D-I-TASSER Q9ULB1-D2

D-I-TASSER results for Q9ULB1-D2

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

Input Sequence in FASTA format

>Q9ULB1 (38 residues)
LADTPVNDGAWHSVRIRRQFRNTTLFIDQVEAKWVEVK

Predicted Secondary Structure

Sequence	20 \| LADTPVNDGAWHSVRIRRQFRNTTLFIDQVEAKWVEVK
Prediction	CCCCCCCCCCCSSSSSSSSCCCCSSSSCCCSSCSSSCC
Confidence	98765568862489998612442899827322025539
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 \| LADTPVNDGAWHSVRIRRQFRNTTLFIDQVEAKWVEVK
Prediction	76734254642341313452551313145445524638
	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

                   |

SS
Seq

CCCCCCCCCCCSSSSSSSSCCCCSSSSCCCSSCSSSCC
LADTPVNDGAWHSVRIRRQFRNTTLFIDQVEAKWVEVK

3najA1

0.03

1.66

1.17

DEthreader

--YDTFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHR

5xauA

0.18

5.97

1.08

SPARKS-K

KTQAGFADGAPHYVAFYSNATGVWLYVDDQLQQMKPHR

2wjsA

0.24

7.39

1.11

MUSTER

PEPNRFHDGREHSVHVERTRGIFTVQIDEDRRHMQNLT

3najA

0.11

3.79

1.17

DEthreader

--DTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHR

3asiA

0.29

8.82

0.96

SPARKS-K

ESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPA

4c1wA

0.22

0.21

6.66

0.63

MapAlign

-APLKVKPGQWNSVTFTVEKGRVRLYVNGVLSRTSLGN

3hbkA

0.11

3.84

0.38

CEthreader

ENIHFNGVGEWNTAVVKVFPNHVEHWLNGVKVLEYERG

3asiA

0.29

8.82

1.09

MUSTER

ESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPA

5xauA

0.18

5.97

0.82

HHsearch

KTQAGFADGAPHYVAFYSNATGVWLYVDDQLQQMKPHR

2erfA

0.22

0.21

6.66

0.59

FFAS-3D

-EEALLATGQWKSITLFVQEDRAQLYIDCEKMENAELD

(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	0.6325

(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	3najA	0.73	1.68	0.105	1.000	model1_3najA.pdb.gz
2	3nv1A	0.73	1.67	0.184	1.000	model1_3nv1A.pdb.gz
3	3wv6A	0.72	1.55	0.132	1.000	model1_3wv6A.pdb.gz
4	1lclA	0.71	1.62	0.081	0.974	model1_1lclA.pdb.gz
5	3b9cA	0.71	1.45	0.135	0.974	model1_3b9cA.pdb.gz
6	2yv8A	0.71	1.72	0.108	0.974	model1_2yv8A.pdb.gz
7	1x50A	0.71	1.46	0.081	0.974	model1_1x50A.pdb.gz
8	2d6nB	0.71	1.96	0.079	1.000	model1_2d6nB.pdb.gz
9	2zhnA	0.70	2.00	0.079	1.000	model1_2zhnA.pdb.gz
10	2nn8A	0.70	1.74	0.053	1.000	model1_2nn8A.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:0097109	1.00	neuroligin family protein binding
GO:0046872	0.79	metal ion binding
GO:0005509	0.77	calcium ion binding
GO:0050839	0.75	cell adhesion molecule binding
GO:0033130	0.75	acetylcholine receptor binding
GO:0005246	0.75	calcium channel regulator 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:0009987	0.90	cellular process
GO:0044763	0.88	single-organism cellular process
GO:0065007	0.84	biological regulation
GO:0050794	0.83	regulation of cellular process
GO:0051179	0.79	localization
GO:0048518	0.78	positive regulation of biological process
GO:0006810	0.78	transport
GO:0048522	0.77	positive regulation of cellular process
GO:0044765	0.77	single-organism transport
GO:0023051	0.77	regulation of signaling
GO:0016043	0.77	cellular component organization
GO:0010646	0.77	regulation of cell communication
GO:2000026	0.76	regulation of multicellular organismal development
GO:1902580	0.76	single-organism cellular localization
GO:0065008	0.76	regulation of biological quality
GO:0051966	0.76	regulation of synaptic transmission, glutamatergic
GO:0051649	0.76	establishment of localization in cell
GO:0051128	0.76	regulation of cellular component organization
GO:0050806	0.76	positive regulation of synaptic transmission
GO:0044802	0.76	single-organism membrane organization
GO:0044707	0.76	single-multicellular organism process
GO:0034613	0.76	cellular protein localization
GO:0032940	0.76	secretion by cell
GO:0022607	0.76	cellular component assembly
GO:0009966	0.76	regulation of signal transduction
GO:0007268	0.76	chemical synaptic transmission
GO:2000463	0.75	positive regulation of excitatory postsynaptic potential
GO:0097119	0.75	postsynaptic density protein 95 clustering
GO:0097118	0.75	neuroligin clustering involved in postsynaptic membrane assembly
GO:0097116	0.75	gephyrin clustering involved in postsynaptic density assembly
GO:0097104	0.75	postsynaptic membrane assembly
GO:0090129	0.75	positive regulation of synapse maturation
GO:0051968	0.75	positive regulation of synaptic transmission, glutamatergic
GO:0051965	0.75	positive regulation of synapse assembly
GO:0050885	0.75	neuromuscular process controlling balance
GO:0030534	0.75	adult behavior
GO:0007612	0.75	learning
GO:0007416	0.75	synapse assembly
GO:0007269	0.75	neurotransmitter secretion
GO:0048519	0.53	negative regulation of biological process
GO:0071625	0.51	vocalization behavior
GO:0042297	0.51	vocal learning
GO:0035176	0.51	social behavior
GO:0048585	0.50	negative regulation of response to stimulus

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:0044425	1.00	membrane part
GO:0044464	0.96	cell part
GO:0044424	0.93	intracellular part
GO:0016020	0.92	membrane
GO:0044444	0.91	cytoplasmic part
GO:0043229	0.91	intracellular organelle
GO:0005886	0.91	plasma membrane
GO:0097458	0.90	neuron part
GO:0097060	0.90	synaptic membrane
GO:0044428	0.90	nuclear part
GO:0043231	0.90	intracellular membrane-bounded organelle
GO:0031090	0.90	organelle membrane
GO:0043025	0.89	neuronal cell body
GO:0042734	0.89	presynaptic membrane
GO:0031982	0.89	vesicle
GO:0031965	0.89	nuclear membrane
GO:0009986	0.89	cell surface
GO:0005783	0.89	endoplasmic reticulum

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	2vz8B	0.602	1.74	0.105	1.000	2.3.1.85	NA
2	0.060	1af0A	0.368	3.56	0.081	0.947	3.4.24.40	NA
3	0.060	1lo8A	0.636	2.25	0.000	1.000	3.1.2.23	NA
4	0.060	3kf5A	0.597	2.56	0.083	0.947	3.2.1.26	NA
5	0.060	2aeyA	0.592	2.77	0.105	1.000	3.2.1.80	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:

No Binding sites was predicted

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

	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.