D-I-TASSER P0DPI2-D1

D-I-TASSER results for P0DPI2-D1

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

Input Sequence in FASTA format

>P0DPI2 (268 residues)
MAAVRVLVASRLAAASAFTSLSPGGRTPSQRAALHLSVPRPAARVALVLSGCGVYDGTEI
HEASAILVHLSRGGAEVQIFAPDVPQMHVIDHTKGQPSEGESRNVLTESARIARGKITDL
ANLSAANHDAAIFPGGFGAAKNLSTFAVDGKDCKVNKEVERVLKEFHQAGKPIGLCCIAP
VLAAKVLRGVEVTVGHEQEEGGKWPYAGTAEAIKALGAKHCVKEVVEAHVDQKNKVVTTP
AFMCETALHYIHDGIGAMVRKVLELTGK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MAAVRVLVASRLAAASAFTSLSPGGRTPSQRAALHLSVPRPAARVALVLSGCGVYDGTEIHEASAILVHLSRGGAEVQIFAPDVPQMHVIDHTKGQPSEGESRNVLTESARIARGKITDLANLSAANHDAAIFPGGFGAAKNLSTFAVDGKDCKVNKEVERVLKEFHQAGKPIGLCCIAPVLAAKVLRGVEVTVGHEQEEGGKWPYAGTAEAIKALGAKHCVKEVVEAHVDQKNKVVTTPAFMCETALHYIHDGIGAMVRKVLELTGK
Prediction	CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHCCHHHCCSSSSCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCSSSSSCHHHHHHHHHCCCCSSSCCCCCCCCCCCCCHHHHHHHHHCCCSSSSCCCCSSSSSCCCCSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
Confidence	9123555421200123222233357765543101024566786599997699998851066899999999981995999928999666446888875556531123488998761687777799756988998499752112223214630024499999999999991991999756999999862995884057742124565256999999809919954777289976996896350017888999999999999999998649
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MAAVRVLVASRLAAASAFTSLSPGGRTPSQRAALHLSVPRPAARVALVLSGCGVYDGTEIHEASAILVHLSRGGAEVQIFAPDVPQMHVIDHTKGQPSEGESRNVLTESARIARGKITDLANLSAANHDAAIFPGGFGAAKNLSTFAVDGKDCKVNKEVERVLKEFHQAGKPIGLCCIAPVLAAKVLRGVEVTVGHEQEEGGKWPYAGTAEAIKALGAKHCVKEVVEAHVDQKNKVVTTPAFMCETALHYIHDGIGAMVRKVLELTGK
Prediction	6422211214412443323313433534344344445453400100000022334100101000100310463504010000546425014226466254453423252043235414405504263010000001201043024224436404226401500430275610000000001001410641400013245544422242025104613041132314300004731000000102453033015004300520161068
	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

CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSSSSCCCCCCCCCHHHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHCCHHHCCSSSSCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCSSSSSCHHHHHHHHHCCCCSSSCCCCCCCCCCCCCHHHHHHHHHCCCSSSSCCCCSSSSSCCCCSSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
MAAVRVLVASRLAAASAFTSLSPGGRTPSQRAALHLSVPRPAARVALVLSGCGVYDGTEIHEASAILVHLSRGGAEVQIFAPDVPQMHVIDHTKGQPSEGESRNVLTESARIARGKITDLANLSAANHDAAIFPGGFGAAKNLSTFAVDGKDCKVNKEVERVLKEFHQAGKPIGLCCIAPVLAAKVLRGVEVTVGHEQEEGGKWPYAGTAEAIKALGAKHCVKEVVEAHVDQKNKVVTTPAFMCETALHYIHDGIGAMVRKVLELTGK

5xr2A

0.14

0.12

3.92

1.17

DEthreader

----------KTD-FDG-------------VE-HKGAYKDGKWKVLMIAAEERYSTGNHPVEMLLPLHHLMEAGFDVDVATLSGYPVKLELWAM---------I--YNKLKEKLKQPKKLADVELGSYLSVFIPGGHAAVVGIS----------ESEDVQQTLDWALDNDRFIVTLCHGPAALLSPLEGYSVCVFPDSLDEGILRLWLVADLLTKQGLKVVNDDMTGRTLKD-RKLLTGDSPLA----S---NELGKLAVNEMLNAIQ

