D-I-TASSER P22888-D3

D-I-TASSER results for P22888-D3

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

Input Sequence in FASTA format

>P22888 (132 residues)
VTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLT
SLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLP
SRETFVNLLEAT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETFVNLLEAT
Prediction	CCCSCCCCHHHHHHHHHCCCCCSCCCCCCCCCCHHHHSSSCCCCCCCSSCCCCCCCCCCCSSSCCCCCCCCSCCHHHHCCCCCCCSSSCCCCCCCCCCHHHHCCCCHHHHCCCCCCCCCCCHHHCHHHHSCC
Confidence	971247874899998657897651854114777333110778997857685747799898676859999754492474288899840187893874681465014066543354547488821264642069
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| VTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETFVNLLEAT
Prediction	744044444312210252340450365105403541233305434055037410613404552165154044036500540553430334434442235414743533332314304503337505444618
	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

CCCSCCCCHHHHHHHHHCCCCCSCCCCCCCCCCHHHHSSSCCCCCCCSSCCCCCCCCCCCSSSCCCCCCCCSCCHHHHCCCCCCCSSSCCCCCCCCCCHHHHCCCCHHHHCCCCCCCCCCCHHHCHHHHSCC
VTKVFSSESNFILEICDNLHITTIPGNAFQGMNNESVTLKLYGNGFEEVQSHAFNGTTLTSLELKENVHLEKMHNGAFRGATGPKTLDISSTKLQALPSYGLESIQRLIATSSYSLKKLPSRETFVNLLEAT

4u7lA

0.22

0.21

6.70

1.50

DEthreader

QLRAFKLPRLTQLDLNRNR-IRLIEGLTFQGLNS-LEVLKLQRNNISKLTDGAFWGLSMHVLHLEYN-SLVEVNSGSLYGLTALHQLHLSNNSIARIHRWSCQKLHELVLSFNNLTRLDEELAELSSLSVLR

1xwdC2

0.48

0.45

13.00

1.94

SPARKS-K

LPDVHKIHSLQLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLE---------

4u7lA

0.24

0.23

7.30

0.45

MapAlign

-VRAFKLPRLTQLDLNRNR-IRLIEGLTFQGL-NSLEVLKLQRNNISKLTDGAFWGLKMHVLHLEYN-SLVEVNSGSLYGLTALHQLHLSNNSIARIHRGFCQKLHELVLSFN-NLTRLDSLAELSSLSVLR

5lfnA

0.19

6.09

0.28

CEthreader

ANSFRAMPNLVSLHLQHC-QIREVAAGAFRGLKQL-IYLYLSHNDIRVLRAGAFDDTELTYLYLDHNK-VTELPRGLLSPLVNLFILQLNNNKIRELRAQGAKDLRWLYLSENALSSLQPGLDDVENLAKFH

3g04C2

0.52

0.45

12.92

1.69

MUSTER

LTKVYSTDIFFILEITDNPYMTSIPVNAFQGLCNETLTLKLYNNGFTSVQGYAFNGTKLDAVYLNKNKYLTVIDKDAFGGVSGPSLLDVSQTSVTALPSKGLEHLKELIARNT-------------------

5xnpA

0.25

0.24

7.51

0.65

HHsearch

RKDFANMTSLVDLTLSRN-TISFITPHAFADLRNLR-ALHLNSNRLTKITNDMFSGSNLHHLILNNNQ-LTLISSTAFDDVFALEELDLSYNNLETIPWEKMVSLHTLSL-DHNMIDNIPK-GTFSHLHKMT

1xwdC2

0.49

0.44

12.76

1.36

FFAS-3D

-----HSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLE---------

2v9tB

0.22

6.92

0.62

EigenThreader

KPGAFSPYKKLRRIDLSNNQISELAPDAFQGL-RSLNSLVLYGNKITELPKSLFEGLFLQLLLLN-ANKINCLRVDAFQDLHNLNLLSLYDNKLQTIAKGPLRAIQTMHLAQNPDCHLKWLADYLHTNPIET

4mqwX

0.49

0.48

14.08

5.04

CNFpred

VHKIHSL-QKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNSAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLEKLVALMEAS

