D-I-TASSER P0DP07-D1

D-I-TASSER results for P0DP07-D1

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

Input Sequence in FASTA format

>P0DP07 (118 residues)
MKHLWFFLLLVAAPRWVLSQVQLQESGPGLVKPSQTLSLTCTVSGGSISSGGYYWSWIRQ
HPGKGLEWIGYIYYSGSTYYNPSLKSLVTISVDTSKNQFSLKLSSVTAADTAVYYCAR

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MKHLWFFLLLVAAPRWVLSQVQLQESGPGLVKPSQTLSLTCTVSGGSISSGGYYWSWIRQHPGKGLEWIGYIYYSGSTYYNPSLKSLVTISVDTSKNQFSLKLSSVTAADTAVYYCAR
Prediction	CCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCSSSSSCCCSSCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCCCCCCCCCSSSSSSCCCCSSSSSSCCCCHHHCSSSSSCC
Confidence	9628999999971642123444321069973865351312567766162798458988509999827889991899812083313535887646777688663456756634444239
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MKHLWFFLLLVAAPRWVLSQVQLQESGPGLVKPSQTLSLTCTVSGGSISSGGYYWSWIRQHPGKGLEWIGYIYYSGSTYYNPSLKSLVTISVDTSKNQFSLKLSSVTAADTAVYYCAR
Prediction	7433131001021243022101144334542333332303120312012344230000012433300010302343314111214132303432343333140423323120222238
	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

                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCSSSSSCCCSSCCCSSSSSSSSCCCCCSSSSSSSSCCCCCCCCCCCCCCSSSSSSCCCCSSSSSSCCCCHHHCSSSSSCC
MKHLWFFLLLVAAPRWVLSQVQLQESGPGLVKPSQTLSLTCTVSGGSISSGGYYWSWIRQHPGKGLEWIGYIYYSGSTYYNPSLKSLVTISVDTSKNQFSLKLSSVTAADTAVYYCAR

6wznA

0.43

0.42

12.42

1.33

DEthreader

SFITC-AWYQKLLIYQSGTQVQLVESGGGLVQPGGSLRLSCAASGLTF--SNYAMNWVRQAPGKGLEWVSSISSRDTTYYADSVKGRFTISRDNSKSTLYLQMNSLRAEDAAVYYCAR

5gruL1

0.70

0.58

16.62

1.12

SPARKS-K

-------------------QVQLKESGPGLVRPSQSLSLTCSVTGYS-ITSGYYWNWIRQFPGNKLEWMGYISYDGSNNYNPSLKGRISITRDTSKNQFFLKLNSVTTDDTATYYCAR

6vy5H

0.52

0.42

12.26

0.45

MapAlign

-------------------EVQLLESGGGLIQPGGSLRLSCAASGFTF--SRFTMSWVRQPPGKGPEWVSGISGSGHTYYADSVKGRFTISRDNSKNTLYLQMNSLKAEDTAVYYCAK

7ckwN

0.55

0.45

12.95

0.26

CEthreader

-------------------QVQLQESGGGLVQPGGSLRLSCAASGFTFSN--YKMNWVRQAPGKGLEWVSDISQSGSISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR

5gruL1

0.72

0.60

17.08

1.18

MUSTER

-------------------QVQLKESGPGLVRPSQSLSLTCSVTGYSITS-GYYWNWIRQFPGNKLEWMGYISYDGSNNYNPSLKGRISITRDTSKNQFFLKLNSVTTDDTATYYCAR

5xcsA

0.52

0.42

12.26

0.40

HHsearch

-------------------EVKLVESGGDLVKPGGSLKLSCAASGFTFSS--YGMSWVRQTPDKRLEWVATISRGGYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCAR

