D-I-TASSER P51530-D1

D-I-TASSER results for P51530-D1

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

Input Sequence in FASTA format

>P51530 (147 residues)
MEQLNELELLMEKSFWEEAELPAELFQKKVVASFPRTKKNHQNIWLMPASEMEKSGSCIG
NLIRMEHVKIVCDGQYLHNFQCKHGAIPVTNLMAGDRVIVSGEERSLFALSRGYVKEINM
TTVTCLLDRNLSVLPESTLFRLDQEEK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MEQLNELELLMEKSFWEEAELPAELFQKKVVASFPRTKKNHQNIWLMPASEMEKSGSCIGNLIRMEHVKIVCDGQYLHNFQCKHGAIPVTNLMAGDRVIVSGEERSLFALSRGYVKEINMTTVTCLLDRNLSVLPESTLFRLDQEEK
Prediction	CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCSSSSCCCSSCCCCSSSSSSSSCCCCCCCCCCCCCCSSSSSCCCCCSSSSSSSSSSSSSCCSSSSSSCCCCCCCCCCCSSSSCCCCC
Confidence	973257999978876511311199999999999988644356652599899987197424739925730214983999999668998767577996299976899859999748999859989999847677789985799537899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MEQLNELELLMEKSFWEEAELPAELFQKKVVASFPRTKKNHQNIWLMPASEMEKSGSCIGNLIRMEHVKIVCDGQYLHNFQCKHGAIPVTNLMAGDRVIVSGEERSLFALSRGYVKEINMTTVTCLLDRNLSVLPESTLFRLDQEEK
Prediction	864354144215521553364425104520453266455334302424175126434010403036445646554131203155552442403441200000554330000212034145630101033504735653103014558
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCSSSSCCCSSCCCCSSSSSSSSCCCCCCCCCCCCCCSSSSSCCCCCSSSSSSSSSSSSSCCSSSSSSCCCCCCCCCCCSSSSCCCCC
MEQLNELELLMEKSFWEEAELPAELFQKKVVASFPRTKKNHQNIWLMPASEMEKSGSCIGNLIRMEHVKIVCDGQYLHNFQCKHGAIPVTNLMAGDRVIVSGEERSLFALSRGYVKEINMTTVTCLLDRNLSVLPESTLFRLDQEEK

5eanA1

0.56

0.50

14.50

1.17

DEthreader

-----------QLAHLKYFSLWCLMLTLESQSKDNRK-T-HQSIWLTPASELEESGNCVGNLVRTEPVSR-VCDQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

5eanA

0.54

15.51

2.55

SPARKS-K

PEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESKDNRKTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

5eanA1

0.56

0.55

15.86

1.29

MapAlign

---LQELALQTLREVRHLKEMQDEILCEVEEYLPSFSKWAEDFIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

4b3fX1

0.17

0.14

4.72

1.10

CEthreader

---------------SAAVESFVTKQLDLLELERDAEVEERRSWQNISLKELQSRGVCLLKLQVSSQRTG-LYGRLLVTFEPRRAALPSNSFTSGDIVGLYDAANEGSQLATGILTRVTQKSVTVAFDS----LDRENSYRLLKLAN

5eanA1

0.52

15.14

1.81

MUSTER

ASIPEAMLSKIQRHLQLAHLKYFSLWCLMLTLESQSKDNTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

5eanA1

0.54

15.51

3.54

HHsearch

VEEMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKRKTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

4b3fX1

0.19

0.16

5.07

1.44

FFAS-3D

------AAVES---FVTKQLDLLELERD------AEVEERRSWQENISLKELQSRGVCLLKLQVSS-QRTGLYGRLLVTFEPRRYALPSNSFTSGDIVGLYDAANEGSQLATGILTRVTQKSVTVAFDS----LDRENSYRLLK---

4b3fX1

0.15

0.13

4.36

1.15

EigenThreader

--------------SAAVESFVTKQLDLLELERDAEVEERRSWQENISLKELQSRGVCLLKLQVSSQ-RTGLYGRLLVTFEPRRYALPSNSFTSGDIVGLYDAANEGSQLATGILTRVTQKSVTVAF----DSLDRENSYRLLKLND

5eanA

0.54

15.51

1.94

CNFpred

PEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDKTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

5eanA

0.56

0.50

14.50

1.17

DEthreader

-----------QLAHLKYFSLWCLMLTLESQSKDNRK-T-HQSIWLTPASELEESGNCVGNLVRTEPVSR-VCDQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREER

