D-I-TASSER P09234-D1

D-I-TASSER results for P09234-D1

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

Input Sequence in FASTA format

>P09234 (159 residues)
MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQG
KIPPTPFSAPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAP
GMRPPMGGHMPMMPGPPMMRPPARPMMVPTRPGMTRPDR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMMRPPARPMMVPTRPGMTRPDR
Prediction	CCCCCCCCCCCSSCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	996212223320025780356666541789999999999998764221011232211234556776667888777788889999999999999899999999999999999999999999999999999999999999999999999999999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMMRPPARPMMVPTRPGMTRPDR
Prediction	744210420322032433423431342440251024103521664244224543543444444444344444443433434434444444444444444444434444343343344443534444524444444444454444444444436346478
	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

CCCCCCCCCCCSSCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMMRPPARPMMVPTRPGMTRPDR

5uz5B

0.18

5.91

1.29

MUSTER

--RYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDIINKHNHKRRHIGKRGRKERENSSQNETLKVTCLSNKEKRHIMHVKKMNQKELAQTSIDTLDGSPDANRFDIGRSRDETCESNPFPRLNNPKKLEPPKILSQWSNTIPKTSIFYS

7jjvA

0.16

0.11

3.77

1.27

SPARKS-K

----------------------------------------------MQCDGLDGADGTSNGQAGASGLAGGPNCNGGKGGKGAPGVGTAGGAGGVGGAGGTGNTNGGAGGSGGNSDVAAGGAGAAGGAAGGAGTGGTGGNGGAKPGGAPGAGGAGTPAG

2vrdA

1.00

0.38

10.74

3.08

HHsearch

MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGK--------------------------------------------------------------------------------------------------

5uz5B

0.15

5.06

1.10

SPARKS-K

--RYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDIINKHNHKRRHIGKRGRKERENSSQNETLKVTCLSNKEKRHIMHVKKMNQKELAQTSIDTLKLLYDGSPGYSKVFVDANRFDIGDLVKASSRSRDETCESNPFPRLNNPKKLEPP

5o9zQ

0.21

0.10

3.19

1.17

SPARKS-K

QPKKFCDYCKCWIADNRP-SVEFHERGKNHKENVAKRISEIKQKSLDKAKEEEKASKEFAAMEAAALKAYQEDLKR-----------------------------------------------------------------------------------

4pw2A3

0.05

2.36

0.48

CEthreader

RDRVKCISGVEGVPLSTQWGPQGYFYAIQIAQYGLSHYSKNLTESHMAAFYAASDWLVRNQDERGGWPIMVTRKLGEGFRALEPGWYSAMAQGYLKAALRATGPFKLPSEQHGVKAVFMNKYDWYEEYPTIPSSFVLNGFIYSLIGLFDLAQTAGEKLG

7abi4

0.04

2.02

0.50

EigenThreader

GWEERAQRLFSTKGKSLESLDTSLFAKNPKSKGTDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTIPYWLYKLHGLNINYICGNGPKAFQRHFAEWRHAHGMRCLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYEDSSGNVVNK

5uz5B

0.21

0.17

5.40

0.76

FFAS-3D

--RYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDKEKRHIMHVKKMNQKELAQTSIYDGSPGYSKVFVDANRFDI-------------------------GDLVKASSRSRDETCESNPFPRLNNPKKLEPPKILSQWSNTIPKTS---

3cw10

0.98

0.33

9.34

0.79

CNFpred

---FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYCKWMEEQAQSLIDKTTAAF------------------------------------------------------------------------------------------------------

2pffA

0.06

0.04

1.96

0.83

DEthreader

GGGGGGGGIIAEIEK-MGVRL--VPELKEFTAKLRKELVETSEVRKAVSIETALEHKVNGNSADAAY-APRA-N--IQLDFPELK---L----EMYKYV-HVSEV--------K-PVGATSSVGVILSGKARARVSLTFK-D----GGGGG--------

