D-I-TASSER O43707-D5

D-I-TASSER results for O43707-D5

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

Input Sequence in FASTA format

>O43707 (154 residues)
GSNPYTTVTPQIINSKWEKVQQLVPKRDHALLEEQSKQQSNEHLRRQFASQANVVGPWIQ
TKMEEIGRISIEMNGTLEDQLSHLKQYERSIVDYKPNLDLLEQQHQLIQEALIFDNKHTN
YTMEHIRVGWEQLLTTIARTINEVENQILTRDAK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GSNPYTTVTPQIINSKWEKVQQLVPKRDHALLEEQSKQQSNEHLRRQFASQANVVGPWIQTKMEEIGRISIEMNGTLEDQLSHLKQYERSIVDYKPNLDLLEQQHQLIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAK
Prediction	CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	9999998799999999999999999999999999999999999999999999899999999999999631468899999999999999999998999999999999999976845776411289999999999999999999999999973149
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| GSNPYTTVTPQIINSKWEKVQQLVPKRDHALLEEQSKQQSNEHLRRQFASQANVVGPWIQTKMEEIGRISIEMNGTLEDQLSHLKQYERSIVDYKPNLDLLEQQHQLIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAK
Prediction	8844346132730462054046205513530551354156245105510630541352055325304534464714145025415523650562464154045015404634135163142335203421530351054225404421344568
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
GSNPYTTVTPQIINSKWEKVQQLVPKRDHALLEEQSKQQSNEHLRRQFASQANVVGPWIQTKMEEIGRISIEMNGTLEDQLSHLKQYERSIVDYKPNLDLLEQQHQLIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAK

5j1iA

0.10

3.56

1.33

DEthreader

----------SPAAPTLRSELELTLGKLEQVRSLSAIYLEKLKTISLVIRGTQGAEEVLRAHEEQLKEAQAVPAPELEATKASLKKLRAQAEAQQPTFDALRDELRGAQEVELDVVERWRERVAQLLERWQAVLAQTDVRQRELEQLGRQLRYY

1sjjA

0.81

22.92

1.27

SPARKS-K

GTNPYTTITPQEINGKWEHVRQLVPRRDQALMEEHARQQQNERLRKQFGAQANVIGPWIQTKMEEIGRISIEMHGTLEDQLNHLRQYEKSIVNYKPKIDQLEGDHQQIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAK

5nl6A

0.18

0.17

5.48

0.71

MapAlign

-----VAPEGLPKSLEGYIANISEAERALRSKLNTAMRNCLIALRKAFADPANATDAKINEYRTFVT--DETSEAPLEEQVATLKAKLEELKQVEAQLPPIEEAEKACEDANIEDNEYTDVSFDDLQFNYEQTVSMFEKKIVYIEAQIN-----

5nl6A

0.18

5.70

0.52

CEthreader

RPVYVAPEGLDPKSLEGYIANISEAERALRSKLNTAMRNCLIALRKAFADPANATDAKINEYRTFVTDETSE--APLEEQVATLKAKLEELKQVEAQLPPIEEAEKACEDANIEDNEYTDVSFDDLQFNYEQTVSMFEKKIVYIEAQINEA---

1sjjA2

0.81

22.92

1.26

MUSTER

GTNPYTTITPQEINGKWEHVRQLVPRRDQALMEEHARQQQNERLRKQFGAQANVIGPWIQTKMEEIGRISIEMHGTLEDQLNHLRQYEKSIVNYKPKIDQLEGDHQQIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAK

5nl6A

0.20

0.19

6.01

1.83

HHsearch

VYVAPEGLDPKSLEGYIANISEAERALRSKLNTA-MRNCL-IALRKAFADPANATDAKINEYRTFVTDETSEAPETLKAKLEELKQVEAQL-------PPIEEAEKACEDANIEDNEYTDVSFDDLQFNYEQTVSMFEKKIVYIEAQINEA---

5nl6A

0.19

0.18

5.67

1.83

FFAS-3D

--VAPEGLDPKSLEGYIANISEAERALRSKLNTAMR--NCLIALRKAFADPANATDAKINEYRTFVTDET--SEAPLEEQVATLKAKLEELKQVEAQLPPIEEAEKACEDANIEDNEYTDVSFDDLQFNYEQTVSMFEKKIVYIEAQINE----

1sjjA2

0.81

22.92

0.92

EigenThreader

GTNPYTTITPQEINGKWEHVRQLVPRRDQALMEEHARQQQNERLRKQFGAQANVIGPWIQTKMEEIGRISIEMHGTLEDQLNHLRQYEKSIVNYKPKIDQLEGDHQQIQEALIFDNKHTNYTMEHIRVGWEQLLTTIARTINEVENQILTRDAK

