D-I-TASSER A8MTB9-D1

D-I-TASSER results for A8MTB9-D1

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

Input Sequence in FASTA format

>A8MTB9 (139 residues)
MDLSRPRWSLWRRVFLMASLLACGICQASGQIFITQTLGIKGYRTVVALDKVPEDVQEYS
WYWGANDSAGNMIISHKPPSAQQPGPMYTGRERVNREGSLLIRPTALNDTGNYTVRVVAG
NETQRATGWLEVLELGSNL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDLSRPRWSLWRRVFLMASLLACGICQASGQIFITQTLGIKGYRTVVALDKVPEDVQEYSWYWGANDSAGNMIISHKPPSAQQPGPMYTGRERVNREGSLLIRPTALNDTGNYTVRVVAGNETQRATGWLEVLELGSNL
Prediction	CCCCCCCCCCCHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCSSSSSSCCCCCCCSSSSSSCCCCCCCCCSSSSSSCCCCSSSCCCCCCSSSSCCCCCSSSSCCCCCCCCSSSSSSSSCCCSSSSSSSSSSSSSCCCC
Confidence	9988898866257999999998347887523587624766895389992799886347887236645787389999468824536776780787289757995257323716999999289628999999999724689
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDLSRPRWSLWRRVFLMASLLACGICQASGQIFITQTLGIKGYRTVVALDKVPEDVQEYSWYWGANDSAGNMIISHKPPSAQQPGPMYTGRERVNREGSLLIRPTALNDTGNYTVRVVAGNETQRATGWLEVLELGSNL
Prediction	8537446221033100100001213342314040443424444402020441273130220231443454220112335544342453433231354030203513572323010202357544403030302525678
	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

CCCCCCCCCCCHHHHHHHHHHHHCCCCCCCSSSSSSCCCCCCCSSSSSSCCCCCCCSSSSSSCCCCCCCCCSSSSSSCCCCSSSCCCCCCSSSSCCCCCSSSSCCCCCCCCSSSSSSSSCCCSSSSSSSSSSSSSCCCC
MDLSRPRWSLWRRVFLMASLLACGICQASGQIFITQTLGIKGYRTVVALDKVPEDVQEYSWYWGANDSAGNMIISHKPPSAQQPGPMYTGRERVNREGSLLIRPTALNDTGNYTVRVVAGNETQRATGWLEVLELGSNL

2fboJ

0.14

0.12

3.94

1.17

DEthreader

---------------T--RTTHTLPCSVVHVSTAEVVQVDEGNDITMTCPCTDCANANVTWYTGPTTGTYQPLANKNQFGITWFSSEIAGRASFSGARNLVIRAAKITDAGRVWCELATGGDADRSSTILKV-------

4y89A

0.27

0.21

6.40

1.12

SPARKS-K

---------------------------AQTNIDVVPFNVAEGKEVLLVVHNESQNLYGYNWYKGERVHANYRIIGYVKNIENAPGPAHNGRETIYPNGTLLIQNVTHNDAGIYTLHVIKENLNEEVTRQFYVF------

4y89A

0.27

0.21

6.40

1.65

FFAS-3D

---------------------------AQTNIDVVPFNVAEGKEVLLVVHNESQNLYGYNWYKGERVHANYRIIGYVKNISNAPGPAHNGRETIYPNGTLLIQNVTHNDAGIYTLHVIKENLNEEVTRQFYVF------

5f1dA

0.23

0.19

5.85

1.47

CNFpred

----------------------------EVTIEAVPPQVAEDNNVLLLVHNLPLALGAFAWYKGNPVSTNAEIVHFVTGNKTTTGPAHSGRETVYSNGSLLIQRVTVKDTGVYTIEMTDEFRRTEATVQFHVHQPVTQP

3f8uD

0.10

0.09

3.19

1.17

DEthreader

------------YPR-APAP--HCEMVSSTVLTTPAPRVRLGQDALLDLSFAYPPPFGLEWRRQHL-GKGHLLLAATPGNQMPAA--QE-GAVAFANGTFWLPRVQPFQEGTYLATIHLPYLQGQVTLELAVYKPPKVS