3nn8A

0.49

0.42

12.05

1.90

FFAS-3D

-------------------QVQLQQSGPEDVKPGASVKISCKASGYSLSTSGMGVNWVKQSPGKGLEWLAHIYWDDDKRYNPSLKSRATLTVDKTSSTVYLELRSLTSEDSSVYYCAR

7dnlH

0.58

0.48

13.88

0.37

EigenThreader

-------------------QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWNDDKNYHPALKSRLTISKDTSSNRVFLNIASVDTADTATYYCAR

5xkuC

0.96

0.81

22.58

1.74

CNFpred

-------------------QVQLQESGPGLVKPSETLSLTCTVSGGSISSGGYYWSWIRQHPGKGLEWIGYIYYSGSTDYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCAG

3wbdA

0.43

0.42

12.42

1.33

DEthreader

TPISC-LYWYLPLIYFSGSQIQLQQSGPELVRPGASVKISCKASGYTF--TDYYIHWVKQRPGEGLEWIGWIYPSGNTKYNEKFKGKATLTVDTSSSTAYMQLSSLTSEDSAVYFCAR

(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	0.7925

(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	6wznA	0.83	2.24	0.456	0.941	model1_6wznA.pdb.gz
2	4rrpA	0.82	2.63	0.482	0.941	model1_4rrpA.pdb.gz
3	3wbdA	0.82	2.69	0.443	0.958	model1_3wbdA.pdb.gz
4	4yjzL	0.82	2.47	0.368	0.941	model1_4yjzL.pdb.gz
5	1tjhH	0.82	0.63	0.525	0.839	model1_1tjhH.pdb.gz
6	2znwA	0.82	2.15	0.602	0.907	model1_2znwA.pdb.gz
7	2iqaH1	0.82	0.70	0.606	0.839	model1_2iqaH1.pdb.gz
8	6vrpA	0.81	0.75	0.525	0.839	model1_6vrpA.pdb.gz
9	3ux9B	0.81	2.44	0.500	0.924	model1_3ux9B.pdb.gz
10	2gjjA	0.81	2.51	0.333	0.932	model1_2gjjA.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:0003823	0.98	antigen binding
GO:0034987	0.88	immunoglobulin receptor 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:0050896	1.00	response to stimulus
GO:0006955	0.99	immune response
GO:0002682	0.84	regulation of immune system process
GO:0006958	0.83	complement activation, classical pathway
GO:0002429	0.83	immune response-activating cell surface receptor signaling pathway
GO:0044763	0.75	single-organism cellular process
GO:0043207	0.75	response to external biotic stimulus
GO:0050871	0.74	positive regulation of B cell activation
GO:0050853	0.74	B cell receptor signaling pathway
GO:0045087	0.74	innate immune response
GO:0042742	0.74	defense response to bacterium
GO:0006911	0.74	phagocytosis, engulfment
GO:0006910	0.74	phagocytosis, recognition

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:0044421	0.92	extracellular region part
GO:0044464	0.86	cell part
GO:0044425	0.77	membrane part
GO:0044459	0.76	plasma membrane part
GO:0072562	0.75	blood microparticle
GO:0043234	0.75	protein complex
GO:0009897	0.75	external side of plasma membrane
GO:0042571	0.74	immunoglobulin complex, circulating

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	0.214	1rjcA	0.705	1.84	0.430	0.788	3.2.1.17	24,26,60,115
2	0.208	1ri8A	0.748	1.39	0.427	0.814	3.2.1.17	25,115
3	0.114	1zvyA	0.772	1.17	0.443	0.822	3.2.1.17	25,60
4	0.067	2bk8A	0.573	1.74	0.104	0.652	2.7.11.1	102
5	0.066	2eo1A	0.549	2.29	0.146	0.644	2.7.11.1	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	0.38	3ffdA	0.777	1.03	0.526	0.822	0.99	III	complex1.pdb.gz	73,74,75,76,77,79
2	0.15	3sgeI	0.697	1.63	0.283	0.780	0.99	III	complex2.pdb.gz	52,54,56,68,71,72,117
3	0.13	1vpoH	0.776	1.05	0.495	0.822	1.04	TES	complex3.pdb.gz	56,68,71,79
4	0.05	1kb53	0.671	1.71	0.281	0.754	0.91	III	complex4.pdb.gz	46,54,71

	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.