D-I-TASSER Q92859-D2

D-I-TASSER results for Q92859-D2

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

Input Sequence in FASTA format

>Q92859 (185 residues)
LPRFTSQPEPSSVYAGNNAILNCEVNADLVPFVRWEQNRQPLLLDDRVIKLPSGMLVISN
ATEGDGGLYRCVVESGGPPKYSDEVELKVLPDPLIILEHAPATTGPLPSAPRDVVASLVS
TRFIKLTWRTPASDPHGDNLTYSVFYTKEGIARERVENTSHPGEMQVTIQNLMPATVYIF
RVMAQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| LPRFTSQPEPSSVYAGNNAILNCEVNADLVPFVRWEQNRQPLLLDDRVIKLPSGMLVISNATEGDGGLYRCVVESGGPPKYSDEVELKVLPDPLIILEHAPATTGPLPSAPRDVVASLVSTRFIKLTWRTPASDPHGDNLTYSVFYTKEGIARERVENTSHPGEMQVTIQNLMPATVYIFRVMAQ
Prediction	CCCSSSCCCCSSSSCCCSSSSSSSSSSCCCCSSSSSSCCSSCCCCCCSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSSCCCCCCCCCCSSSSSSSSSCCCCCSSSSSSSCCCCSSSSSCCCCCCCSSSSSSSSC
Confidence	98089368648994893199999999648978999999999689997899179879993765123489999999789853889999999358652235677555568998657899981699869999789988998714799999838999759999873884799982887993289999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| LPRFTSQPEPSSVYAGNNAILNCEVNADLVPFVRWEQNRQPLLLDDRVIKLPSGMLVISNATEGDGGLYRCVVESGGPPKYSDEVELKVLPDPLIILEHAPATTGPLPSAPRDVVASLVSTRFIKLTWRTPASDPHGDNLTYSVFYTKEGIARERVENTSHPGEMQVTIQNLMPATVYIFRVMAQ
Prediction	63443450562404454505041405251404031314654056763143365220304604561314010203153345302403030335442434533443644454425040333455414445443465442523202021346535523232214374230204444354434323408
	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

CCCSSSCCCCSSSSCCCSSSSSSSSSSCCCCSSSSSSCCSSCCCCCCSSSCCCCSSSSCCCCHHHCSSSSSSSSSCCCCSSSSSSSSSSSCCCCCCCCCCCCCCCCCCCCCSSSSSSSCCCCCSSSSSSCCCCCCCCCCSSSSSSSSSCCCCCSSSSSSSCCCCSSSSSCCCCCCCSSSSSSSSC
LPRFTSQPEPSSVYAGNNAILNCEVNADLVPFVRWEQNRQPLLLDDRVIKLPSGMLVISNATEGDGGLYRCVVESGGPPKYSDEVELKVLPDPLIILEHAPATTGPLPSAPRDVVASLVSTRFIKLTWRTPASDPHGDNLTYSVFYTKEGIARERVENTSHPGEMQVTIQNLMPATVYIFRVMAQ

6iaaA2

0.22

6.81

1.31

SPARKS-K

PPIILQGPANQTLAVDGTALLKCKATGDPLPVISWLKEGFTFPGDPRATIQEQGTLQIKNLRISDTGTYTCVATSSSG-ETSWSAVLDVTESGA--TISKNYDLSDLPGPPSKPQVTDVTKNSVTLSWQ-PGTPGTLPASAYIIEAFSQSVSNSWQTVANHVKTTLYTVRGLRPNTIYLF-VRAI

6iaaA2

0.22

0.21

6.66

1.22

MUSTER

PPIILQGPANQTLAVDGTALLKCKATGDPLPVISWLKEGFTFPGDPRATIQEQGTLQIKNLRISDTGTYTCVATSSSG-ETSWSAVLDVTESGAT--ISKNYDLSDLPGPPSKPQVTDVTKNSVTLSWQPG-TPGTLPASAYIIEAFSQSVSNSWQTVANHVKTTLYTVRGLRPNTIYLF-VRAI

