D-I-TASSER P02787-D1

D-I-TASSER results for P02787-D1

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

Input Sequence in FASTA format

>P02787 (182 residues)
MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVK
KASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVAR
SMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMY
LG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG
Prediction	CCHHHHHHHHHHHHHHHHCCCCCCSSSSSCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCHHHHHHHHHCCCCCSSSSCHHHHSSCCCCCCCCSSSSSSSSCCCCCCCSSSSSSSSSSSCCCHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCHHHHCC
Confidence	94168999999999875028998579986496999999999999986335788727998369999999999809984999671230010147789812367874368888536999999995897106899828542136888787753546744333433423345266698898466358
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG
Prediction	33000111211101111332465401000235523510540263045334764130312355236301530474401000034520130124634132002132447654422100000024545553044045433532346434413023244134010342043025136513352238
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHCCCCCCSSSSSCCHHHHHHHHHHHHHHHHHCCCCCCCSSSSSCCCHHHHHHHHHCCCCCSSSSCHHHHSSCCCCCCCCSSSSSSSSCCCCCCCSSSSSSSSSSSCCCHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSSCCCCCCHHHHCC
MRLAVGALLVCAVLGLCLAVPDKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

6wb6A

0.21

0.20

6.45

1.33

DEthreader

--VRSCHTGGYKPLELRGHGPELVVRLCVTSNVALSKCRAMSVFAFSRD--IRPILDCVQENSEDACLKSVQDNGSDLASVDDMRVAAAAKK-YNLHPVFHEVYGELTSAMAPSRTWVAAKDFLSDVSIAHTPLSLAQMLA-TRPDLFNIYGEFLKNNVIFNNAAKGLATTE-KLDFEKFKI

6uj6A1

0.99

0.88

24.62

2.73

SPARKS-K

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVARSIGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

1d4nA

0.99

0.87

24.47

0.84

MapAlign

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYL-

1d4nA1

1.00

0.88

24.77

0.84

CEthreader

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

1d4nA1

0.99

0.87

24.47

2.16

MUSTER

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQFPSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

6uj6A1

0.96

0.85

23.88

2.67

HHsearch

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEPQTFYSHTVVARSIGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

6uj6A1

0.98

0.87

24.32

2.48

FFAS-3D

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQVPSHTVVARSIGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

1d4nA1

1.00

0.88

24.77

1.08

EigenThreader

---------------------DKTVRWCAVSEHEATKCQSFRDHMKSVIPSDGPSVACVKKASYLDCIRAIAANEADAVTLDAGLVYDAYLAPNNLKPVVAEFYGSKEDPQTFSHTVVARSMGGKEDLIWELLNQAQEHFGKDKSKEFQLFSSPHGKDLLFKDSAHGFLKVPPRMDAKMYLG

3s9lC

0.38

0.35

10.26

1.82

CNFpred

AKMYLGYEYVTAIRNLRE-DECKPVKWCALSHHERLKCDEWSVNSV-------GKIECVSAETTEDCIAKIMNGEADAMSLDGGFVYIAGK--CGLVPVLAENYDK-PEAG-PNHAVVTRKD--KEACVHKILRQQQHLFGSDVTDNFCLFRSE-TKDLLFRDDTVCLAKLHDRNTYEKYLG

6xr0M

0.27

0.26

7.91

1.33

DEthreader

KGGSYSESLC-------DPNLPPYLRWCVLSTPEIQKCGDMAVAFRRQR--LKPEIQCVSAKSPQHCMERIQAEQVDAVTLSGEDIYTAGKT-YGLVPAAGEHYAPEDSSSIPPHAVMVRPD-TNIFTVYGLLDKAQDLFGDDHNKNFKMFDSSNYGQLLFKDATVRAVPVGEKTTYRGWLY

(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	0.7476

(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	1d4nA	0.87	0.72	0.981	0.885	model1_1d4nA.pdb.gz
2	6uj6A	0.85	1.07	0.994	0.885	model1_6uj6A.pdb.gz
3	6xr0M	0.84	2.57	0.290	0.967	model1_6xr0M.pdb.gz
4	1b1xA	0.83	1.65	0.587	0.879	model1_1b1xA.pdb.gz
5	3mc2A1	0.82	1.46	0.631	0.879	model1_3mc2A1.pdb.gz
6	1ryxA1	0.79	2.28	0.472	0.874	model1_1ryxA1.pdb.gz
7	3i6vA	0.48	3.63	0.105	0.648	model1_3i6vA.pdb.gz
8	1zcjA	0.41	5.22	0.094	0.709	model1_1zcjA.pdb.gz
9	2x58A	0.41	5.30	0.076	0.692	model1_2x58A.pdb.gz
10	3hemA	0.37	5.42	0.058	0.643	model1_3hemA.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:0005506	0.94	iron ion binding
GO:0005102	0.59	receptor binding
GO:0008199	0.57	ferric iron binding
GO:1990459	0.54	transferrin receptor binding
GO:0008198	0.54	ferrous iron binding
GO:0015091	0.53	ferric iron transmembrane transporter 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:0050896	0.93	response to stimulus
GO:0044699	0.81	single-organism process
GO:0009987	0.81	cellular process
GO:0065007	0.80	biological regulation
GO:0006810	0.76	transport
GO:0048522	0.74	positive regulation of cellular process
GO:0006826	0.74	iron ion transport
GO:0043207	0.69	response to external biotic stimulus
GO:0065008	0.65	regulation of biological quality
GO:0051707	0.65	response to other organism
GO:0044763	0.65	single-organism cellular process
GO:0009617	0.61	response to bacterium
GO:0006879	0.58	cellular iron ion homeostasis
GO:0042221	0.55	response to chemical
GO:0070887	0.51	cellular response to chemical stimulus
GO:0010038	0.51	response to metal ion
GO:0097286	0.50	iron ion import
GO:0051130	0.50	positive regulation of cellular component organization

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	0.87	cell part
GO:0044424	0.83	intracellular part
GO:0044444	0.79	cytoplasmic part
GO:0043226	0.76	organelle
GO:0043227	0.74	membrane-bounded organelle
GO:0044421	0.71	extracellular region part
GO:0043229	0.70	intracellular organelle
GO:0043231	0.69	intracellular membrane-bounded organelle
GO:0031988	0.69	membrane-bounded vesicle
GO:0005615	0.68	extracellular space
GO:0016023	0.64	cytoplasmic, membrane-bounded vesicle
GO:0005576	0.62	extracellular region

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	2de3B	0.536	4.27	0.058	0.769	3.13.1.3	NA
2	0.060	1dbiA	0.471	5.01	0.083	0.775	3.4.21.-	NA
3	0.060	1gc5A	0.477	4.92	0.072	0.769	2.7.1.147	NA
4	0.060	1m21A	0.487	4.72	0.063	0.753	3.5.1.-	NA
5	0.060	2df4A	0.474	4.11	0.071	0.681	6.3.5.-	84

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.36	3tajA	0.744	1.98	0.356	0.819	0.60	NBO	complex1.pdb.gz	179,180,182

	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.