D-I-TASSER Q0P6H9-D2

D-I-TASSER results for Q0P6H9-D2

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

Input Sequence in FASTA format

>Q0P6H9 (263 residues)
PAPGPGDSNIFWGLQISDIHLSRFRDPGRAVDLEKFCSETIDIIQPALVLATGDLTDAKT
KEQLGSRQHEVEWQTYQGILKKTRVMEKTKWLDIKGNHDAFNIPSLDSIKNYYRKYSAVR
RDGSFHYVHSTPFGNYSFICVDATVNPGPKRPYNFFGILDKKKMEELLLLAKESSRSNHT
IWFGHFTTSTILSPSPGIRSIMSSAIAYLCGHLHTLGGLMPVLHTRHFQGTLELEVGDWK
DNRRYRIFAFDHDLFSFADLIFG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| PAPGPGDSNIFWGLQISDIHLSRFRDPGRAVDLEKFCSETIDIIQPALVLATGDLTDAKTKEQLGSRQHEVEWQTYQGILKKTRVMEKTKWLDIKGNHDAFNIPSLDSIKNYYRKYSAVRRDGSFHYVHSTPFGNYSFICVDATVNPGPKRPYNFFGILDKKKMEELLLLAKESSRSNHTIWFGHFTTSTILSPSPGIRSIMSSAIAYLCGHLHTLGGLMPVLHTRHFQGTLELEVGDWKDNRRYRIFAFDHDLFSFADLIFG
Prediction	CCCCCCCCCCSSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCSSSSSCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCSSSSSSSCCCSSSSSSCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCHHHHHHHCCCSSSSSCCCCCCCCCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSSSCCSSSSSSSSCC
Confidence	99998899858999982456587778127999999999998731998999947753677655554311489999999999997414787189947888887776642167777763013577762269995159689999838777777776542433599999999999984789990999987996214686344777631966999477677421113035642797599997203458817999996996899821329
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| PAPGPGDSNIFWGLQISDIHLSRFRDPGRAVDLEKFCSETIDIIQPALVLATGDLTDAKTKEQLGSRQHEVEWQTYQGILKKTRVMEKTKWLDIKGNHDAFNIPSLDSIKNYYRKYSAVRRDGSFHYVHSTPFGNYSFICVDATVNPGPKRPYNFFGILDKKKMEELLLLAKESSRSNHTIWFGHFTTSTILSPSPGIRSIMSSAIAYLCGHLHTLGGLMPVLHTRHFQGTLELEVGDWKDNRRYRIFAFDHDLFSFADLIFG
Prediction	74447556210000000001004243562153035004400640302000000000113445424454345115304500541562643300000000122223424234400441244444432212241644300000000233332421210213025610530352067167431100000000102244343134135402000001102324424421222463110000010354320000001442000201538
	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                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSSSSSSCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCSSSSCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCSSSSSCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCSSSSSSSCCCSSSSSSCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCCCCCHHHHHHHCCCSSSSSCCCCCCCCCCCCSSSSCCCCSSSSSSSSCCCCCSSSSSSSSCCSSSSSSSSCC
PAPGPGDSNIFWGLQISDIHLSRFRDPGRAVDLEKFCSETIDIIQPALVLATGDLTDAKTKEQLGSRQHEVEWQTYQGILKKTRVMEKTKWLDIKGNHDAFNIPSLDSIKNYYRKYSAVRRDGSFHYVHSTPFGNYSFICVDATVNPGPKRPYNFFGILDKKKMEELLLLAKESSRSNHTIWFGHFTTSTILSPSPGIRSIMSSAIAYLCGHLHTLGGLMPVLHTRHFQGTLELEVGDWKDNRRYRIFAFDHDLFSFADLIFG

5fi9A

0.15

0.14

4.64

1.33

DEthreader

PSPPAPGAPVSRVLFLTDLHWDHEYLEWPLRTLESLLKGLGPAGPFEMVYWTGDIPAHDV-WQQSRQDQLRALTTITDLVRKF--LGPVPVYPAVGNHESTPGQSSQWLYEAMAKAWELLLRGFYALTPR---PGLRLISLNMNFCSRENFWL---STDPAGQLQWLVEELQAAERGDKVHIIGHIPPGHCLKSSWNYYKIIAYLAGQFFGHTH-V---D--EFEIFYPLAVAFLAPSTTLNPGYRVYQIDSSVVDHETYILN