2nziA

0.25

7.70

1.96

FFAS-3D

-PHFKEELRNLNVRYQSNATLVCKVTGHPKPIVKWYRQGKEIIADGLKYRIGYHQLIIASVTDDDATVYQVRATNQGGSVSGTASLEVAKNRFGIDQKTVELDVADVPDPPRGVKVSDVSRDSVNLTWTEPASDGGSKITNYIVEKCATTAERWLRVG--QARETRYTVINLFGKTSYQFRVIAE

6iaaA

0.23

0.22

6.95

2.45

CNFpred

PPIILQGPANQTLAVDGTALLKCKATGDPLPVISWLKEGFTFPRDPRATIQEQGTLQIKNLRISDTGTYTCVATSSSGE-TSWSAVLDVTESGATIS--KNYDLSDLPGPPSKPQVTDVTKNSVTLSWQPGT-PGTLPASAYIIEAFSQSNSWQTVANHVK--TTLYTVRGLRPNTIYLFMVRAI

5i99A

0.20

0.15

4.69

1.00

DEthreader

APDFRNPMKMVQVQVGSLVILDCKPRASPRALSFWKKGDMMVREQARVSFLNDGGLKIMNVTKADAGTYTCTAENQ-FGKANGTTHLVVTEP-T--------------------RIILAPSNLPCQVQH-P-------------MFAWLTDFKFEKVGG-----SSGDLMGKYV-CMVQT-----

6iaaA

0.22

6.81

1.27

SPARKS-K

PPIILQGPANQTLAVDGTALLKCKATGDPLPVISWLKEGFTFPGDPRATIQEQGTLQIKNLRISDTGTYTCVATSSSG-ETSWSAVLDVTESGA--TISKNYDLSDLPGPPSKPQVTDVTKNSVTLSWQ-PGTPGTLPASAYIIEAFSQSVSNSWQTVANHVKTTLYTVRGLRPNTIYLF-VRAI

4pbxA

0.26

0.25

7.84

0.50

MapAlign

FPNIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDPNGRIKQLRSGALQIESSEETDQGKYECVATNSAGVRYSSPANLYVRVRGPPSESVVTRTGEQAPSAPRNVQARMLSATTMIVQWEEPVEP-NGLIRGYRVYYTMHPVGNWQKHNVD-D-SLLTTVGSLLEDETYTVRVLAF

6iaaA2

0.20

6.39

0.57

CEthreader

PPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSLLFPNQRCSVSPTGDLTITNIQRSDAGYYICQALTVAGS-ILAKAQLEVTDVLTDATISKNYDLSDLPGPPSKPQVTDVTKNSVTLSWQPGTPGT-LPASAYIIEAFSQSVSNSWQTVANHVKTTLYTVRGLRPNTIYLFVRAIN

6iaaA

0.22

0.21

6.66

1.20

MUSTER

PPIILQGPANQTLAVDGTALLKCKATGDPLPVISWLKEGFTFPGDPRATIQEQGTLQIKNLRISDTGTYTCVATSSSG-ETSWSAVLDVTESGAT--ISKNYDLSDLPGPPSKPQVTDVTKNSVTLSWQPG-TPGTLPASAYIIEAFSQSVSNSWQTVANHVKTTLYTVRGLRPNTIYLF-VRAI

6iaaA2

0.23

7.11

0.58

HHsearch

PPQFVVRPRDQIVAQGRTVTFPCETKGNPQPAVFWQKEGSQNLPNSRCSVSPTGDLTITNIQRSDAGYYICQALTVAG-SILAKAQLEVTDVPIIVTESKNYDLSDLPGPPSKPQVTDVTKNSVTLSWQPGT-PGTLPASAYIIEAFSQSSNSWQTVAN-HVKTTLYTVRGLRPNTIYLF-VRAI

