D-I-TASSER P09884-D4

D-I-TASSER results for P09884-D4

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

Input Sequence in FASTA format

>P09884 (145 residues)
VLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPD
PSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFS
YSRFYAKPLAALVTYKGREILMHTK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTK
Prediction	CCCCCCCCSCCCSSSSSCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
Confidence	9889988713847999612112678998557833334555422256898635642247875221264369999999999999998741799989987600999999998621114246657777898999999999999999739
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| VLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTK
Prediction	7543454226420020104211110023231334333343344333364443443453344424431222104401520451454346375354334334141302211000211221343030213400410033035105618
	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                 140

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCSCCCSSSSSCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCSSSSCCCCCCCSSCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCC
VLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTK

3cfrA2

0.26

0.23

7.25

1.17

DEthreader

FVK-P--PNRY-VMSFDLTSLYPSIIRQVNISPETI-AGT-F--KV---APLAPNGMMYYKD-RDGVVPTEITKVFNQRKEHKGYMLAANYAQRTEVAGMTAQINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQIEI

3iayA

0.34

0.33

9.92

2.64

SPARKS-K

VIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCN--KATVERLNLKIDEDYVITPNTKRRRGILPIILDELISARKRAKKDLRDE-KDPFKRDVLNGRQLALKISANSVYGFTGATVGKLPCLAISSSVTAYGRTMILKTK

5n2eA3

0.27

0.26

8.04

1.24

MapAlign

-FAPKQKMFSNNVLIFDYNSLYPNVCIFGNLSPETLVGVVTVHCEPRLPNLISEIAIFD--RSIEGTIPRLLRTFLAERARYKKMLKQA-TSSTEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYL-

3cfrA2

0.25

7.70

0.95

CEthreader

VKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVASPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRAQRTEVAGMTAQINRKALINGLAGALGNVWFRYYDLRNATAITTFGQMALQWIE

4fvmA3

0.59

0.54

15.64

1.89

MUSTER

VFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNKEDID---------ELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTET-DPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTR

4q5vA

0.98

0.90

25.12

2.52

HHsearch

VLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVEQ-------------IPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTK

4fvmA3

0.59

0.54

15.64

2.17

FFAS-3D

VFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRN---------KEDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKTET-DPHKRVQCDIRQQALKLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTR

5n2eA3

0.28

8.63

1.22

EigenThreader

VFAPKQKMFSNNVLIFDYNSLYPNVCIFGNLSPETSTNRLEELLQKYPPPRYITEPRLPNLRSIEGTIPRLLRTFLAERARYKKMLKQA-TSSTEKAIYDSMQYTYKIVANSVYGLMGFRNSALYSYASAKSCTSIGRRMILYLE

4q5vA

1.00

0.91

25.49

1.69

CNFpred

VLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRV-------------EQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTK

4m8oA

0.22

0.21

6.51

1.17

DEthreader

HVES---AGVFRIYHVDVASMYPNIMTTNRLQPDSIKAER-KL--AW---IVEREAIVC-Q-RENPFYVDTVKSFRDRRYEFKGLAKTWNLAKKMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMAR

(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	0.7723

(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	3cfrA	0.85	2.11	0.234	0.959	model1_3cfrA.pdb.gz
2	3iayA2	0.80	2.58	0.321	0.945	model1_3iayA2.pdb.gz
3	6tnyA	0.79	2.58	0.328	0.945	model1_6tnyA.pdb.gz
4	4q5vA2	0.78	2.37	1.000	0.910	model1_4q5vA2.pdb.gz
5	6wyaA	0.78	2.39	0.343	0.897	model1_6wyaA.pdb.gz
6	5n2eA	0.78	2.70	0.259	0.945	model1_5n2eA.pdb.gz
7	6wjvA	0.77	3.08	0.222	0.959	model1_6wjvA.pdb.gz
8	4m8oA	0.76	3.12	0.203	0.966	model1_4m8oA.pdb.gz
9	1s5jA2	0.74	3.26	0.309	0.945	model1_1s5jA2.pdb.gz
10	4fvmA	0.74	2.58	0.567	0.897	model1_4fvmA.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	0.99	catalytic activity
GO:0016787	0.68	hydrolase activity
GO:0004518	0.66	nuclease activity
GO:0004527	0.65	exonuclease activity
GO:0008408	0.64	3'-5' exonuclease activity
GO:0008296	0.58	3'-5'-exodeoxyribonuclease activity
GO:1901363	0.56	heterocyclic compound binding
GO:0097159	0.56	organic cyclic compound binding
GO:0016740	0.53	transferase activity
GO:0016772	0.52	transferase activity, transferring phosphorus-containing groups
GO:0016779	0.50	nucleotidyltransferase 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:0006259	0.98	DNA metabolic process
GO:0050896	0.95	response to stimulus
GO:0006281	0.94	DNA repair
GO:0016070	0.54	RNA metabolic process
GO:0006271	0.50	DNA strand elongation involved in DNA replication

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:0044446	0.99	intracellular organelle part
GO:0061695	0.97	transferase complex, transferring phosphorus-containing groups
GO:0044428	0.84	nuclear part
GO:0044427	0.79	chromosomal part
GO:0044454	0.78	nuclear chromosome part
GO:0043226	0.58	organelle
GO:0043229	0.57	intracellular organelle
GO:0043227	0.52	membrane-bounded organelle
GO:0043231	0.51	intracellular membrane-bounded organelle
GO:0005658	0.51	alpha DNA polymerase:primase complex

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	1ygeA	0.463	4.86	0.021	0.772	1.13.11.12	NA
2	0.060	3mddA	0.494	4.44	0.061	0.738	1.3.99.3	NA
3	0.060	1ukwA	0.489	4.54	0.070	0.745	1.3.99.3	NA
4	0.060	2iukA	0.442	4.64	0.100	0.717	1.13.11.12	NA
5	0.060	2fonB	0.517	4.43	0.081	0.793	1.3.3.6	82

	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	0.27	3spzA	0.851	2.11	0.227	0.959	0.24	QNA	complex1.pdb.gz	111,112,115,116,118,119,121
2	0.16	3ldsA	0.847	2.15	0.248	0.959	0.24	UUU	complex2.pdb.gz	112,114,115,119
3	0.07	2dtuC	0.738	3.12	0.266	0.938	0.12	QNA	complex3.pdb.gz	111,114,138
4	0.05	3suoA	0.849	2.12	0.248	0.959	0.27	TTP	complex4.pdb.gz	21,22,107,111
5	0.05	3cq8A	0.849	2.13	0.248	0.959	0.26	TTP	complex5.pdb.gz	35,36,67,68,117
6	0.04	3tafD	0.757	3.02	0.270	0.952	0.21	QNA	complex6.pdb.gz	71,113,115,130,136,137
7	0.04	2dtuA	0.743	3.10	0.270	0.952	0.24	UUU	complex7.pdb.gz	114,118,127,128,129
8	0.04	2oyqD	0.726	3.39	0.270	0.952	0.29	QNA	complex8.pdb.gz	118,133,134
9	0.04	1wafB	0.738	3.14	0.270	0.952	0.24	GMP	complex9.pdb.gz	114,132,133
10	0.04	2atqA	0.749	2.96	0.270	0.952	0.19	GDP	complex10.pdb.gz	114,118,126,127,128

	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.