D-I-TASSER O43660-D2

D-I-TASSER results for O43660-D2

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

Input Sequence in FASTA format

>O43660 (121 residues)
MPKPQWHPPWKLYRVISGHNAIINTLTVNSDGVLVSGADNGTMHLWDWRTGYNFQRVHAA
VQPGSLDSESGIFACAFDQSESRLLTAEADKTIKVYREDDTATEETHPVSWKPEIIKRKR
F

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPKPQWHPPWKLYRVISGHNAIINTLTVNSDGVLVSGADNGTMHLWDWRTGYNFQRVHAAVQPGSLDSESGIFACAFDQSESRLLTAEADKTIKVYREDDTATEETHPVSWKPEIIKRKRF
Prediction	CCCCCSCCCCCSSSSSCCCCCCSSSSSSCCCCSSSSSSCCCSSSSSSCCCCCSSSSSSCCCCCCCCCCCCCSSSSSSCCCCCSSSSSCCCCCSSSSSCCCCCCSSSCCCCCCCCCSSSSSC
Confidence	9988728998088986388985899999799949996389929998288893789851766666678787189999879999899981899099984889953100021588984898479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPKPQWHPPWKLYRVISGHNAIINTLTVNSDGVLVSGADNGTMHLWDWRTGYNFQRVHAAVQPGSLDSESGIFACAFDQSESRLLTAEADKTIKVYREDDTATEETHPVSWKPEIIKRKRF
Prediction	7654616263521320443533020004244110001034423344316224314405435454434154343030314634330101233133024375743544340624463041318
	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

CCCCCSCCCCCSSSSSCCCCCCSSSSSSCCCCSSSSSSCCCSSSSSSCCCCCSSSSSSCCCCCCCCCCCCCSSSSSSCCCCCSSSSSCCCCCSSSSSCCCCCCSSSCCCCCCCCCSSSSSC
MPKPQWHPPWKLYRVISGHNAIINTLTVNSDGVLVSGADNGTMHLWDWRTGYNFQRVHAAVQPGSLDSESGIFACAFDQSESRLLTAEADKTIKVYREDDTATEETHPVSWKPEIIKRKRF

4lg8A

0.17

5.41

1.33

DEthreader

DTIRIWSVPASCVQVVRAHESAVTGLSLHATGYLLSSSDDQYWAFSDIQTGRVLTKVTDETS-----G-CSLTCAQFHPDGLIFGTGTMDSQIKIWDLKERTNVANFPHTAVVSLIFDQSH

6f3tA

0.16

0.15

4.95

1.51

SPARKS-K

RVARLWATDHQPLRIFAGHLADVNCTRFHPNSYVATGSADRTVRLWDVLNGNCVRIFTG--------HKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHGHTDTVCSLRFSRDGEILASG

5o9zL

0.18

0.15

4.86

0.34

MapAlign

-KIKVWKQSGQCLRRFERHSKGVTCLSFSKDSQILSASFDQTIRIHGLKSGKTLKEFRG--------HSSFVNEATFTQDGHYIISASSDGTVKIWNMKTTECSNTFKNSV----------

5nnzB

0.16

0.15

4.95

0.26

CEthreader

KTCKLWDTNGKCVATLTGHDDEILDSCFDYTGLIATASADGTARIFSAATRKCIAKLEG--------HEGEISKISFNPQGNHLLTGSSDKTARIWDAQTGQCLQVLEGHTDEIFSCAFNY

1b9xA3

0.27

0.21

6.34

1.44

MUSTER

-----------------GHTGDVMSLSLAPDTLFVSGACDASAKLWDVREGMCRQTFTG--------HESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYS---HDNIICGIT-

3dm0A

0.21

0.20

6.29

0.63

HHsearch

KSIILWKTKGVAQRRLTGHSHFVEDVVLSSDGFALSGSWDGELRLWDLAAGVSTRRFVG--------HTKDVLSVAFSLDNRQIVSASRDRTIKLWNTLGEHRDWVSCVRFSPNTLQTIVS

6zwmC2

0.13

0.12

4.31

1.43

FFAS-3D

---YVWNTQLIPKTKIPAHTRYALQCRFSPDSLLATCSADQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVETGEIKRE--YGGHQKAVVCLAF

6zwmC2

0.12

4.12

0.48

EigenThreader

GNCYVWLTGQLIPTKIPAHTRYALQCRFSPDTLLATCSADQTCKIWRTSNFSLMTELSIKSGNPGESSRGWMWGCAFSGDSQYIVTASSDNLARLWCVETGEIKREYGAVVCLAFNDSVLG

