D-I-TASSER P28328-D2

D-I-TASSER results for P28328-D2

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

Input Sequence in FASTA format

>P28328 (76 residues)
APNSDNTLATSGKECALCGEWPTMPHTIGCEHIFCYFCAKSSFLFDVYFTCPKCGTEVHS
LQPLKSGIEMSEVNAL

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| APNSDNTLATSGKECALCGEWPTMPHTIGCEHIFCYFCAKSSFLFDVYFTCPKCGTEVHSLQPLKSGIEMSEVNAL
Prediction	CCCCCCCCCCCCCSCCCCCCCCCCCSSCCCCCHHHHHHHHHHHHCCCCCCCCCCCCSCCCCCCCCCCCSSSCCCCC
Confidence	9987322244689285468837776881886546899999998148898799999743554554467556345579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| APNSDNTLATSGKECALCGEWPTMPHTIGCEHIFCYFCAKSSFLFDVYFTCPKCGTEVHSLQPLKSGIEMSEVNAL
Prediction	8467774456475401003432431341513121014004421445762412414550562641546144442648
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCSCCCCCCCCCCCSSCCCCCHHHHHHHHHHHHCCCCCCCCCCCCSCCCCCCCCCCCSSSCCCCC
APNSDNTLATSGKECALCGEWPTMPHTIGCEHIFCYFCAKSSFLFDVYFTCPKCGTEVHSLQPLKSGIEMSEVNAL

6yxeA

0.20

6.32

1.33

DEthreader

PSKVVIQDITMELHCPLCNDWFRDPLMLSCGHNFCEACIQDFWRLAKETFCPECKMLCQYNCTFNP-VLDKLVEKI

5ferA

0.20

6.30

2.47

SPARKS-K

--MAELCPLAEELSCSICLEPFKEPVTTPCGHNFCGSCLNETWAVQGPYLCPQCRAVYQARPQLHKNTVLCNVVEQ

5dkaA

0.28

0.22

6.84

0.79

MapAlign

-----------SFDCAVCLEVLHQPVRTRCGHVFCRSCIATSLK-NNKWTCPYCRAYLPSEGVPATDVAMKSE---

5dkaA

0.25

0.21

6.54

0.51

CEthreader

----------TSFDCAVCLEVLHQPVRTRCGHVFCRSCIATSLKNNKW-TCPYCRAYLPSEGVPATDVAKRMKSEY

5ferA

0.20

6.30

2.16

MUSTER

--MAELCPLAEELSCSICLEPFKEPVTTPCGHNFCGSCLNETWAVGSPYLCPQCRAVYQARPQLHKNTVLCNVVEQ

4qplA

0.25

0.21

6.53

1.23

HHsearch

--------SLTVPECAICLQTCVHPVSLPCKHVFCYLCVKGASWL--GKRCALCRQEIPEDF--LDKPSPEELKRG

3ztgA

0.20

6.32

1.09

FFAS-3D

PLGSEDDPIPDELLCLICKDIMTDAVVICCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFLRQAVN-

2kreA

0.09

3.46

0.92

EigenThreader

NARAEIDYSDDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHL--LNSPTDPFNRQTLTESMLEPVPELKEQIQAW

3fl2A

0.21

6.67

2.10

CNFpred

PFQLFLSKVEETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRA-QVFSCPACRYDLGRSYAMQVNQPLQTVLNQ

1jm7A

0.22

0.21

6.66

1.33

DEthreader

EVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKGPSQCPLCKNDITRSLQEST-RFSQ-LVEL

