D-I-TASSER Q3LFD5-D1

D-I-TASSER results for Q3LFD5-D1

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

Input Sequence in FASTA format

>Q3LFD5 (160 residues)
MDGVLFRAHQCQYVHPCVHVYVTVGLMDPLCERKEKASKQERENPLAHLAAWGLVGLHNI
GQTCCLNSLIQVFVMNVDFARILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVWP
LELAYCLQKYNVPLFVQHDAAQLYLKLWNLIKDQIADVHL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDGVLFRAHQCQYVHPCVHVYVTVGLMDPLCERKEKASKQERENPLAHLAAWGLVGLHNIGQTCCLNSLIQVFVMNVDFARILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVWPLELAYCLQKYNVPLFVQHDAAQLYLKLWNLIKDQIADVHL
Prediction	CCCSSSSCCCCCCCCCCHHHHCCHHHCHHHHCCHHHCCHCHCCCCCCCCCCCCCCCCSCCCCCHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCSCHHHHHHHHHCCCCCCCCSHHHHHHHHHHHHHHHHHCCCCCC
Confidence	9960320454420365222201221011443001101100002543235678987723178117999999999907699999995467887655313699999999999996899822789999998076888764065999999999999997348999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDGVLFRAHQCQYVHPCVHVYVTVGLMDPLCERKEKASKQERENPLAHLAAWGLVGLHNIGQTCCLNSLIQVFVMNVDFARILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVWPLELAYCLQKYNVPLFVQHDAAQLYLKLWNLIKDQIADVHL
Prediction	7633135245353344224232344214323646654555546454644564311103021110000010001110430030024242555454432200310230032035365420304401510444514322022224243135643476167478
	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                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCSSSSCCCCCCCCCCHHHHCCHHHCHHHHCCHHHCCHCHCCCCCCCCCCCCCCCCSCCCCCHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCSCHHHHHHHHHCCCCCCCCSHHHHHHHHHHHHHHHHHCCCCCC
MDGVLFRAHQCQYVHPCVHVYVTVGLMDPLCERKEKASKQERENPLAHLAAWGLVGLHNIGQTCCLNSLIQVFVMNVDFARILKRITVPRGADEQRRSVPFQMLLLLEKMQDSRQKAVWPLELAYCLQKYNVPLFVQHDAAQLYLKLWNLIKDQIADVHL

4q8hA

0.12

0.09

3.33

1.00

DEthreader

--PETSD-IQTY----------TSI------P----------FD-FTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENF---ETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTREEDFIKMPQKFNRFLLSQLIKEEAQTHN

5chtA1

0.77

0.55

15.57

1.64

SPARKS-K

---------------------------------------------GPGDSPHGLVGLHNIGQTCCLNSLLQVFMMNMDFRMILKRITVPRSAEERKRSVPFQLLLLLEKMQDSRQKAVLPTELVQCLQKYNVPLFVQHDAAQLYLTIWNLTKDQITDTDL

6tbmQ

0.15

0.14

4.85

1.05

MapAlign

-----SCPHLKQILTSNAKDTVYRNYGLAVMNNLGTETIIDGSRPPSLKASTGLRGFINMGATCFMSSIVQTIVHNPFVRDYFLSGYHAKCTKKMDTCITCCIDEIFKVFYGDETKGYGPTALLTAAWRVKLAGYSEQDAHEFWQFLLDEIHKSDTCRCI

6tbmQ

0.17

5.56

0.79

CEthreader

QTGYIFCFRCGDYVGDQRLEFIRQSKQGERTEPIMNNLGTETIRPPSLKASTGLRGFINMGATCFMSSIVQTIVHNPFVRDYFLSGYHAKCTKKMDTCITCCIDEIFKVFYGTDEKGYGPTALLTAAWRVKLAGYSEQDAHEFWQFLLDEIHKSDTELHP

5chtA1

0.77

0.55

15.57

1.69

MUSTER

---------------------------------------------GPGDSPHGLVGLHNIGQTCCLNSLLQVFMMNMDFRMILKRITVPRSAEERKRSVPFQLLLLLEKMQDSRQKAVLPTELVQCLQKYNVPLFVQHDAAQLYLTIWNLTKDQITDTDL

6tbmQ

0.15

5.05

1.85

HHsearch

TGHVFGIDSQYIFCFRCGDYVGDQRLEFIRQSKQGERTEPIETIIPSLKASTGLRGFINMGATCFMSSIVQTIVHNPFVRDYFLSGYHAKCTKKMDTCITCCIDEIFKVFYGTETKGYGPTALLTAAWRVKNAGYSEQDAHEFWQFLLDEIHKSDTELHP

5chtA1

0.79

0.54

15.37

1.93

FFAS-3D

-------------------------------------------------SPHGLVGLHNIGQTCCLNSLLQVFMMNMDFRMILKRITVPRSAEERKRSVPFQLLLLLEKMQDSRQKAVLPTELVQCLQKYNVPLFVQHDAAQLYLTIWNLTKDQITDTD-

4zuxe

0.14

4.71

1.47

EigenThreader

LNTMKCGTCHEINSGAWNHSHFLSHSKQIGHIFGINSNNCTKTMVPSMERRDGLSGLINMGSTAFMSSILQCLIHNPYFIRHSMSHSNNCKVRSPDKCFSCALDKIVHELYGALNRQTGFIYLLTCAWKINLAGYSQQDAHEFWQFIINQIHQSYVCECI

