D-I-TASSER A8MZ36-D2

D-I-TASSER results for A8MZ36-D2

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

Input Sequence in FASTA format

>A8MZ36 (123 residues)
EPGQPVHALQGCTWQLSALAEQQRRILQQDWSDLMADPAGVRREYEHFKQHELLSQEQSV
NQLEEDGKRMVELRHPAVGPIQAHQEALKMEWQNFLNLCICQETQLQHVEDYSRILCPSS
SPH

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EPGQPVHALQGCTWQLSALAEQQRRILQQDWSDLMADPAGVRREYEHFKQHELLSQEQSVNQLEEDGKRMVELRHPAVGPIQAHQEALKMEWQNFLNLCICQETQLQHVEDYSRILCPSSSPH
Prediction	CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Confidence	941699999999999999999999999734355567989999999999998999989999999999999999299973579999999999999999999999999998999999998711489
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| EPGQPVHALQGCTWQLSALAEQQRRILQQDWSDLMADPAGVRREYEHFKQHELLSQEQSVNQLEEDGKRMVELRHPAVGPIQAHQEALKMEWQNFLNLCICQETQLQHVEDYSRILCPSSSPH
Prediction	856403510340351141036315412554155634426414642551446405533641550374044025761464640542363045205413400402553054154144026416668
	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 AttentionPotential. 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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
EPGQPVHALQGCTWQLSALAEQQRRILQQDWSDLMADPAGVRREYEHFKQHELLSQEQSVNQLEEDGKRMVELRHPAVGPIQAHQEALKMEWQNFLNLCICQETQLQHVEDYSRILCPSSSPH

3lbxB

0.11

3.83

1.50

DEthreader

GTADKFRFFSMARDLLSWMESIIRQIETQERD--VSSVELLMKYHQGIN-AEIETRSKNFSACLELGESLLQRQHQASEEIREKLQQVMSRRKEMNEKWEARWERLRMLLEVCQFSRDASVAE

3edvA1

0.09

3.41

1.53

SPARKS-K

MRHRLFQLNREVDDLEQWIAEREVVAGSHELGQDYEHVTMLQERFREFARDTGNIGQERVDTVNHLADELINSGHSDAATIAEWKDGLNEAWADLLELIDTRTQILAASYELHKFYHDAKEIF

5j1iA

0.12

0.11

4.03

0.76

MapAlign

---RCQRCISELKDIRLQLEACETRTVHRLRLPLARECAQRIAEQQKAQA-EVEGLGKGVARLSAEAEKVL-ALSPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVL

3edvA1

0.09

3.41

0.54

CEthreader

MRHRLFQLNREVDDLEQWIAEREVVAGSHELGQDYEHVTMLQERFREFARDTGNIGQERVDTVNHLADELINSGHSDAATIAEWKDGLNEAWADLLELIDTRTQILAASYELHKFYHDAKEIF

3edvA1

0.09

3.41

1.46

MUSTER

MRHRLFQLNREVDDLEQWIAEREVVAGSHELGQDYEHVTMLQERFREFARDTGNIGQERVDTVNHLADELINSGHSDAATIAEWKDGLNEAWADLLELIDTRTQILAASYELHKFYHDAKEIF

3pe0A

0.24

7.35

1.87

HHsearch

-LESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALM-RELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAE

1cunA2

0.15

0.13

4.37

1.77

FFAS-3D

---EYQQFVANVEEEEAWINEKMTLVASEDYGDTLAAIQGLLKKHEAF-ETDFTVHKDRVNDVCANGEDLIKKNNHHVENITAKMKGLKGKVSDLEKAAAQRKAKLDENS-------------

3lbxB

0.11

3.83

0.82

EigenThreader

STADKFRFFSMARDLLSWMESIIRQIETQERD--VSSVELLMKYHQGINA-EIETRSKNFSACLELGESLLQRQHQASEEIREKLQQVMSRRKEMNEKWEARWERLRMLLEVCQFSRDASVAE

3pe0A

0.24

7.35

1.03

CNFpred

-LESLHSFVAAATKELMWLNEKEEEEVGFDWSDRNTNMTAKKESYSALM-RELELKEKKIKELQNAGDRLLREDHPARPTVESFQAALQTQWSWMLQLCCCIEAHLKENAAYFQFFSDVREAE

1u4qA

0.11

3.83

1.50

DEthreader

NEHRLHQFFRDMDDEESWIKEKKLLVS-SEDY-GRDGVQNLRKKHKRLEAE-LAAHEPAIQGVLDTGKKLSDDNTIGKEEIQQRLAQFVDHWKELKQLAAARGQRLEESLEYQQFVANVEEEE

(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

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Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8317

(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 AttentionPotential, 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