4bsrA

0.21

0.20

6.50

1.50

DEthreader

LLPLPSLRFLEELRLAGNA-LTYIPKGAFTGLYS-LKVLMLQNNQLRHVPTEALQNLSLQSLRLDAN-HISYVPPSCFSGLHSLRHLWLDDNALEIPVFRSLSALQAMTLALNKIHHIPDYFGNLSSLVVLH

(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	0.8836

(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	4u7lA	0.89	1.67	0.217	0.977	model1_4u7lA.pdb.gz
2	5z8xA	0.88	1.66	0.209	0.977	model1_5z8xA.pdb.gz
3	4kt1A	0.87	1.46	0.244	0.962	model1_4kt1A.pdb.gz
4	4p8sA2	0.87	1.66	0.209	0.977	model1_4p8sA2.pdb.gz
5	4bsrA	0.87	1.66	0.225	0.977	model1_4bsrA.pdb.gz
6	4lxrA	0.87	1.57	0.188	0.970	model1_4lxrA.pdb.gz
7	1p8tA	0.87	1.75	0.208	0.985	model1_1p8tA.pdb.gz
8	5xnpA	0.87	1.71	0.211	0.970	model1_5xnpA.pdb.gz
9	5lfnA	0.87	1.84	0.233	0.977	model1_5lfnA.pdb.gz
10	3zyiA1	0.87	1.88	0.217	0.977	model1_3zyiA1.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:0038023	0.81	signaling receptor activity
GO:0004888	0.80	transmembrane signaling receptor activity
GO:0004930	0.79	G-protein coupled receptor activity
GO:0016500	0.66	protein-hormone receptor activity
GO:0008528	0.61	G-protein coupled peptide receptor 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:0065007	0.94	biological regulation
GO:0050794	0.93	regulation of cellular process
GO:0080090	0.85	regulation of primary metabolic process
GO:0031323	0.85	regulation of cellular metabolic process
GO:0019220	0.83	regulation of phosphate metabolic process
GO:0007165	0.83	signal transduction
GO:0050790	0.77	regulation of catalytic activity
GO:0048518	0.68	positive regulation of biological process
GO:0048522	0.67	positive regulation of cellular process
GO:0044699	0.66	single-organism process
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0045937	0.62	positive regulation of phosphate metabolic process
GO:0007186	0.61	G-protein coupled receptor signaling pathway
GO:0031326	0.59	regulation of cellular biosynthetic process
GO:0045935	0.58	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.58	positive regulation of cellular biosynthetic process
GO:0043085	0.57	positive regulation of catalytic activity
GO:0007187	0.57	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0007190	0.56	activation of adenylate cyclase activity
GO:0007188	0.55	adenylate cyclase-modulating G-protein coupled receptor signaling pathway
GO:0032502	0.54	developmental process
GO:0009755	0.54	hormone-mediated signaling pathway
GO:0007189	0.54	adenylate cyclase-activating G-protein coupled receptor signaling pathway

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	0.97	cell part
GO:0044425	0.70	membrane part
GO:0044459	0.68	plasma membrane part
GO:0016021	0.68	integral component of membrane
GO:0005887	0.66	integral component of plasma membrane
GO:0044424	0.58	intracellular 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	0.060	1vblA	0.615	4.14	0.070	0.962	4.2.2.2	NA
2	0.060	2uveA	0.631	4.03	0.093	0.977	3.2.1.82	NA
3	0.060	1k5cA	0.610	4.04	0.072	0.947	3.2.1.15	NA
4	0.060	2z8gB	0.608	3.96	0.016	0.955	3.2.1.57	79,103
5	0.060	2ahxB	0.620	3.46	0.100	0.894	2.7.10.1	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	0.17	2xwtC	0.829	2.15	0.194	0.977	1.63	UUU	complex1.pdb.gz	26,27,30,52,55
2	0.08	3a79B	0.808	2.20	0.159	0.955	1.30	UUU	complex2.pdb.gz	42,43,63,65,88,90
3	0.04	2z7xA	0.812	2.13	0.188	0.970	0.60	PCJ	complex3.pdb.gz	5,39,43,50,51,57,67,68,70,71,72,73,74,96

	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.