2dksA

0.28

0.24

7.27

1.05

SPARKS-K

-------------------GSSGSSGTAQLTIEAVPSNAAEGKEVLLLVHNLPQDPRGYNWYKGETVDANRRIIGYVISNQITPGPAYSNRETIYPNASLLMRNVTRNDTGSYTLQVIKLNLMSEVTGQFSVHPETPKP

3ebaA

0.10

0.08

2.89

0.42

MapAlign

----------------------------QVQLVESGGSVQAGGSLRLSCS-ASGYTYISGWFRQAPGKGLEWVAAIRSSDGTYYADSVKGRFTISQTVYLQMNSLKPEDTAMYYCAATEIGIYYWGGTQVTVSS-----

5my6B

0.13

0.10

3.48

0.34

CEthreader

----------------------------QVQLQESGGGVQAGGSLKLTCAASIFNSCGMGWYRQSPGRERELVSRISGDGDTWHKESVKGRFTISQTLYLQMNSLKPEDTAVYFCAVCYNLETYWGGTQVTVSS-----

2dksA

0.28

0.24

7.26

0.84

MUSTER

---------------------GSSGSSGTAQLTIEAVNAAEGKEVLLLVHNLPQDPRGYNWYKGETVDANRRIIGYVISNQITPGPAYSNRETIYPNASLLMRNVTRNDTGSYTLQVIKLNLSEEVTGQFSVHPETPKP

2ch8A1

0.17

0.12

3.80

0.37

HHsearch

------------------------------------VTAFLGERVTLTSYWRRVPEIEVSWFKLGPGEEQVLIGRMHHDVIF-IEWPFRGFFDIHRTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVV------