3l3bB

0.33

0.26

7.84

1.56

SPARKS-K

-----------------------------------------ALNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESVGEVR-NILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFDDY----ILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKKVKVTIGEDSNG-----------LIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYLK-

3l3bB

0.34

0.26

7.92

0.89

MapAlign

------------------------------------------LNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESV-GEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFD----DYILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKKVKVTIGE-------------DGLIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYL--

3l3bB

0.34

0.27

8.04

0.74

CEthreader

-----------------------------------------ALNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESV-GEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFD----DYILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKKVKVTIGEDSNG-----------LIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYLK-

3l3bB

0.35

0.27

8.14

1.32

MUSTER

-----------------------------------------ALNSAVILAGCGHMDGSEIREAVLVMLELDRHNVNFKCFAPNKNQKQVVDHKKKESV-GEVRNILVESARIARGSVYDIEQIRVEEFDMLVIPGGYGVAKNFSNLFDD----YILPEFKNAVREFYNAKKPIGAVCISPAVVVALLKKVKVTIGEDSNG-----------LIDKMGGVHVDCPTIKSVKDDVNRIFSCSAYMRNDSLYNVYLGIQDMISSMVNYLK-

4i2nA

0.15

0.14

4.65

2.02

HHsearch

PTPDPAEDNAFFPSAYSLSQFTASKSDLS-GAHYPTPYQGGRWKILVVGADERYLTGNHPVETLLPMYHLDKAGFSFDIATLSGNPVKF-EWWAMPREDQEVNGLY-SKYQSSFRQPLKLSDVIDSDYIGVFIPGGHGALMGL----------PDSQEVKAVLQWAMKQNKFIISLCHGPAAFVGLFAGYKIVAFPDEMDAGHLTW-KFGEQLQAIGFELLNT-GISGQVFQDRKMLTGDSPLAGNALGQLAAKALLAE------VEQ

1oy1A

0.45

0.35

10.36

2.11

FFAS-3D

------------------------------------------KKIGVILSGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEATETRN--VLIEAARITRGEIRPLAQADAAELDALIVPGGFGAAKNLSNFASLGSECTVDREL-KALAQAHQAGKPL-GFCIAPALPKIFDFPLRLTIGTDID----------TAEVLEEGAEHVPCPVDDIVVDEDNKIVTTPAYL-AQNIAEAASGIDKLVSRVLVLAEL

1oy1A

0.40

0.32

9.35

0.90

EigenThreader

------------------------------------------KKIGVILSGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEATETRNVLIEAARITRG--EIRPLAQADAAELDALIVPGGFGAAKNLSNFASLGSECTVDRELKALAQAHQ-AGKPLGF-CIAPALPKIFDFPLRLTIGTD----------IDTAEVLEEGAEHVPCPVDDIVVDEDNKIVTTPAYLAQN-IAEAASGIDKLVSRVLVLAEL

1vhqA

0.47

0.37

10.88

2.19

CNFpred

------------------------------------------KKIGVILSGCGVYDGSEIHEAVLTLLAISRSGAQAVCFAPDKQQVDVINHLTGEAM-TETRNVLIEAARITRGEIRPLAQADAAELDALIVPGGFGAAKNLSNFASLGSECTVDRELKALAQAMHQAGKPLGFMMIAPAMLPKIFDPLRLTIGTDI---------DTAEVLEEMGAEHVPCPVDDIVVDEDNKIVTTPAYMLAQNIAEAASGIDKLVSRVLVLAE-

4i2nA

0.17

0.13

4.32

1.17

DEthreader

----------KSD-LS--------------GA-HY-PTPYQGWKILVVGADERYSTGNHPVETLLPMYHLDKAGFSFDIATLSGNPVKFEWWAM----------VN-LYSKYQSSQPLKLSDVALSDYIGVFIPGGHGALMGLP----------DSQEVKAVLQWAMKQNKFIISLCHGPAAFLDLFAGYKIVAFPDEMDAQPMHLWKFGEQLQAIGFELLNTGISGQVFQD-RKMLTGDSPLA----G---NALGQLAAKALLAEVE