1hciA

0.70

0.69

19.75

1.13

CNFpred

SSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHIRVGWELLLTTIARTINEVETQILTRD--

6m3qF

0.11

0.10

3.75

1.33

DEthreader

--------PDSEQISRRQSQVDRLYVALKELGEERRVSLEQQYWLYQLSRQVDELEHWIAEKEVVAGS-PELGQDHVSVLQEKFSEFAETGTAGRERLAAVNQMVDELIECGHTAAATMAEWKDGLNEAWAELLELMGTRAQLLAASRELHKGA

(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	0.772

(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	1sjjA2	0.88	1.89	0.778	0.994	model1_1sjjA2.pdb.gz
2	6m3qF	0.81	2.47	0.104	0.942	model1_6m3qF.pdb.gz
3	6sl2A	0.79	2.79	0.086	0.987	model1_6sl2A.pdb.gz
4	1g8xA	0.79	2.76	0.132	0.968	model1_1g8xA.pdb.gz
5	3kbuB	0.77	2.76	0.078	0.942	model1_3kbuB.pdb.gz
6	3edvA	0.77	2.58	0.068	0.896	model1_3edvA.pdb.gz
7	3r6nA	0.77	2.82	0.087	0.903	model1_3r6nA.pdb.gz
8	2ycuA2	0.74	2.89	0.081	0.948	model1_2ycuA2.pdb.gz
9	1u4qA	0.72	3.61	0.101	0.961	model1_1u4qA.pdb.gz
10	3pe0A	0.64	3.10	0.109	0.831	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	0.91	cytoskeletal protein binding
GO:0046983	0.90	protein dimerization activity
GO:0042803	0.89	protein homodimerization activity
GO:0017166	0.84	vinculin binding
GO:0051393	0.82	alpha-actinin 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	0.97	single-organism process
GO:0009987	0.97	cellular process
GO:0044763	0.96	single-organism cellular process
GO:0016043	0.93	cellular component organization
GO:0044767	0.88	single-organism developmental process
GO:0030029	0.88	actin filament-based process
GO:0006996	0.87	organelle organization
GO:1902589	0.86	single-organism organelle organization
GO:0048869	0.86	cellular developmental process
GO:0048856	0.86	anatomical structure development
GO:0007010	0.86	cytoskeleton organization
GO:0045214	0.85	sarcomere organization
GO:0048468	0.84	cell development
GO:0055002	0.83	striated muscle cell development
GO:0048741	0.82	skeletal muscle fiber development

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:0044424	0.98	intracellular part
GO:0044444	0.95	cytoplasmic part
GO:0044422	0.94	organelle part
GO:0043226	0.94	organelle
GO:0044446	0.93	intracellular organelle part
GO:0044430	0.91	cytoskeletal part
GO:0043229	0.91	intracellular organelle
GO:0042995	0.87	cell projection
GO:0044449	0.86	contractile fiber part
GO:0030054	0.86	cell junction
GO:0016020	0.85	membrane
GO:0005925	0.85	focal adhesion
GO:0005856	0.85	cytoskeleton
GO:0044448	0.83	cell cortex part
GO:0030863	0.82	cortical cytoskeleton
GO:0001725	0.82	stress fiber
GO:0044425	0.81	membrane part
GO:0005911	0.81	cell-cell junction
GO:0005886	0.81	plasma membrane
GO:0044459	0.80	plasma membrane part
GO:0030864	0.79	cortical actin cytoskeleton
GO:0005913	0.79	cell-cell adherens junction
GO:1990357	0.78	terminal web
GO:0097433	0.78	dense body
GO:0090637	0.78	inner dense plaque of desmosome
GO:0090636	0.78	outer dense plaque of desmosome
GO:0042383	0.78	sarcolemma
GO:0031252	0.78	cell leading edge
GO:0030486	0.78	smooth muscle dense body
GO:0030027	0.78	lamellipodium
GO:0016328	0.78	lateral plasma membrane
GO:0005923	0.78	bicellular tight junction
GO:0005915	0.78	zonula adherens

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	0.067	2e2aA	0.520	2.64	0.069	0.643	2.7.1.69	NA
2	0.067	3k1sA	0.529	2.64	0.038	0.662	2.7.1.69	NA
3	0.060	2ohyB	0.453	4.26	0.064	0.675	5.4.3.6	NA
4	0.060	1ezfB	0.470	3.97	0.034	0.656	2.5.1.21	NA
5	0.060	1z0hB	0.242	5.42	0.031	0.442	3.4.24.69	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:

No Binding sites was predicted

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

	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.