(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	0.7066

(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	7bbdB	0.82	1.86	0.203	0.974	model1_7bbdB.pdb.gz
2	5olmA	0.82	1.41	0.211	0.934	model1_5olmA.pdb.gz
3	6yxeA	0.81	1.67	0.189	0.974	model1_6yxeA.pdb.gz
4	1jm7A	0.81	1.50	0.230	0.974	model1_1jm7A.pdb.gz
5	2y43A	0.81	1.46	0.211	0.934	model1_2y43A.pdb.gz
6	5ferA	0.80	1.52	0.222	0.934	model1_5ferA.pdb.gz
7	1z6uA	0.79	1.79	0.243	0.974	model1_1z6uA.pdb.gz
8	6wi7A	0.79	2.20	0.230	0.974	model1_6wi7A.pdb.gz
9	3fl2A	0.79	1.81	0.227	0.987	model1_3fl2A.pdb.gz
10	2cklA	0.79	1.84	0.236	0.947	model1_2cklA.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:0003824	0.80	catalytic activity
GO:0019787	0.78	ubiquitin-like protein transferase activity
GO:0004842	0.71	ubiquitin-protein transferase activity
GO:0043167	0.68	ion binding
GO:0046914	0.67	transition metal ion binding
GO:0008270	0.66	zinc ion binding
GO:0061659	0.53	ubiquitin-like protein ligase 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:0009987	1.00	cellular process
GO:0071704	0.88	organic substance metabolic process
GO:0044238	0.88	primary metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0016043	0.83	cellular component organization
GO:0006996	0.82	organelle organization
GO:0007031	0.81	peroxisome organization
GO:0044699	0.73	single-organism process
GO:0044763	0.70	single-organism cellular process
GO:0051179	0.66	localization
GO:1902578	0.65	single-organism localization
GO:0006810	0.65	transport
GO:0044765	0.64	single-organism transport
GO:0015031	0.64	protein transport
GO:0017038	0.62	protein import
GO:0065007	0.57	biological regulation
GO:0050794	0.56	regulation of cellular process
GO:0051649	0.55	establishment of localization in cell
GO:0051641	0.55	cellular localization
GO:0043170	0.55	macromolecule metabolic process
GO:1902580	0.54	single-organism cellular localization
GO:0055085	0.54	transmembrane transport
GO:0044260	0.54	cellular macromolecule metabolic process
GO:0006886	0.54	intracellular protein transport
GO:0065002	0.53	intracellular protein transmembrane transport
GO:0044710	0.53	single-organism metabolic process
GO:0006625	0.53	protein targeting to peroxisome
GO:1902589	0.52	single-organism organelle organization
GO:0044743	0.52	intracellular protein transmembrane import
GO:0044281	0.51	small molecule metabolic process
GO:0016558	0.51	protein import into peroxisome matrix

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:0044444	0.93	cytoplasmic part
GO:0043226	0.85	organelle
GO:0043231	0.84	intracellular membrane-bounded organelle
GO:0044446	0.83	intracellular organelle part
GO:0044439	0.71	peroxisomal part
GO:0042579	0.69	microbody
GO:0016020	0.58	membrane
GO:0005778	0.55	peroxisomal membrane
GO:0032991	0.51	macromolecular complex
GO:0044428	0.50	nuclear part

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	0.098	3eb6A	0.637	2.02	0.200	0.789	6.3.2.19	NA
2	0.060	3i3kA	0.432	4.08	0.030	0.816	1.14.13.70	NA
3	0.060	1z0zC	0.478	4.11	0.000	0.895	2.7.1.23	NA
4	0.060	3dojA	0.472	3.45	0.033	0.789	1.1.1.79	70
5	0.060	1xg7A	0.474	3.77	0.044	0.868	4.2.99.18	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	0.10	3eb50	0.624	1.82	0.183	0.789	1.05	III	complex1.pdb.gz	3,5,6,9,10,12,13,16,27,30,31,32,63,65,66,67,68,69
2	0.05	3ztgA	0.724	2.34	0.187	0.974	1.28	ZN	complex2.pdb.gz	29,30,51,53,54
3	0.04	3eb61	0.637	2.02	0.200	0.789	1.09	III	complex3.pdb.gz	7,11,16,17,18,19,20,42,52,53,55
4	0.04	1rmd0	0.729	2.35	0.176	0.961	0.83	III	complex4.pdb.gz	7,8,11,12,16,31,32,33,67,69,73

	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.