(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	0.4132

(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	7c6oA	0.49	5.26	0.026	0.837	model1_7c6oA.pdb.gz
2	2a0uA	0.48	5.32	0.047	0.830	model1_2a0uA.pdb.gz
3	2epgB	0.47	4.67	0.022	0.774	model1_2epgB.pdb.gz
4	1uc2A	0.47	5.00	0.049	0.792	model1_1uc2A.pdb.gz
5	4fyeA2	0.47	5.00	0.075	0.761	model1_4fyeA2.pdb.gz
6	4eplA	0.46	5.02	0.040	0.755	model1_4eplA.pdb.gz
7	3ecsC	0.43	5.04	0.051	0.742	model1_3ecsC.pdb.gz
8	1vb5B	0.40	5.27	0.050	0.711	model1_1vb5B.pdb.gz
9	3irhC	0.38	4.98	0.034	0.629	model1_3irhC.pdb.gz
10	3btpA	0.36	5.65	0.043	0.667	model1_3btpA.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:1901363	0.99	heterocyclic compound binding
GO:0097159	0.99	organic cyclic compound binding
GO:0003723	0.98	RNA binding
GO:0030627	0.95	pre-mRNA 5'-splice site 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:0009987	1.00	cellular process
GO:0022607	0.99	cellular component assembly
GO:0000395	0.98	mRNA 5'-splice site recognition
GO:0008152	0.59	metabolic process
GO:0071704	0.57	organic substance metabolic process
GO:0044237	0.55	cellular metabolic process
GO:0043170	0.55	macromolecule metabolic process
GO:0044238	0.54	primary metabolic process
GO:0044260	0.53	cellular macromolecule metabolic process
GO:0034641	0.52	cellular nitrogen compound metabolic process
GO:0006139	0.51	nucleobase-containing compound metabolic process
GO:0016070	0.50	RNA 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:0044446	1.00	intracellular organelle part
GO:0044428	0.99	nuclear part
GO:0032991	0.97	macromolecular complex
GO:0030529	0.95	intracellular ribonucleoprotein complex
GO:0005685	0.93	U1 snRNP
GO:0005681	0.92	spliceosomal complex
GO:0071010	0.90	prespliceosome
GO:0005684	0.90	U2-type spliceosomal complex
GO:0000243	0.89	commitment complex

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	1dkpA	0.443	5.36	0.052	0.780	3.1.3.2 3.1.3.26	NA
2	0.060	2p2wA	0.441	5.20	0.072	0.767	2.3.3.-	NA
3	0.060	1fohC	0.374	5.63	0.039	0.717	1.14.13.7	NA
4	0.060	2v4wD	0.442	5.02	0.055	0.742	2.3.3.10	108
5	0.060	1cc1L	0.451	5.35	0.029	0.792	1.12.99.6	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	1pjlF	0.450	4.69	0.062	0.717	0.14	NAD	complex1.pdb.gz	75,76,77
2	0.01	1gz4A	0.431	4.78	0.068	0.730	0.15	ATP	complex2.pdb.gz	103,129,130,134
3	0.01	1eflC	0.458	4.72	0.054	0.736	0.16	NAD	complex3.pdb.gz	75,90,91,92
4	0.01	1pj4C	0.458	4.83	0.052	0.742	0.21	ATP	complex4.pdb.gz	54,55,143
5	0.01	1pjlA	0.411	5.10	0.064	0.730	0.11	NAD	complex5.pdb.gz	61,91,141
6	0.01	1do8B	0.457	4.82	0.052	0.742	0.15	NAD	complex6.pdb.gz	112,113,114
7	0.01	1do8A	0.451	5.03	0.058	0.755	0.13	NAD	complex7.pdb.gz	78,81,107,108,109,110
8	0.01	1uwkA	0.464	5.08	0.049	0.799	0.14	URO	complex8.pdb.gz	90,91,92,95,100,136
9	0.01	3myrB	0.462	5.17	0.045	0.792	0.21	NFV	complex9.pdb.gz	74,75,140

	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.