D-I-TASSER B3KNS4-D1

D-I-TASSER results for B3KNS4-D1

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

Input Sequence in FASTA format

>B3KNS4 (109 residues)
MDKPCGCPPGVCDHGTGDRRDPWYSTVGLLPPVRAMSQRNLNAKTEQGPTGVTMTSNPIT
WGQIKKTTQEAEKLLERQGQAKTPDSMFLAMLAVVSCASIGSGEPPTGN

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MDKPCGCPPGVCDHGTGDRRDPWYSTVGLLPPVRAMSQRNLNAKTEQGPTGVTMTSNPITWGQIKKTTQEAEKLLERQGQAKTPDSMFLAMLAVVSCASIGSGEPPTGN
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
Confidence	9998789832012554222487777789994189999860334689998887657999978999999999999999709989867999999999985036888999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MDKPCGCPPGVCDHGTGDRRDPWYSTVGLLPPVRAMSQRNLNAKTEQGPTGVTMTSNPITWGQIKKTTQEAEKLLERQGQAKTPDSMFLAMLAVVSCASIGSGEPPTGN
Prediction	8754241354226443654454425654333314403644045545645454447442332331441053045215656454424301020111121343674635688
	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

                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
MDKPCGCPPGVCDHGTGDRRDPWYSTVGLLPPVRAMSQRNLNAKTEQGPTGVTMTSNPITWGQIKKTTQEAEKLLERQGQAKTPDSMFLAMLAVVSCASIGSGEPPTGN

1kgzB

0.11

3.97

0.48

CEthreader

DEVAIHTPTQVAELNNGEIESYQLSPQDFGLQSYSLNALQGGTPEENRDILARLLQGKGDAAHARQVAANVALLLKLFGQDNLRHNAQLALETIRSGTAFERVTALAAR

3o0rC

0.05

2.21

0.57

EigenThreader

-FTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSVGCHTLLGYFAPELGNVVGRREGFNTFLQAWMKIQQFHLSEGQVDDLAEFLKWSSKIWPPNKEG--

3mveA1

0.12

0.10

3.55

0.43

FFAS-3D

----------------EKNGFSWYRNLGVDPQEQVLARIASSKHSRTDELDTVMGYHSGNWYEWTRLGMEHQKRAGEMTNEAASEALFSASLCYSIAGYPHLKSDN---

4ic9A

0.13

0.10

3.50

0.68

SPARKS-K

-----------------------GQGRDWKMAIKRCSNVAVG-VGGKSKKFGREPGDIPTLDQLRLVICDLQERREKFGSSK-EIDMAIVTLKVFAVAGLLNMTVSTAA

5cwqA

0.18

0.06

2.09

0.45

CNFpred

-------------------------------------------------------------EKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLA---------

5uot0

0.05

2.09

1.00

DEthreader

-------NNYRVLLEATVPRRLTELIMIQKSLPLLEGQIRESHQKTELRRCGAKMFDKLVEGRLYNKIRE-D--------PSMLQKAMEIIQQAFINVAKKHFGEFTAK

6ip0A

0.06

2.72

0.74

MapAlign

-VSRLPKSTLRLLETSIPGVTEPMLYIGMLFSMFAWHVEDHYLYSINYQHCGASKTWYGIPGSAALKFEKVVKECVYNDDIFPPKTLLDHVPVYKAVQGFSHGFNCGEA

5ue0A1

0.20

0.17

5.60

0.58

MUSTER

LDDVDNEMAAIAMQGFRSMIEQFNVNNPATAELQAMEAQ-LTAMSDQL---VGADGELP------AEIQAIKDALAQAL--KQADGLATAMGQVAFAAAVGGGSAGTAG

7kdsA2

0.20

0.09

2.94

0.49

HHsearch

-----------------------------------------------------------TYGDLLREVSKVAGVLQSWGIKKMNAQAIIAMLAIARLGAAHSVIFAGFS

3fh2A

0.06

2.49

0.44

CEthreader

VLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDAVRQEVEEIIGQGSQPTPRAKKVLELSLREGLQMGHKIGTEFLLLGLIREGEGVAAQVLVKLGAD

(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	0.5042

(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	3ondA	0.50	4.24	0.074	0.853	model1_3ondA.pdb.gz
2	5ezmA	0.50	4.50	0.037	0.872	model1_5ezmA.pdb.gz
3	5hb4B	0.50	4.38	0.038	0.862	model1_5hb4B.pdb.gz
4	6r9tA	0.50	4.38	0.084	0.853	model1_6r9tA.pdb.gz
5	5bvrA	0.50	4.38	0.064	0.844	model1_5bvrA.pdb.gz
6	3ce6A2	0.50	4.35	0.042	0.862	model1_3ce6A2.pdb.gz
7	6p25B2	0.49	4.73	0.046	0.872	model1_6p25B2.pdb.gz
8	1v8bA	0.49	4.38	0.062	0.872	model1_1v8bA.pdb.gz
9	5nvrA	0.48	4.22	0.047	0.780	model1_5nvrA.pdb.gz
10	3n58A	0.48	4.24	0.063	0.835	model1_3n58A.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:0044822	1.00	poly(A) RNA binding
GO:0008134	0.66	transcription factor binding
GO:0001078	0.66	transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001047	0.66	core promoter binding
GO:0000978	0.66	RNA polymerase II core promoter proximal region sequence-specific DNA 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:0044763	0.47	single-organism cellular process
GO:0044281	0.47	small molecule metabolic process
GO:0044237	0.40	cellular 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:0044428	1.00	nuclear part
GO:0043231	1.00	intracellular membrane-bounded organelle
GO:0005737	0.85	cytoplasm
GO:0044444	0.69	cytoplasmic part
GO:0016020	0.52	membrane
GO:0005794	0.52	Golgi apparatus
GO:0005654	0.52	nucleoplasm
GO:0005634	0.52	nucleus

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	0.060	1v8bC	0.493	4.37	0.062	0.872	3.3.1.1	NA
2	0.060	2o2rC	0.454	4.27	0.097	0.798	1.5.1.6	NA
3	0.060	3b4wA	0.445	4.24	0.059	0.780	1.2.1.-	NA
4	0.060	2j6lB	0.435	4.13	0.100	0.761	1.2.1.31 1.2.1.3	NA
5	0.060	3ihyC	0.442	4.66	0.057	0.789	2.7.1.137	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	3rhoA	0.454	4.07	0.099	0.771	0.34	NAP	complex1.pdb.gz	6,7,10,16,60,63
2	0.01	2nt8A	0.459	4.45	0.040	0.798	0.30	ATP	complex2.pdb.gz	37,39,40,41,65
3	0.01	1d8tA	0.309	4.71	0.043	0.587	0.21	GDP	complex3.pdb.gz	50,51,52,53,96,97
4	0.01	1d8tA	0.309	4.71	0.043	0.587	0.16	III	complex4.pdb.gz	74,77,79
5	0.01	3rhlA	0.453	4.19	0.089	0.780	0.13	NAP	complex5.pdb.gz	6,8,9,10,13,14,64,67,68
6	0.01	1etuA	0.304	4.37	0.044	0.532	0.23	GDP	complex6.pdb.gz	5,68,69,88,89
7	0.01	1v8bA	0.492	4.38	0.062	0.872	0.34	NAD	complex7.pdb.gz	78,91,95
8	0.01	1efu0	0.395	4.56	0.081	0.743	0.14	III	complex8.pdb.gz	63,66,67,70,73,74,77

	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.