5chtA

0.81

0.55

15.53

1.17

CNFpred

----------------------------------------------------GLVGLHNIGQTCCLNSLLQVFMMNMDFRMILKRITVPRSAEERKRSVPFQLLLLLEKMQDSRQKAVLPTELVQCLQKYNVPLFVQHDAAQLYLTIWNLTKDQITDTDL

4q8hA1

0.12

0.09

3.33

1.00

DEthreader

--PETSD-IQTY----------TSI------P----------FD-FTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENF---ETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTREEDFIKMPQKFNRFLLSQLIKEEAQTHN

(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	0.7172

(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	5chtA	0.64	2.46	0.754	0.713	model1_5chtA.pdb.gz
2	4q8hA1	0.63	3.28	0.092	0.781	model1_4q8hA1.pdb.gz
3	3ihpB3	0.61	2.01	0.214	0.700	model1_3ihpB3.pdb.gz
4	6r5kA2	0.61	2.94	0.085	0.750	model1_6r5kA2.pdb.gz
5	6h4hA	0.60	2.79	0.217	0.713	model1_6h4hA.pdb.gz
6	4czwA	0.60	2.63	0.109	0.719	model1_4czwA.pdb.gz
7	2f1zB	0.60	3.18	0.154	0.738	model1_2f1zB.pdb.gz
8	3mhhA2	0.57	2.60	0.196	0.669	model1_3mhhA2.pdb.gz
9	2ayoA	0.57	2.89	0.182	0.669	model1_2ayoA.pdb.gz
10	2gfoA1	0.56	2.57	0.171	0.650	model1_2gfoA1.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:0016787	0.99	hydrolase activity
GO:0008234	0.98	cysteine-type peptidase activity
GO:0019783	0.97	ubiquitin-like protein-specific protease activity
GO:0004843	0.87	thiol-dependent ubiquitin-specific protease 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:0009987	0.94	cellular process
GO:0071704	0.88	organic substance metabolic process
GO:0044260	0.87	cellular macromolecule metabolic process
GO:0044238	0.87	primary metabolic process
GO:0050794	0.80	regulation of cellular process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0019538	0.65	protein metabolic process
GO:0031323	0.64	regulation of cellular metabolic process
GO:0044267	0.60	cellular protein metabolic process
GO:0050896	0.59	response to stimulus
GO:0006508	0.59	proteolysis
GO:0006464	0.59	cellular protein modification process
GO:0070647	0.58	protein modification by small protein conjugation or removal
GO:0034641	0.56	cellular nitrogen compound metabolic process
GO:2000112	0.55	regulation of cellular macromolecule biosynthetic process
GO:0090304	0.55	nucleic acid metabolic process
GO:0051252	0.55	regulation of RNA metabolic process
GO:0010468	0.55	regulation of gene expression
GO:0016579	0.54	protein deubiquitination
GO:0006355	0.54	regulation of transcription, DNA-templated
GO:0051716	0.50	cellular response to stimulus
GO:0048519	0.50	negative regulation of biological process
GO:0006950	0.50	response to stress

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:0044424	1.00	intracellular part
GO:0043229	0.96	intracellular organelle
GO:0043231	0.93	intracellular membrane-bounded organelle
GO:0005634	0.89	nucleus
GO:0005737	0.72	cytoplasm
GO:0044444	0.58	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	0.060	2f1yA	0.265	5.09	0.010	0.475	3.1.2.15	23,74
2	0.060	2nyfA	0.441	5.00	0.079	0.744	4.3.1.5	NA
3	0.060	1lwdA	0.430	4.62	0.040	0.694	1.1.1.42	NA
4	0.060	1l9mB	0.442	4.89	0.045	0.750	2.3.2.13	NA
5	0.060	1k0wA	0.437	4.95	0.079	0.738	5.1.3.4	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	3r0iA	0.433	4.77	0.040	0.681	0.28	C0K	complex1.pdb.gz	56,66,67,70
2	0.01	3anmB	0.429	4.72	0.040	0.675	0.31	SYD	complex2.pdb.gz	19,57,58,60,66
3	0.01	2avw0	0.497	4.08	0.078	0.731	0.12	III	complex3.pdb.gz	57,58,59,60,61
4	0.01	1t1sA	0.432	4.56	0.032	0.669	0.18	CBQ	complex4.pdb.gz	32,52,54
5	0.01	1q0hA	0.433	4.84	0.048	0.694	0.13	NDP	complex5.pdb.gz	57,58,59,60
6	0.01	1q0qA	0.434	4.73	0.063	0.688	0.21	DXP	complex6.pdb.gz	54,67,71,105
7	0.01	3anlA	0.430	4.78	0.040	0.681	0.12	NDP	complex7.pdb.gz	8,11,31,53,54,55
8	0.01	3mqsC	0.256	5.42	0.028	0.456	0.36	III	complex8.pdb.gz	54,56,58,81,112
9	0.01	2eghA	0.434	4.36	0.058	0.669	0.12	NDP	complex9.pdb.gz	21,22,23,58,76
10	0.01	1t1sB	0.433	4.68	0.048	0.675	0.13	CBQ	complex10.pdb.gz	26,58,68

	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.