(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	0.8901

(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	6iaaA2	0.91	1.45	0.225	0.962	model1_6iaaA2.pdb.gz
2	2fboJ	0.56	4.41	0.164	0.805	model1_2fboJ.pdb.gz
3	3dmkA	0.55	4.24	0.086	0.735	model1_3dmkA.pdb.gz
4	1cs6A	0.55	4.16	0.168	0.724	model1_1cs6A.pdb.gz
5	5e4iA	0.54	4.10	0.175	0.703	model1_5e4iA.pdb.gz
6	3p3yA	0.54	3.88	0.146	0.703	model1_3p3yA.pdb.gz
7	3lafA	0.54	4.44	0.184	0.735	model1_3lafA.pdb.gz
8	1bihA	0.53	4.21	0.086	0.730	model1_1bihA.pdb.gz
9	5whzL	0.53	4.29	0.138	0.719	model1_5whzL.pdb.gz
10	1yewA	0.52	4.68	0.082	0.811	model1_1yewA.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:0042802	0.44	identical protein binding
GO:0003824	0.38	catalytic activity
GO:0004872	0.37	receptor activity
GO:0008092	0.36	cytoskeletal protein binding
GO:0005198	0.36	structural molecule activity
GO:0004672	0.35	protein kinase activity
GO:0008307	0.34	structural constituent of muscle
GO:0051371	0.33	muscle alpha-actinin binding
GO:0004888	0.33	transmembrane signaling receptor activity
GO:0097367	0.30	carbohydrate derivative binding
GO:0004674	0.30	protein serine/threonine kinase 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:0044699	0.91	single-organism process
GO:0009987	0.86	cellular process
GO:0044763	0.84	single-organism cellular process
GO:0032502	0.79	developmental process
GO:0044767	0.77	single-organism developmental process
GO:0065007	0.68	biological regulation
GO:0050789	0.67	regulation of biological process
GO:0050794	0.66	regulation of cellular process
GO:0048856	0.65	anatomical structure development
GO:0006928	0.63	movement of cell or subcellular component
GO:0048869	0.61	cellular developmental process
GO:0016043	0.59	cellular component organization
GO:0051239	0.54	regulation of multicellular organismal process
GO:0050793	0.54	regulation of developmental process
GO:2000026	0.53	regulation of multicellular organismal development
GO:0051128	0.52	regulation of cellular component organization
GO:0045595	0.52	regulation of cell differentiation
GO:0045664	0.51	regulation of neuron differentiation
GO:0010975	0.50	regulation of neuron projection development
GO:0009653	0.50	anatomical structure morphogenesis

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	0.95	cell part
GO:0044425	0.56	membrane part
GO:0044424	0.55	intracellular part
GO:0044459	0.50	plasma membrane part
GO:0043226	0.48	organelle
GO:0016020	0.48	membrane
GO:0044444	0.46	cytoplasmic part
GO:0031224	0.46	intrinsic component of membrane
GO:0016021	0.45	integral component of membrane
GO:0044422	0.44	organelle part
GO:0097458	0.43	neuron part
GO:0043227	0.42	membrane-bounded organelle
GO:0005886	0.41	plasma membrane
GO:0042995	0.40	cell projection
GO:0031226	0.39	intrinsic component of plasma membrane
GO:0043005	0.37	neuron projection
GO:0005887	0.37	integral component of plasma membrane
GO:0044446	0.36	intracellular organelle part
GO:0030424	0.35	axon
GO:0044421	0.34	extracellular region part
GO:0043229	0.34	intracellular organelle
GO:0043234	0.33	protein complex
GO:0044449	0.30	contractile fiber part

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	0.155	2wwmD	0.466	1.29	0.198	0.492	2.7.11.1	66,68
2	0.060	1u2hA	0.471	0.96	0.300	0.486	2.7.11.1	38,41,84
3	0.060	2gqhA	0.418	1.97	0.224	0.465	2.7.11.1	42,51,72
4	0.060	1j2gA	0.440	4.82	0.071	0.703	1.7.3.3	NA
5	0.060	3ebgA	0.465	5.45	0.027	0.805	3.4.11.-	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	2ibg0	0.492	4.13	0.089	0.654	0.49	III	complex1.pdb.gz	33,34,36,72,80,81,82,83,84
2	0.01	1uh2A	0.339	5.04	0.027	0.557	0.42	GLC	complex2.pdb.gz	21,35,38
3	0.01	3tygH	0.273	6.42	0.054	0.551	0.51	UUU	complex3.pdb.gz	15,90,91
4	0.01	1fcc0	0.408	4.90	0.063	0.665	0.62	III	complex4.pdb.gz	6,8,20,22,50,52,55,83

	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.