3d03A

0.14

0.12

4.15

1.32

SPARKS-K

----------MLLAHISDTHFRSRGEKIDVNAANADVVSQLNALRPDAVVVSGDIVNCGR---------PEEYQVARQILGSL----NYPLYLIPGNHD-----DKALFLEYLQPLCPQLGSDANNMRCAVDDFATRLLFIDSSRAGTS------KGWLTDETISWLEAQLFEGGDKP-ATIFMHHPPLPLGNAQHRLLALVERFTRIFCGHNHSLTTQYRQALISTLPGTVHQVPYCDLSPASCLMHRQVGEQWVSYQHSLA

2xmoA

0.12

0.11

3.77

0.95

MapAlign

-------DRNLSMVVTTDVHYFAGKQLAYSDEITDAFLADVESKKTDVLIISGDLTNNG---------EKTSHEELAKKLTQV-EKNGTQVFVVPGNHDIWARISPTDFSKIYSDFGAISSDLSYLAAP---SSKVWLLMLDTAIYNMQQGNPTTEGGLTAGTLDWIKESSALAKKNAKLIPVLHHNLTYTINYNQQVIDALTEMDFSLSGHIH------TQNIRSAGKEITDIVTNASVFPHKYGNITYSAKNFTYQSQKL-

3tghA

0.10

0.09

3.26

0.59

CEthreader

-------KCQLRFASLGDWGKDTK----GQILNAKYFKQFIKNERVTFIVSPGSNFIDGVKGL----NDPAWKNLYEDVYSEEKGDMYMPFFTVLGTRDWTGNYNAQLLKGQTNYPKWIMPNYWYHYFTHFTVSAAAFIFIDTWVLSSNFPY----KKIHEKAWNDLKSQLSVAKKADFIIVVGDQPIYGSSYLAYYLLPLLKDVDLYISGHDN-------NMEVIEDNDMAHITCGSFSSDIGFCVHELSNNGIVTKFVSSK

1warA

0.14

4.77

1.15

MUSTER

EAEAEFATPALRFVAVGDWGGVPPFHTAREMANAKEIARTVQILGADFILSLGDNFY---FTGVQDINDKRFQETFEDVFSD-RSLRKVPWYVLAGNHDHL--GNVSAQIAYSKISRWNFPSPFYRLHFKIPNVSVAIFMLDTVTLCGNSDDFLSQQPERRTQLSWLKKQLAAA-REDYVLVAGHYPVWSIAEHGKQLRPLLATYTAYLCGHDHNFMDPSKRHQRKVPNGYLRFHYGTEDSLGGFAYVEISSKEMTVTYIEAS

2xmoA

0.13

0.12

4.22

1.77

HHsearch

---PIEKDRNLSMVVTTDVHYFAPSLTAYSDEITDAFLADVESKKTDVLIISGDLTNNGEK---------TSHEELAKKLTQVEK-NGTQVFVVPGNHDINNPWARISPTDFSKIYSDFGYEFSLSYLA-APSSKVWLLMLDTAIYKTNMGNPTTEGGLTAGTLDWIKESSALAKNGAKLIPVLHHNLTDHNNYNQQVIDALTEGDFSLSGHIHTQNIRSAKS--TDGKEITDIVTNALSFPHKYGNITYSAKNFTYQSQKLD

2xmoA

0.13

0.12

4.12

1.57

FFAS-3D

PI---EKDRNLSMVVTTDVHYFDGKQLAYSDEITDAFLADVESKKTDVLIISGDLTNNGE---------KTSHEELAKKLTQV-EKNGTQVFVVPGNHDINNPWARKFEKSDFGYEDAISSDEFSLSYLAAPSSKVWLLMLDTAIYKTNQGNPTTEGGLTAGTLDWIKESSALAKNGAKLIPVLHHNLTDHNDVKQQVIDALTAMDFSLSGHIHTQNIR----SAKSTDGITDIVTNALSVPHKYGNITYSAKNFTYQSQKLD