5m23A

0.17

0.16

5.17

1.59

CNFpred

KTLKIWDVSGKCLKTLKGHSNYVFCCNFNPSNLIVSGSFDESVRIWDVKTGKCLKTLPAH--------SDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASG-NPPVSFVKFSPNGKYILAA

2oajA3

0.07

2.77

1.33

DEthreader

NSMIVYDDRDQLSFKLDLQKSPIVSIQWNPDITVLISYEY-VTLTYSLVENEIKQSFIYELPASEKRT-PKVIQSLYHPNSLHIITIHEDNSLVFWDANSGHMIMARTVIVLILMLPPAGC

(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	0.7634

(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	1b9xA	0.84	2.08	0.183	0.950	model1_1b9xA.pdb.gz
2	2pbiD	0.84	2.09	0.165	0.950	model1_2pbiD.pdb.gz
3	3iytA3	0.83	2.07	0.133	0.934	model1_3iytA3.pdb.gz
4	2h9lA	0.83	2.01	0.212	0.934	model1_2h9lA.pdb.gz
5	1vyhT	0.83	2.07	0.177	0.934	model1_1vyhT.pdb.gz
6	5o9zL	0.82	2.11	0.159	0.934	model1_5o9zL.pdb.gz
7	4j87A	0.82	2.15	0.168	0.934	model1_4j87A.pdb.gz
8	4lg8A	0.82	2.27	0.165	0.950	model1_4lg8A.pdb.gz
9	3jcrD	0.82	2.14	0.212	0.934	model1_3jcrD.pdb.gz
10	5nrlH	0.82	2.09	0.150	0.934	model1_5nrlH.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:0003723	0.44	RNA binding
GO:0044877	0.42	macromolecular complex binding
GO:0008092	0.41	cytoskeletal protein binding
GO:0030234	0.36	enzyme regulator activity
GO:0046983	0.31	protein dimerization activity
GO:0043028	0.31	cysteine-type endopeptidase regulator activity involved in apoptotic process
GO:0042802	0.31	identical protein binding
GO:0016505	0.31	peptidase activator activity involved in apoptotic process
GO:0045502	0.30	dynein binding
GO:0017069	0.30	snRNA binding
GO:0015631	0.30	tubulin 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:0009987	0.86	cellular process
GO:0044260	0.75	cellular macromolecule metabolic process
GO:0044238	0.75	primary metabolic process
GO:0006396	0.71	RNA processing
GO:0008380	0.62	RNA splicing
GO:0006397	0.61	mRNA processing
GO:0000377	0.61	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
GO:0000398	0.59	mRNA splicing, via spliceosome

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	0.88	intracellular organelle part
GO:0032991	0.87	macromolecular complex
GO:0044428	0.82	nuclear part
GO:0043234	0.80	protein complex
GO:0030529	0.75	intracellular ribonucleoprotein complex
GO:1902494	0.71	catalytic complex
GO:1990234	0.70	transferase complex
GO:0044427	0.68	chromosomal part
GO:0044454	0.66	nuclear chromosome part
GO:0031461	0.66	cullin-RING ubiquitin ligase complex
GO:0005681	0.66	spliceosomal complex
GO:0080008	0.65	Cul4-RING E3 ubiquitin ligase complex
GO:0071013	0.65	catalytic step 2 spliceosome
GO:0071011	0.65	precatalytic spliceosome
GO:0005662	0.64	DNA replication factor A complex
GO:0000974	0.64	Prp19 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	2d0vA	0.731	2.97	0.108	0.967	1.1.99.8	NA
2	0.060	1gjqA	0.770	2.65	0.084	0.984	1.7.99.1 1.7.2.1	NA
3	0.060	2d5lA	0.676	3.23	0.103	0.917	3.4.14.-	NA
4	0.060	3gvjA	0.702	3.16	0.061	0.942	3.2.1.129	28
5	0.060	3c75J	0.710	2.54	0.083	0.884	1.4.99.3	26,45

	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	0.16	3p4fA	0.825	2.07	0.204	0.934	0.54	III	complex1.pdb.gz	22,24,39,71,72,73,89
2	0.14	3smrA	0.825	2.11	0.186	0.934	0.48	NP7	complex2.pdb.gz	24,25,39,72,73,74
3	0.04	2xl2A	0.828	2.00	0.212	0.934	0.40	III	complex3.pdb.gz	16,26,28,33
4	0.04	1a0rB	0.836	2.10	0.183	0.950	0.60	FAR	complex4.pdb.gz	17,36,38,40,42,44,46
5	0.04	2bcj5	0.839	2.03	0.174	0.950	0.47	III	complex5.pdb.gz	20,22,24,39,40,41,70,71,73,89
6	0.04	1tbg2	0.840	2.04	0.174	0.950	0.42	III	complex6.pdb.gz	20,21,39,40,41,70

	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.