO:0044446	0.92	intracellular organelle part
GO:0043226	0.91	organelle
GO:0042995	0.89	cell projection
GO:0005929	0.88	cilium
GO:0044430	0.81	cytoskeletal part
GO:0044441	0.78	ciliary part
GO:0005815	0.77	microtubule organizing center
GO:0036064	0.76	ciliary basal body
GO:0005930	0.57	axoneme
GO:0044444	0.52	cytoplasmic 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	0.067	1tjcA	0.838	1.51	0.196	1.000	1.14.11.2	NA
2	0.066	1fyjA	0.583	1.95	0.122	0.706	6.1.1.15 6.1.1.17	NA
3	0.060	1ayxA	0.635	2.87	0.176	0.980	3.2.1.3	44
4	0.060	2fbnA	0.817	1.46	0.235	1.000	5.2.1.8	NA
5	0.060	1w0dD	0.661	2.95	0.102	0.941	1.1.1.85	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	0.32	1elrA	0.854	1.05	0.294	1.000	0.70	III	complex1.pdb.gz	8,20,24,27,30,31

	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.