(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	0.7493

(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	3l3bB	0.76	1.13	0.343	0.784	model1_3l3bB.pdb.gz
2	1oy1A	0.76	1.30	0.474	0.787	model1_1oy1A.pdb.gz
3	5xr2A	0.67	3.09	0.151	0.791	model1_5xr2A.pdb.gz
4	4i2nA	0.67	3.10	0.145	0.791	model1_4i2nA.pdb.gz
5	1n57A	0.66	3.18	0.149	0.780	model1_1n57A.pdb.gz
6	1u9cA	0.61	2.92	0.181	0.698	model1_1u9cA.pdb.gz
7	3n7tA	0.61	3.16	0.158	0.720	model1_3n7tA.pdb.gz
8	3miiA	0.61	2.95	0.144	0.698	model1_3miiA.pdb.gz
9	4p5pA	0.60	2.95	0.153	0.694	model1_4p5pA.pdb.gz
10	2vrnA	0.58	2.95	0.141	0.653	model1_2vrnA.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:0016836	0.91	hydro-lyase activity
GO:0019172	0.84	glyoxalase III activity
GO:0097159	0.58	organic cyclic compound binding
GO:1901363	0.57	heterocyclic compound binding
GO:0043167	0.52	ion binding
GO:0043169	0.51	cation binding
GO:0003676	0.51	nucleic acid binding

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:0044763	1.00	single-organism cellular process
GO:0044710	1.00	single-organism metabolic process
GO:0044237	1.00	cellular metabolic process
GO:0044281	0.88	small molecule metabolic process
GO:0061727	0.86	methylglyoxal catabolic process to lactate
GO:0019243	0.75	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione
GO:0065007	0.73	biological regulation
GO:0050789	0.73	regulation of biological process
GO:0050794	0.72	regulation of cellular process
GO:0044238	0.68	primary metabolic process
GO:0019222	0.66	regulation of metabolic process
GO:0080090	0.65	regulation of primary metabolic process
GO:0031323	0.65	regulation of cellular metabolic process
GO:1901576	0.61	organic substance biosynthetic process
GO:0044249	0.61	cellular biosynthetic process
GO:0060255	0.59	regulation of macromolecule metabolic process
GO:2000112	0.58	regulation of cellular macromolecule biosynthetic process
GO:0019219	0.58	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.58	regulation of gene expression
GO:1903506	0.57	regulation of nucleic acid-templated transcription
GO:0043170	0.55	macromolecule metabolic process
GO:0044711	0.54	single-organism biosynthetic process
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0006629	0.52	lipid metabolic process
GO:0008299	0.51	isoprenoid biosynthetic process
GO:0006807	0.51	nitrogen compound metabolic process
GO:0048518	0.50	positive regulation of biological process
GO:0034641	0.50	cellular nitrogen compound 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:0044444	1.00	cytoplasmic part
GO:0043226	0.99	organelle
GO:0005739	0.98	mitochondrion

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	0.066	1i7qB	0.458	3.91	0.136	0.586	4.1.3.27	NA
2	0.066	1i7sB	0.456	3.85	0.138	0.582	4.1.3.27	54,176
3	0.066	1qdlB	0.462	4.10	0.085	0.590	4.1.3.27	NA
4	0.060	2jfdA	0.366	5.65	0.069	0.586	2.3.1.85	NA
5	0.060	1enpA	0.484	4.47	0.139	0.657	1.3.1.9	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	0.04	1vcoA	0.519	4.57	0.114	0.716	0.45	GLN	complex1.pdb.gz	135,136,137,177,178,181
2	0.03	2ab00	0.557	2.60	0.200	0.623	0.86	III	complex2.pdb.gz	59,60,61,64,65,67,68,71,72,195,196,240,242,256
3	0.03	2qioA	0.489	4.34	0.117	0.653	0.42	NAD	complex3.pdb.gz	61,62,134,241
4	0.03	3k31A	0.492	4.48	0.113	0.668	0.50	NAD	complex4.pdb.gz	135,182,242,243
5	0.03	1rw70	0.610	2.97	0.157	0.702	0.68	III	complex5.pdb.gz	189,191,219,220,221,228,229,230,231,262
6	0.01	2ad5A	0.515	5.15	0.084	0.746	0.65	CTP	complex6.pdb.gz	162,163,164,167

	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.