D-I-TASSER Q96NU0-D3

D-I-TASSER results for Q96NU0-D3

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

Input Sequence in FASTA format

>Q96NU0 (160 residues)
TFQFRTWNRAGHLLFGELQRGSGSFVLFLKDGKLKLSLFQAGQSPRNVTAGAGLNDGQWH
SVSFSAKWSHMNVVVDDDTAVQPLVAVLIDSGDTYYFGGCLGNSSGSGCKSPLGGFQGCL
RLITNMTADSAWTVVRHGGPDAVTLRGAPSGHPLSAVSFA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| TFQFRTWNRAGHLLFGELQRGSGSFVLFLKDGKLKLSLFQAGQSPRNVTAGAGLNDGQWHSVSFSAKWSHMNVVVDDDTAVQPLVAVLIDSGDTYYFGGCLGNSSGSGCKSPLGGFQGCLRLITNMTADSAWTVVRHGGPDAVTLRGAPSGHPLSAVSFA
Prediction	CSSSSSCCCCSSSSSSCCCCCCCSSSSSSSCCSSSSSSSSCCCCSSSSSSCCCCCCCCCSSSSSSSSCCSSSSSSSCCCCCSCCCCSSSCCCCCSSSSCCCCCCCCCCCCCCCCCCSSSSSSSSSCCSCCCHHHHHHCCCCCSSSCCCCCCCCCCCCCCC
Confidence	9389967999489997589998789999999999999981999529998077214996289999997999999992876400255422348995899407775455444457899035747879877125404321057653067488999986775579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| TFQFRTWNRAGHLLFGELQRGSGSFVLFLKDGKLKLSLFQAGQSPRNVTAGAGLNDGQWHSVSFSAKWSHMNVVVDDDTAVQPLVAVLIDSGDTYYFGGCLGNSSGSGCKSPLGGFQGCLRLITNMTADSAWTVVRHGGPDAVTLRGAPSGHPLSAVSFA
Prediction	7664314444203010236744100001347432201022344331303354403443103020314653020202343434444444043733010021245454463444352020002203336462424324442453330431347313413327
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSSCCCCSSSSSSCCCCCCCSSSSSSSCCSSSSSSSSCCCCSSSSSSCCCCCCCCCSSSSSSSSCCSSSSSSSCCCCCSCCCCSSSCCCCCSSSSCCCCCCCCCCCCCCCCCCSSSSSSSSSCCSCCCHHHHHHCCCCCSSSCCCCCCCCCCCCCCC
TFQFRTWNRAGHLLFGELQRGSGSFVLFLKDGKLKLSLFQAGQSPRNVTAGAGLNDGQWHSVSFSAKWSHMNVVVDDDTAVQPLVAVLIDSGDTYYFGGCLGNSSGSGCKSPLGGFQGCLRLITNMTADSAWTVVRHGGPDAVTLRGAPSGHPLSAVSFA

1dykA2

0.24

0.20

6.24

1.17

DEthreader

EFEFRTTRPTGVLLGVS-SQKMDGMGIEMIDEKLMFHVDNGAG-RFTAIYDAHMCNGQWHKVTAKKIKNRLELVVDGNQ-VDAQSNTSADTNDPVFVGGFPGGLNQFGLTTNI-RFRGCIRSLKLTKGT----------------------GKPLEVNFP

2wjsA2

0.21

0.19

5.96

1.54

SPARKS-K

MFKFRTFSSSALLMYLATRDLKDFMSVELSDGHVKVSYDLGS-GMTSVVSNQNHNDGKWKAFTLSRIQKQANISIVDISSSGNNFGLDLKADDKIYFGGLPTLRNLRP-EVNVKKYSGCLKDIEISRTPYNI----LSSPDYVGVTKGC-----------

1dykA

0.17

5.55

0.68

MapAlign

ELEVRTEAESGLLFYMARINHADFATVQLRNGFPYFSYDLG-SGDTSTMIPTKINDGQWHKIKIVRVKQEGILYVDDASSQTISKADILDVVGILYVGGLPINYTTRRIGPVTYSLDGCVRNLHMTTRPTGVLLGVSSQKMDGMGIEMIDEKLMFHVDNG

1q56A

0.15

0.14

4.63

0.54

CEthreader

ELSIKTEATQGLILWSGKGERSDYIALAIVDGFVQMMYDLGS-KPVVLRSTVPINTNHWTHIKAYRVQREGSLQVGNEAPITGSSATQLDTDGALWLGGMERLSVAHKLPKAYTGFIGCIRDVIVDRQELHLVEDALNNPTILHCSAK------------

1dykA2

0.23

0.21

6.67

1.29

MUSTER

EFEFRTTRPTGVLLGVSSQK-MDGMGIEMIDEKLMFHVDNGAGRFTAIYDPGHMCNGQWHKVTAKKIKNRLELVVDGNQVDAQSPNTSADTNDPVFVGGFPGGLN-QFGLTTNIRFRGCIRSLKLTKGTGKPLEV--NFAKALELRGVQPVSPT------

2wjsA

0.13

0.12

4.36

1.71

HHsearch

VVHVKTAVADNLLFYLGSAKFIDFLAIEMRKGKVSFLWDVGSGVGRVEYPDLTIDDSYWYRIEASRTGRNGSISVRALDGYHSVGYTILDVNAMLFVGGLTGKIKK-ADAVRVITFTGCMGETYFDNKPI-F-REKEGDCKGCLVSRPIWYPNISTVMFK