(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	0.7859

(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

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

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3f8uD	0.71	2.92	0.081	0.863	model1_3f8uD.pdb.gz
2	4fomA	0.71	1.70	0.145	0.791	model1_4fomA.pdb.gz
3	2dksA	0.70	2.35	0.265	0.820	model1_2dksA.pdb.gz
4	2fboJ	0.70	2.01	0.128	0.806	model1_2fboJ.pdb.gz
5	2petA	0.70	2.01	0.152	0.806	model1_2petA.pdb.gz
6	4frwA	0.70	2.09	0.198	0.799	model1_4frwA.pdb.gz
7	5opiC	0.69	2.73	0.102	0.835	model1_5opiC.pdb.gz
8	5a2fA	0.69	1.57	0.152	0.755	model1_5a2fA.pdb.gz
9	3mj6A	0.69	2.92	0.163	0.835	model1_3mj6A.pdb.gz
10	4bfiB	0.69	1.90	0.119	0.784	model1_4bfiB.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	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0004872	0.64	receptor activity
GO:0042802	0.58	identical protein binding
GO:0046983	0.55	protein dimerization activity
GO:0097367	0.54	carbohydrate derivative binding
GO:1901681	0.50	sulfur compound 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	0.91	cellular process
GO:0044699	0.78	single-organism process
GO:0044763	0.76	single-organism cellular process
GO:0071704	0.74	organic substance metabolic process
GO:0044237	0.74	cellular metabolic process
GO:0044260	0.72	cellular macromolecule metabolic process
GO:0044238	0.72	primary metabolic process
GO:0043412	0.71	macromolecule modification
GO:0065007	0.69	biological regulation
GO:0050789	0.69	regulation of biological process
GO:0050794	0.68	regulation of cellular process
GO:0032501	0.65	multicellular organismal process
GO:0016192	0.64	vesicle-mediated transport
GO:0032502	0.63	developmental process
GO:0044767	0.61	single-organism developmental process
GO:0051239	0.59	regulation of multicellular organismal process
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0048518	0.58	positive regulation of biological process
GO:0022414	0.58	reproductive process
GO:0048519	0.57	negative regulation of biological process
GO:0048869	0.56	cellular developmental process
GO:0048583	0.56	regulation of response to stimulus
GO:0048523	0.56	negative regulation of cellular process
GO:0032879	0.55	regulation of localization
GO:0009653	0.55	anatomical structure morphogenesis
GO:0007165	0.55	signal transduction
GO:0050793	0.54	regulation of developmental process
GO:0048856	0.54	anatomical structure development
GO:0031323	0.54	regulation of cellular metabolic process
GO:0023051	0.54	regulation of signaling
GO:0010646	0.54	regulation of cell communication
GO:0007166	0.54	cell surface receptor signaling pathway
GO:0006928	0.54	movement of cell or subcellular component
GO:2000026	0.53	regulation of multicellular organismal development
GO:1902531	0.53	regulation of intracellular signal transduction
GO:0051246	0.53	regulation of protein metabolic process
GO:0048585	0.53	negative regulation of response to stimulus
GO:0050896	0.52	response to stimulus
GO:0050790	0.52	regulation of catalytic activity
GO:0048522	0.52	positive regulation of cellular process
GO:0045595	0.52	regulation of cell differentiation
GO:0031324	0.52	negative regulation of cellular metabolic process
GO:0010605	0.52	negative regulation of macromolecule metabolic process
GO:0010604	0.52	positive regulation of macromolecule metabolic process
GO:0009968	0.52	negative regulation of signal transduction
GO:0003008	0.52	system process
GO:0001932	0.52	regulation of protein phosphorylation
GO:0051240	0.51	positive regulation of multicellular organismal process
GO:0051128	0.51	regulation of cellular component organization
GO:0051094	0.51	positive regulation of developmental process
GO:0048646	0.51	anatomical structure formation involved in morphogenesis
GO:0022603	0.51	regulation of anatomical structure morphogenesis
GO:0016477	0.51	cell migration
GO:0010628	0.51	positive regulation of gene expression
GO:0007155	0.51	cell adhesion
GO:0006725	0.50	cellular aromatic compound 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:0044464	1.00	cell part
GO:0043226	0.90	organelle
GO:0044424	0.89	intracellular part
GO:0044444	0.85	cytoplasmic part
GO:0043229	0.80	intracellular organelle
GO:0016020	0.79	membrane
GO:0043227	0.74	membrane-bounded organelle
GO:0005886	0.73	plasma membrane
GO:0005737	0.68	cytoplasm
GO:0044422	0.67	organelle part
GO:0043231	0.59	intracellular membrane-bounded organelle
GO:0044425	0.55	membrane part
GO:0044421	0.51	extracellular region part
GO:0005829	0.51	cytosol

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	0.281	2edwA	0.552	2.02	0.188	0.633	2.7.11.1	46,64,109,115
2	0.214	2wwmD	0.570	1.99	0.189	0.647	2.7.11.1	64,114,127
3	0.202	1u2hA	0.570	1.68	0.167	0.633	2.7.11.1	60
4	0.163	2eo1A	0.544	2.27	0.146	0.626	2.7.11.1	62
5	0.153	1zv5A	0.621	2.46	0.095	0.741	3.2.1.17	128

	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	0.11	1ct8B	0.668	2.33	0.089	0.784	0.65	TAA	complex1.pdb.gz	62,64,113,128
2	0.10	1yegH	0.667	2.19	0.072	0.777	0.89	BPN	complex2.pdb.gz	63,65,113,115,129
3	0.09	1xgyI	0.663	2.45	0.089	0.784	0.63	III	complex3.pdb.gz	62,64,71,114,126
4	0.08	1yecH	0.667	2.20	0.072	0.777	0.64	PNB	complex4.pdb.gz	62,64,114,115,117,123
5	0.07	1mh5B	0.663	2.18	0.064	0.770	0.67	HAL	complex5.pdb.gz	61,63,71,114,127,129
6	0.02	2fr4H	0.653	2.45	0.081	0.777	0.70	QNA	complex6.pdb.gz	63,114,127,128
7	0.02	3qumH	0.657	2.29	0.081	0.777	0.72	UUU	complex7.pdb.gz	39,40,41

	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.