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Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3edvA	0.93	1.28	0.089	1.000	model1_3edvA.pdb.gz
2	3kbuB	0.92	1.41	0.114	1.000	model1_3kbuB.pdb.gz
3	6m3pA	0.92	1.39	0.098	1.000	model1_6m3pA.pdb.gz
4	1u4qA	0.91	1.30	0.132	0.984	model1_1u4qA.pdb.gz
5	6m3qF	0.90	1.56	0.089	1.000	model1_6m3qF.pdb.gz
6	3lbxB	0.90	1.35	0.108	0.976	model1_3lbxB.pdb.gz
7	3r6nA	0.90	1.58	0.205	0.992	model1_3r6nA.pdb.gz
8	3fb2B	0.89	1.33	0.093	0.959	model1_3fb2B.pdb.gz
9	1sjjA	0.86	1.89	0.139	0.992	model1_1sjjA.pdb.gz
10	3pe0A	0.84	1.97	0.240	0.984	model1_3pe0A.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:0008092	0.84	cytoskeletal protein binding
GO:0003779	0.75	actin binding
GO:0008017	0.66	microtubule 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:0044699	0.96	single-organism process
GO:0009987	0.93	cellular process
GO:0044763	0.92	single-organism cellular process
GO:0032502	0.87	developmental process
GO:0048856	0.79	anatomical structure development
GO:0016043	0.79	cellular component organization
GO:0048869	0.75	cellular developmental process
GO:0044767	0.75	single-organism developmental process
GO:0065007	0.74	biological regulation
GO:0050789	0.71	regulation of biological process
GO:0050794	0.70	regulation of cellular process
GO:0006996	0.68	organelle organization
GO:1902589	0.67	single-organism organelle organization
GO:0007010	0.65	cytoskeleton organization
GO:0065008	0.64	regulation of biological quality
GO:0030029	0.64	actin filament-based process
GO:0032501	0.63	multicellular organismal process
GO:0048518	0.62	positive regulation of biological process
GO:0051128	0.61	regulation of cellular component organization
GO:0048646	0.61	anatomical structure formation involved in morphogenesis
GO:0030036	0.61	actin cytoskeleton organization
GO:0051493	0.60	regulation of cytoskeleton organization
GO:0044707	0.60	single-multicellular organism process
GO:1901880	0.59	negative regulation of protein depolymerization
GO:0051494	0.59	negative regulation of cytoskeleton organization
GO:0048522	0.59	positive regulation of cellular process
GO:0044087	0.59	regulation of cellular component biogenesis
GO:0051239	0.58	regulation of multicellular organismal process
GO:0030030	0.58	cell projection organization
GO:0051240	0.57	positive regulation of multicellular organismal process
GO:0051130	0.57	positive regulation of cellular component organization
GO:0051094	0.57	positive regulation of developmental process
GO:0050769	0.56	positive regulation of neurogenesis
GO:0048513	0.56	animal organ development
GO:0031346	0.56	positive regulation of cell projection organization
GO:0010975	0.56	regulation of neuron projection development
GO:0009653	0.56	anatomical structure morphogenesis
GO:0007017	0.55	microtubule-based process
GO:0048812	0.54	neuron projection morphogenesis
GO:0007409	0.53	axonogenesis
GO:0048639	0.52	positive regulation of developmental growth
GO:0044700	0.52	single organism signaling
GO:0000226	0.52	microtubule cytoskeleton organization
GO:0051491	0.51	positive regulation of filopodium assembly
GO:0048813	0.51	dendrite morphogenesis
GO:0045773	0.51	positive regulation of axon extension
GO:0035149	0.51	lumen formation, open tracheal system
GO:0035147	0.51	branch fusion, open tracheal system
GO:0030716	0.51	oocyte fate determination
GO:0016319	0.51	mushroom body development
GO:0016204	0.51	determination of muscle attachment site
GO:0016203	0.51	muscle attachment
GO:0016199	0.51	axon midline choice point recognition
GO:0007475	0.51	apposition of dorsal and ventral imaginal disc-derived wing surfaces
GO:0007424	0.51	open tracheal system development
GO:0007423	0.51	sensory organ development
GO:0007026	0.51	negative regulation of microtubule depolymerization
GO:0001578	0.51	microtubule bundle formation

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:0044424	1.00	intracellular part
GO:0043226	0.96	organelle
GO:0043229	0.93	intracellular organelle
GO:0005737	0.92	cytoplasm
GO:0043232	0.91	intracellular non-membrane-bounded organelle
GO:0005856	0.90	cytoskeleton
GO:0044444	0.85	cytoplasmic part
GO:0044422	0.80	organelle part
GO:0030054	0.79	cell junction
GO:0044446	0.75	intracellular organelle part
GO:0005912	0.74	adherens junction
GO:0044430	0.73	cytoskeletal part
GO:0030055	0.65	cell-substrate junction
GO:0097458	0.62	neuron part
GO:0005924	0.62	cell-substrate adherens junction
GO:0044463	0.58	cell projection part
GO:0042995	0.57	cell projection
GO:0099513	0.56	polymeric cytoskeletal fiber
GO:0035371	0.56	microtubule plus-end
GO:0033267	0.55	axon part
GO:0005874	0.54	microtubule
GO:0045169	0.53	fusome
GO:0044295	0.52	axonal growth cone
GO:0030175	0.52	filopodium
GO:0005927	0.52	muscle tendon junction
GO:0000235	0.52	astral microtubule

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

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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	0.144	3eabA	0.519	2.82	0.023	0.707	3.6.4.3	16,57,65
2	0.094	2e2aA	0.611	2.96	0.049	0.829	2.7.1.69	NA
3	0.067	1cxzB	0.517	2.86	0.108	0.675	2.7.11.13	NA
4	0.060	2o36A	0.606	3.23	0.063	0.821	3.4.24.15	NA
5	0.060	1s4bP	0.610	3.27	0.063	0.821	3.4.24.15	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

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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	0.04	1czqA	0.340	0.95	0.136	0.358	1.32	III	complex1.pdb.gz	13,16,19,23,24
	2	0.01	3mylX	0.402	4.02	0.030	0.626	0.41	POP	complex2.pdb.gz	8,9,10,11,12,67

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.