5fi9A2

0.13

0.12

4.25

1.08

EigenThreader

PSPPAPGAPVSRVLFLTDLHWDHEYLDLPLRTLESLLKGLGPAGPFEMVYWTGDIPAHDVWQQSRQDQLRALTTITDLVRKFLGP---VPVYPAVGNHESTPVNGFPPLYEAMAKAWEPWLPGFYALTPRP---GLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVEELQAAENRGKVHIIGHIPPGHCLKSWSWNYYKIIARYEQFFGHTHVD----EFEIFYDESRPLAVAFLAPNLNPGYRVYQIDGNYDHETYILNL

2xmoA

0.13

0.12

4.08

1.63

CNFpred

---------NLSMVVTTDVHYFAPSL-AYSDEITDAFLADVESKKTDVLIISGDLTNNG---------EKTSHEELAKKLTQVEKN-GTQVFVVPGNHDINNTISPTDFSKIYSDFGAISSDFSLSYLAAP-SSKVWLLMLDTAIYKTNMGNPTTEGGLTAGTLDWIKESSALAKNGAKLIPVLHHNLTDTINYNQQVIDALTEMDFSLSGHIHTQNIRSAKS-----KEITDIVTNALSVPHKYGNITYSAKNFTYQSQKLD

5fi9A2

0.15

0.14

4.64

1.33

DEthreader

PSPPAPGAPVSRVLFLTDLHWDHEYLEWPLRTLESLLKGLGPAGPFEMVYWTGDIPAHDV-WQQSRQDQLRALTTITDLVRKF--LGPVPVYPAVGNHESTPGQSSQWLYEAMAKAWELLLRGFYALTPR---PGLRLISLNMNFCSRENFWL---STDPAGQLQWLVEELQAAERGDKVHIIGHIPPGHCLKSSWNYYKIIAYLAGQFFGHTH-V---D--EFEIFYPLAVAFLAPSTTLNPGYRVYQIDSSVVDHETYILN

