D-I-TASSER Q6PCE3-D1

D-I-TASSER results for Q6PCE3-D1

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

Input Sequence in FASTA format

>Q6PCE3 (233 residues)
MAENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLRWDKNPKTKEQIENLLRNGMNKELRDR
LCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFKQRGFVVGYDTRGQ
VTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTPFVPYAVQKLKAVAGVMITASHNRKE
DNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLRWDKNPKTKEQIENLLRNGMNKELRDRLCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFKQRGFVVGYDTRGQVTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTPFVPYAVQKLKAVAGVMITASHNRKEDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQ
Prediction	CCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCSCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSCCCCCCCCHHHHHHHHHCCCSSSSSSCCCCCCCCCCSSSSCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	98644565317888523457798999999999924999789999999999199999999982798656853021148998702499999999999999999778666862999864888877677769999999999998199799859999982889999984896579995478992227379977998839999999999999863555455543122002300004589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MAENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLRWDKNPKTKEQIENLLRNGMNKELRDRLCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFKQRGFVVGYDTRGQVTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTPFVPYAVQKLKAVAGVMITASHNRKEDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQ
Prediction	76646656233411532453337503620550174452760262045116653462036104651442113020312532232023001200200030026317745521000000014444441204300310030014340301104431101000100332503000000000004620000012640140346115401620563154265425461154252464228
	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                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCSCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSCCCCCCCCHHHHHHHHHCCCSSSSSSCCCCCCCCCCSSSSCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC
MAENTEGDLNSNLLHAPYHTGDPQLDTAIGQWLRWDKNPKTKEQIENLLRNGMNKELRDRLCCRMTFGTAGLRSAMGAGFCYINDLTVIQSTQGMYKYLERCFSDFKQRGFVVGYDTRGQVTSSCSSQRLAKLTAAVLLAKDVPVYLFSRYVPTPFVPYAVQKLKAVAGVMITASHNRKEDNGYKVYWETGAQITSPHDKEILKCIEECVEPWNGSWNDNLVDTSPLKRDPLQ

2fuvA1

0.22

0.16

5.02

1.00

DEthreader

-----------------------------------QYY-VLK--P-----------EA-GNAEAVKFGTSGHRGSAGRH-S-FNEPHILAIAQAIAEERAKNG--IT-GPCYVGKDT-H-----ALSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHNLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLGLQVKRISLDAA-ASGHVKAVDL

1tuoA1

0.29

0.18

5.50

1.78

SPARKS-K

------------------------------------------------------------MSAPIRFGTEGFRGVIARE---FTFATLHRLAEAYGRHLLER----GGGLVVVGHDTRF------LADAFARALSGHLAGMGLKVVLLKGPVPTPLLSFAVRHLKAAGGAMLTASHNPPQYLGVKFKDATGGPIAQEEAKAIEALVPEEARALEGAYETL-------------

2fuvA

0.20

0.17

5.35

1.13

MapAlign

--------------------AIHNRAGQPAQQSDLINVAQLTAQYYVL------KPEAGNAEHAVKFGTSGHRG-SAG-RHSFNEPHILAIAQAIAEERAKN--GIT-GPCYVGKDTH------ALSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLGLV-KRISLDAA-ASGHVKAVDL

2fuvA1

0.19

0.16

5.24

0.79

CEthreader

------------------------AIHNRAGQPAQQSDLINVAQLTAQYYVLKPE--AGNAEHAVKFGTSGHRGSAGRH--SFNEPHILAIAQAIAEERAKNG---ITGPCYVGKDTHA------LSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHNLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLAQGVKRISLDAAASGHVKAVDLV

1tuoA1

0.29

0.18

5.50

1.38

MUSTER

------------------------------------------------------------MSAPIRFGTEGFRGVIARE---FTFATLHRLAEAYGRHLLER----GGGLVVVGHDTRF------LADAFARALSGHLAGMGLKVVLLKGPVPTPLLSFAVRHLKAAGGAMLTASHNPPQYLGVKFKDATGGPIAQEEAKAIEALVPEEARALEGAYETL-------------

2fuvA

0.22

0.18

5.81

2.40

HHsearch

AIHNRAG-------QPAQQSDLINVAQLTAQYYVLKPEAGN-------------------AEHAVKFGTSGHRGSAGRH--SFNEPHILAIAQAIAEERAKNG---ITGPCYVGKDTHA------LSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHNLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLAVKRISLDAA---ASGHGVDPLG

1tuoA1

0.30

0.18

5.61

1.66

FFAS-3D

------------------------------------------------------------MSAPIRFGTEGFRGVIAREFT---FATLHRLAEAYGRHLLE----RGGGLVVVGHDTRF------LADAFARALSGHLAGMGLKVVLLKGPVPTPLLSFAVRHLKAAGGAMLTASHNPPQYLGVKFKDATGGPIAQEEAKAIEALVPEEARALEGAYE---------------

2fuvA1

0.18

0.15

5.01

1.12

EigenThreader

IHNRAGQPA-------QQSDLINVAQLTAQYYVLKPEAG------------NAE--------HAVKFGTSGHRGSAGR--HSFNEPHILAIAQAIAEERAKN---GITGPCYVGKDTHA------LSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHNKKDGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLAGGLQGVKRISLDAAASGHLVQP