5mc9A2

0.17

0.14

4.75

1.62

FFAS-3D

VILFSTFSPNGLLFYLASNGTKDFLSIELVRGRVKVMVDL-GSGPLTLMTDRRYNNGTWYKIAFQRNRKQGLLAVFDAYTPGAASDLNRLEKDLIYVGGLPHSKAVRK-GVSSRSYVGCIKNLEISRSTFDL------LRNSYGVRG-------------

5mc9A3

0.16

0.15

4.97

1.08

EigenThreader

LATFATKNSSGILLVALGKDHVPFFSIMLLEGRIEVHVNSGDGTLRKALHAGSYSDGQEHSISLVRNRRVITIQVDENSPVEMKLGGKTIDISNLYIGGLPEDKATPMLKMRTSFHGCIKNVVL-----DAQLLD--FTHATGSEQTCLLAEEPM-----

3poyA

0.21

0.19

5.95

1.76

CNFpred

TLSFKTLQRNGLMLHTGK--SADYVNLALKNGAVSLVINLGS-GAFEALVEPKFNDNAWHDVKVTRNLRQVTISVDGILTTTGYT-TMLGSDDFFYVGGSPSTADLPGSPV-SNNFMGCLKEVVYKNVRLELSRLAKQGDPKMKIHG-------------

2r16A

0.22

0.19

5.93

1.17

DEthreader

SLRFRSQRAYGILMATTSRDSADTLRLELDAGRVKLTVNLG-KGPETLFAGYNLNDNEWHTVRVVRRGKSLKLTVDDQQAMTGQMAHTRLEFHNIETGIIT-ERRYL-SSVPS-NFIGHLQSLT-FNG----MAYI--CKNGDID----------YCELA

(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	0.771

(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	1dykA1	0.79	1.88	0.183	0.869	model1_1dykA1.pdb.gz
2	2jd4A2	0.78	2.16	0.179	0.875	model1_2jd4A2.pdb.gz
3	3poyA1	0.77	2.07	0.215	0.869	model1_3poyA1.pdb.gz
4	2wjsA1	0.75	2.23	0.130	0.863	model1_2wjsA1.pdb.gz
5	1q56A	0.75	2.32	0.148	0.863	model1_1q56A.pdb.gz
6	2r16A	0.73	2.62	0.189	0.856	model1_2r16A.pdb.gz
7	1kdkA	0.72	2.81	0.214	0.875	model1_1kdkA.pdb.gz
8	3asiA3	0.71	2.31	0.185	0.812	model1_3asiA3.pdb.gz
9	1h30A	0.69	2.74	0.130	0.838	model1_1h30A.pdb.gz
10	1h6s1	0.34	5.72	0.048	0.644	model1_1h6s1.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:0005102	0.76	receptor binding
GO:0098772	0.56	molecular function regulator
GO:0005509	0.56	calcium ion binding
GO:0008289	0.52	lipid binding
GO:0004857	0.52	enzyme inhibitor activity
GO:0072341	0.51	modified amino acid binding
GO:0043028	0.51	cysteine-type endopeptidase regulator activity involved in apoptotic process
GO:0030295	0.51	protein kinase activator activity
GO:0022843	0.51	voltage-gated cation channel activity
GO:0005543	0.51	phospholipid binding
GO:0005262	0.51	calcium channel activity
GO:0004869	0.51	cysteine-type endopeptidase inhibitor 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	0.94	single-organism process
GO:0044763	0.77	single-organism cellular process
GO:0032502	0.62	developmental process
GO:0065007	0.61	biological regulation
GO:0044767	0.60	single-organism developmental process
GO:0050794	0.55	regulation of cellular process
GO:0016043	0.54	cellular component organization

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	0.74	cell part
GO:0044421	0.69	extracellular region part
GO:0044425	0.45	membrane part
GO:0016020	0.44	membrane
GO:0043226	0.39	organelle
GO:0044424	0.38	intracellular part
GO:0043227	0.35	membrane-bounded organelle
GO:0016021	0.35	integral component of membrane
GO:0005615	0.35	extracellular space
GO:0031012	0.34	extracellular matrix
GO:0044459	0.33	plasma membrane part
GO:0097458	0.32	neuron part
GO:0044420	0.30	extracellular matrix component

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	0.066	1lclA	0.526	3.19	0.107	0.700	3.1.1.5	NA
2	0.066	2ifwA	0.626	3.84	0.068	0.900	3.4.23.32	NA
3	0.066	3d6eB	0.587	2.57	0.088	0.713	3.2.1.73	NA
4	0.060	3ffzA	0.601	2.78	0.089	0.731	3.4.24.69	NA
5	0.060	1ajkA	0.610	4.12	0.083	0.838	3.2.1.73	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	0.07	1lhuA	0.720	2.79	0.214	0.875	0.72	EST	complex1.pdb.gz	14,16,23,25,40,64,66,93,95,126
2	0.04	2wjsA	0.762	2.11	0.174	0.863	0.81	CA	complex2.pdb.gz	23,40,86,90
3	0.04	3mw2A	0.711	2.12	0.194	0.806	0.64	UUU	complex3.pdb.gz	10,11,29,34,36
4	0.04	2r1dH	0.709	2.18	0.186	0.806	0.54	III	complex4.pdb.gz	98,115,118,119,120
5	0.03	1b09E	0.663	3.17	0.077	0.838	0.53	PC	complex5.pdb.gz	28,100,114
6	0.03	2a3xD	0.674	2.94	0.064	0.844	0.51	CPK	complex6.pdb.gz	25,27,100,114
7	0.02	3l2yI	0.664	3.23	0.079	0.850	0.56	OPE	complex7.pdb.gz	26,28,100

	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.