(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	0.8573

(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	5fi9A	0.82	2.93	0.139	0.947	model1_5fi9A.pdb.gz
2	5ebbA	0.81	2.82	0.126	0.928	model1_5ebbA.pdb.gz
3	5karA	0.80	2.76	0.155	0.920	model1_5karA.pdb.gz
4	2xmoA	0.80	2.57	0.116	0.905	model1_2xmoA.pdb.gz
5	1warA	0.80	3.03	0.132	0.932	model1_1warA.pdb.gz
6	2nxfA	0.78	2.72	0.153	0.893	model1_2nxfA.pdb.gz
7	3ib8A	0.76	2.47	0.156	0.844	model1_3ib8A.pdb.gz
8	3d03A	0.76	2.06	0.156	0.829	model1_3d03A.pdb.gz
9	1kbpA	0.74	2.49	0.140	0.837	model1_1kbpA.pdb.gz
10	4ltyC	0.71	3.34	0.150	0.856	model1_4ltyC.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	0.97	hydrolase activity
GO:0042578	0.96	phosphoric ester hydrolase activity
GO:0008081	0.92	phosphoric diester hydrolase activity
GO:0004115	0.90	3',5'-cyclic-AMP phosphodiesterase activity
GO:0046872	0.89	metal ion binding
GO:0046914	0.88	transition metal ion binding
GO:0005506	0.86	iron ion binding
GO:0008199	0.85	ferric iron binding
GO:1901363	0.80	heterocyclic compound binding
GO:0097159	0.80	organic cyclic compound binding
GO:0016791	0.78	phosphatase activity
GO:0003993	0.77	acid phosphatase activity
GO:0000166	0.76	nucleotide binding
GO:0008198	0.70	ferrous iron binding
GO:0030145	0.54	manganese ion binding
GO:0042301	0.50	phosphate ion binding
GO:0008663	0.50	2',3'-cyclic-nucleotide 2'-phosphodiesterase 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	0.98	cellular process
GO:0008152	0.93	metabolic process
GO:0044237	0.92	cellular metabolic process
GO:0006796	0.87	phosphate-containing compound metabolic process
GO:0065007	0.86	biological regulation
GO:0050794	0.85	regulation of cellular process
GO:0044699	0.85	single-organism process
GO:0016311	0.85	dephosphorylation
GO:0050896	0.81	response to stimulus
GO:0048523	0.81	negative regulation of cellular process
GO:0044763	0.81	single-organism cellular process
GO:0006950	0.80	response to stress
GO:0071704	0.72	organic substance metabolic process
GO:0065008	0.72	regulation of biological quality
GO:0048518	0.72	positive regulation of biological process
GO:0048522	0.71	positive regulation of cellular process
GO:0044238	0.71	primary metabolic process
GO:0042592	0.71	homeostatic process
GO:0044707	0.70	single-multicellular organism process
GO:0009605	0.70	response to external stimulus
GO:1901700	0.69	response to oxygen-containing compound
GO:0045453	0.69	bone resorption
GO:0033993	0.69	response to lipid
GO:0032879	0.69	regulation of localization
GO:0031667	0.69	response to nutrient levels
GO:0030154	0.69	cell differentiation
GO:0010035	0.69	response to inorganic substance
GO:0070723	0.68	response to cholesterol
GO:0033591	0.68	response to L-ascorbic acid
GO:0033555	0.68	multicellular organismal response to stress
GO:0030335	0.68	positive regulation of cell migration
GO:0030316	0.68	osteoclast differentiation
GO:0010043	0.68	response to zinc ion
GO:0007162	0.68	negative regulation of cell adhesion
GO:0001503	0.68	ossification
GO:0006807	0.65	nitrogen compound metabolic process
GO:0044710	0.63	single-organism metabolic process
GO:0034641	0.63	cellular nitrogen compound metabolic process
GO:1901360	0.61	organic cyclic compound metabolic process
GO:0046483	0.61	heterocycle metabolic process
GO:0006139	0.60	nucleobase-containing compound metabolic process
GO:0016043	0.58	cellular component organization
GO:0019637	0.57	organophosphate metabolic process
GO:1901575	0.56	organic substance catabolic process
GO:0044712	0.56	single-organism catabolic process
GO:0044248	0.56	cellular catabolic process
GO:0042545	0.55	cell wall modification
GO:1901135	0.54	carbohydrate derivative metabolic process
GO:0044281	0.54	small molecule metabolic process
GO:1901564	0.53	organonitrogen compound metabolic process
GO:1901565	0.52	organonitrogen compound catabolic process
GO:0046434	0.52	organophosphate catabolic process
GO:0051704	0.51	multi-organism process
GO:0009405	0.50	pathogenesis
GO:0006198	0.50	cAMP catabolic 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:0044464	0.98	cell part
GO:0044424	0.95	intracellular part
GO:0043226	0.87	organelle
GO:0043227	0.86	membrane-bounded organelle
GO:0043229	0.79	intracellular organelle
GO:0043231	0.78	intracellular membrane-bounded organelle
GO:0044444	0.73	cytoplasmic part
GO:0044446	0.60	intracellular organelle part
GO:0016020	0.50	membrane

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	0.117	2nxfA	0.778	2.72	0.153	0.893	3.6.1.16 3.6.1.53 3.6.1.13	98
2	0.067	2r17B	0.483	3.34	0.136	0.586	3.1.3.3	181
3	0.066	1f89A	0.567	4.92	0.086	0.825	3.5.-.-	NA
4	0.066	2w1vA	0.556	4.81	0.071	0.806	3.5.1.3	NA
5	0.060	1emsA	0.576	4.56	0.053	0.802	3.6.1.29	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	0.63	1warA	0.797	3.03	0.132	0.932	1.73	FE	complex1.pdb.gz	18,54,97,185,212
2	0.35	2zo9B	0.755	2.07	0.156	0.829	1.48	UUU	complex2.pdb.gz	18,20,54,97,98,212,214
3	0.29	1kbpB	0.736	2.49	0.140	0.837	1.18	FE	complex3.pdb.gz	18,54,57,98,214

	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.