3na5A

0.21

0.16

5.06

1.38

CNFpred

------------------------VAQLTAQYYVLKPEAGN-------------------AEHAVKFGTSGHRGSAGR--HSFNEPHILAIAQAIAEERAKN---GITGPCYVGKDTHA------LSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHNLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLAGGVKRISLDAAMASGHVKAVDL

2fuvA

0.22

0.16

5.02

1.00

DEthreader

-----------------------------------QYY-VLK--P-----------EA-GNAEAVKFGTSGHRGSAGRH-S-FNEPHILAIAQAIAEERAKNG--IT-GPCYVGKDT-H-----ALSEPAFISVLEVLAANGVDVIVQEGFTPTPAVSNAILVHNLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANALLGLQVKRISLDAA-ASGHVKAVDL

(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	0.7442

(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	2fuvA	0.68	2.38	0.185	0.747	model1_2fuvA.pdb.gz
2	2z0fB	0.65	2.72	0.175	0.738	model1_2z0fB.pdb.gz
3	1kfqA1	0.61	2.61	0.177	0.700	model1_1kfqA1.pdb.gz
4	1c4gA1	0.61	2.37	0.208	0.682	model1_1c4gA1.pdb.gz
5	1tuoA	0.60	1.65	0.275	0.639	model1_1tuoA.pdb.gz
6	1wqaA	0.58	2.49	0.255	0.639	model1_1wqaA.pdb.gz
7	2f7lA	0.57	2.75	0.273	0.631	model1_2f7lA.pdb.gz
8	1k2yX	0.56	2.82	0.212	0.639	model1_1k2yX.pdb.gz
9	3i3wA	0.56	2.26	0.259	0.614	model1_3i3wA.pdb.gz
10	1yooA	0.40	5.14	0.047	0.622	model1_1yooA.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	1.00	catalytic activity
GO:0016740	0.65	transferase activity
GO:0016772	0.61	transferase activity, transferring phosphorus-containing groups
GO:0016773	0.60	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.60	kinase activity
GO:0047933	0.59	glucose-1,6-bisphosphate synthase 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:0071704	1.00	organic substance metabolic process
GO:0044238	1.00	primary metabolic process
GO:0009987	0.95	cellular process
GO:0044237	0.93	cellular metabolic process
GO:0009058	0.91	biosynthetic process
GO:1901576	0.90	organic substance biosynthetic process
GO:0044249	0.90	cellular biosynthetic process
GO:0044699	0.75	single-organism process
GO:0006807	0.71	nitrogen compound metabolic process
GO:0034641	0.70	cellular nitrogen compound metabolic process
GO:1901360	0.69	organic cyclic compound metabolic process
GO:0046483	0.69	heterocycle metabolic process
GO:0044710	0.69	single-organism metabolic process
GO:0006725	0.69	cellular aromatic compound metabolic process
GO:0006139	0.68	nucleobase-containing compound metabolic process
GO:0044281	0.67	small molecule metabolic process
GO:1901135	0.65	carbohydrate derivative metabolic process
GO:0044271	0.60	cellular nitrogen compound biosynthetic process
GO:0005975	0.60	carbohydrate metabolic process
GO:0034654	0.59	nucleobase-containing compound biosynthetic process
GO:1901137	0.58	carbohydrate derivative biosynthetic process
GO:0044763	0.55	single-organism cellular process
GO:0044723	0.53	single-organism carbohydrate metabolic process
GO:0019318	0.50	hexose 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:0044424	1.00	intracellular part
GO:0005829	0.99	cytosol

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	2dq4A	0.473	5.37	0.044	0.747	1.1.1.103	NA
2	0.060	1vj0A	0.478	5.68	0.043	0.768	1.1.1.1	NA
3	0.060	2vwqA	0.486	5.28	0.100	0.755	1.1.1.47	NA
4	0.060	1p0fA	0.483	5.32	0.044	0.747	1.1.1.2	92,170
5	0.060	1agnA	0.489	5.47	0.063	0.764	1.1.1.1	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	0.18	2h4lX	0.556	2.74	0.224	0.631	0.17	R1P	complex1.pdb.gz	72,75,84,169,171,172,173
2	0.08	2vwgA	0.489	5.40	0.106	0.764	0.28	NAP	complex2.pdb.gz	91,115,170,203
3	0.08	1qlhA	0.481	5.53	0.059	0.760	0.31	NAD	complex3.pdb.gz	87,114,128,130,172
4	0.07	1ju9B	0.481	5.55	0.058	0.760	0.30	NAD	complex4.pdb.gz	92,93,94,134,173
5	0.07	1agnA	0.489	5.47	0.063	0.764	0.23	NAD	complex5.pdb.gz	92,114,134,194,195,197
6	0.06	3btoC	0.483	5.48	0.048	0.760	0.26	SSB	complex6.pdb.gz	69,71,170,202
7	0.06	1u3vA	0.486	5.57	0.049	0.768	0.18	HPL	complex7.pdb.gz	72,95,199
8	0.06	6adhA	0.477	5.57	0.048	0.760	0.24	NAD	complex8.pdb.gz	91,131,148,172,173
9	0.05	1ldyA	0.483	5.47	0.044	0.755	0.26	CXF	complex9.pdb.gz	70,72,169,198
10	0.05	3hudA	0.479	5.52	0.044	0.760	0.20	NAD	complex10.pdb.gz	66,68,134

	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.