(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	0.7205

(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	5eanA1	0.76	3.29	0.537	0.905	model1_5eanA1.pdb.gz
2	4b3fX	0.63	2.95	0.148	0.796	model1_4b3fX.pdb.gz
3	4flnA	0.40	4.94	0.037	0.667	model1_4flnA.pdb.gz
4	2efxA	0.35	5.29	0.034	0.660	model1_2efxA.pdb.gz
5	2wjvA3	0.34	5.04	0.026	0.619	model1_2wjvA3.pdb.gz
6	3euwA	0.33	5.64	0.082	0.626	model1_3euwA.pdb.gz
7	2xzlA3	0.32	5.05	0.025	0.565	model1_2xzlA3.pdb.gz
8	1ii0B	0.32	5.01	0.070	0.571	model1_1ii0B.pdb.gz
9	1sxjC1	0.32	5.19	0.061	0.558	model1_1sxjC1.pdb.gz
10	1lv7A1	0.31	4.99	0.030	0.551	model1_1lv7A1.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	1.00	hydrolase activity
GO:0004520	0.97	endodeoxyribonuclease activity
GO:0017108	0.96	5'-flap endonuclease activity
GO:0003676	0.87	nucleic acid binding
GO:0008094	0.86	DNA-dependent ATPase activity
GO:0043139	0.85	5'-3' DNA helicase activity
GO:0043142	0.83	single-stranded DNA-dependent ATPase activity
GO:0003677	0.83	DNA binding
GO:0016890	0.61	site-specific endodeoxyribonuclease activity, specific for altered base

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:0044260	1.00	cellular macromolecule metabolic process
GO:0044238	1.00	primary metabolic process
GO:0034641	1.00	cellular nitrogen compound metabolic process
GO:0034645	0.99	cellular macromolecule biosynthetic process
GO:0006259	0.99	DNA metabolic process
GO:0006260	0.98	DNA replication
GO:0022402	0.84	cell cycle process
GO:0033567	0.83	DNA replication, Okazaki fragment processing
GO:0031570	0.83	DNA integrity checkpoint
GO:0000729	0.82	DNA double-strand break processing
GO:0000076	0.81	DNA replication checkpoint
GO:0065007	0.66	biological regulation
GO:0016070	0.66	RNA metabolic process
GO:0006281	0.66	DNA repair
GO:2000112	0.65	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.65	regulation of nucleobase-containing compound metabolic process
GO:0006401	0.65	RNA catabolic process
GO:0051054	0.64	positive regulation of DNA metabolic process
GO:0032042	0.64	mitochondrial DNA metabolic process
GO:0031328	0.64	positive regulation of cellular biosynthetic process
GO:0010557	0.64	positive regulation of macromolecule biosynthetic process
GO:0006275	0.64	regulation of DNA replication
GO:0006261	0.63	DNA-dependent DNA replication
GO:0043137	0.62	DNA replication, removal of RNA primer
GO:0045740	0.61	positive regulation of DNA replication
GO:0006284	0.61	base-excision repair
GO:0006264	0.61	mitochondrial DNA replication

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:0044446	0.96	intracellular organelle part
GO:0044444	0.96	cytoplasmic part
GO:0032991	0.96	macromolecular complex
GO:0043234	0.95	protein complex
GO:0005760	0.93	gamma DNA polymerase complex
GO:0043231	0.55	intracellular membrane-bounded organelle
GO:0005634	0.53	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	1ewyA	0.455	3.44	0.074	0.639	1.18.1.2	NA
2	0.060	2b5oB	0.451	3.50	0.104	0.619	1.18.1.2	58,62,113
3	0.060	1gpzA	0.453	4.06	0.057	0.667	3.4.21.41	NA
4	0.060	1fuiA	0.530	4.32	0.056	0.789	5.3.1.25	NA
5	0.060	1qfyA	0.445	3.46	0.096	0.619	1.18.1.2	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:

Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
1	0.06	1amoA	0.529	4.28	0.080	0.816	0.26	FMN	complex1.pdb.gz	42,43,44,45,143
2	0.06	1amoA	0.529	4.28	0.080	0.816	0.16	NAP	complex2.pdb.gz	52,101,110,112,114
3	0.01	1cqxA	0.540	4.74	0.092	0.871	0.23	FAD	complex3.pdb.gz	96,112,113,114,115,129
4	0.01	3ozuA	0.545	4.63	0.088	0.864	0.20	UUU	complex4.pdb.gz	36,37,40,41,108
5	0.01	1cqxA	0.540	4.74	0.092	0.871	0.18	HEM	complex5.pdb.gz	56,96,97
6	0.01	3ozvA	0.533	4.51	0.081	0.837	0.27	DGG	complex6.pdb.gz	40,43,52,55
7	0.01	1cqxB	0.543	4.69	0.092	0.871	0.11	DGG	complex7.pdb.gz	39,40,43,46,55
8	0.01	1ja0A	0.530	4.34	0.063	0.844	0.11	NAP	complex8.pdb.gz	126,127,128,130,131
9	0.01	3fjoA	0.467	3.89	0.063	0.680	0.11	FAD	complex9.pdb.gz	94,95,98,100,102
10	0.01	1tllB	0.524	4.10	0.047	0.769	0.16	NAP	complex10.pdb.gz	41,44,45,49,57,112

	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.