D-I-TASSER P13473-D2

D-I-TASSER results for P13473-D2

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

Input Sequence in FASTA format

>P13473 (190 residues)
GTYSVNNGNDTCLLATMGLQLNITQDKVASVININPNTTHSTGSCRSHTALLRLNSSTIK
YLDFVFAVKNENRFYLKEVNISMYLVNGSVFSIANNNLSYWDAPLGSSYMCNKEQTVSVS
GAFQINTFDLRVQPFNVTQGKYSTAQDCSADDDNFLVPIAVGAALAGVLILVLLAYFIGL
KHHHAGYEQF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| GTYSVNNGNDTCLLATMGLQLNITQDKVASVININPNTTHSTGSCRSHTALLRLNSSTIKYLDFVFAVKNENRFYLKEVNISMYLVNGSVFSIANNNLSYWDAPLGSSYMCNKEQTVSVSGAFQINTFDLRVQPFNVTQGKYSTAQDCSADDDNFLVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF
Prediction	CSSSSCCCCCSSSSSSSSSSSSSSSSCSCSSSSSCCCCCSSSSSCCCCSSSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSSSSCCCCCCCCCCCCCCCSSSCCCCCSSSSCCCCSSSSCCCSSSSSSSSSSSSSSCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCCCC
Confidence	9379927994377798258999994013116871899861201406977899999589777999999927956999999999991787521345776425882589618957972797459689999788999775589922561376897666515899999999999999997631020363245339
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| GTYSVNNGNDTCLLATMGLQLNITQDKVASVININPNTTHSTGSCRSHTALLRLNSSTIKYLDFVFAVKNENRFYLKEVNISMYLVNGSVFSIANNNLSYWDAPLGSSYMCNKEQTVSVSGAFQINTFDLRVQPFNVTQGKYSTAQDCSADDDNFLVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF
Prediction	8604046643200102020303041644443230416445352515553030203166333020202244743131431303131445523544444143040325310304453404235403030340301013166651142430442544302111212332233333210100123356541565
	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                 160                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CSSSSCCCCCSSSSSSSSSSSSSSSSCSCSSSSSCCCCCSSSSSCCCCSSSSSSSSCCCCSSSSSSSSCCCCSSSSSSSSSSSSCCCCCCCCCCCCCCCSSSCCCCCSSSSCCCCSSSSCCCSSSSSSSSSSSSSSCCCCCCCCCSSCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHSSSCCCCCCCCC
GTYSVNNGNDTCLLATMGLQLNITQDKVASVININPNTTHSTGSCRSHTALLRLNSSTIKYLDFVFAVKNENRFYLKEVNISMYLVNGSVFSIANNNLSYWDAPLGSSYMCNKEQTVSVSGAFQINTFDLRVQPFNVTQGKYSTAQDCSADDDNFLVPIAVGAALAGVLILVLLAYFIGLKHHHAGYEQF

5gv0A

0.36

0.28

8.46

1.17

DEthreader

SKYNVTGNNGTCLLASMALQLNITYLTVTRAFNISPND-TSSGSCGINLVTLKVENK-NRALELQFGMNASSLFFLQGVRLNMTLPDVPTFSISNHSLKALQATVGNSYKCNTEEHIFVSKMLSLNVFSVQVQAFKVDSDRFGSVEECVQDG--------------------------------------

4akmA

0.27

0.21

6.46

2.38

SPARKS-K

GIYQVLNGSRLCIKAEMGIQLIVQDKESRRYFNIDPNATQASGNCGTRKSNLLLNFQ-GGFVNLTFTKDEES-YYISEVGAYLTVSDPTVYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDECS-----------------------------------------

5gv0A

0.35

0.28

8.32

1.37

MapAlign

SKYNVTGNNGTCLLASMALQLNITYKTVTRAFNISP-NDTSSGSCGINLVTLKVEN-KNRALELQFGMNSSSLFFLQGVRLNMTLALVPTFSISNHSLKALQATVGNSYKCNTEEHIFVSKMLSLNVFSVQVQAFKVDSDRFGSVEECVQDG--------------------------------------

4akmA

0.27

0.21

6.46

1.56

CEthreader

GIYQVLNGSRLCIKAEMGIQLIVQDKEPRRYFNIDPNATQASGNCGTRKSNLLLNFQ-GGFVNLTFTKD-EESYYISEVGAYLTVSDETVYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDECS-----------------------------------------

4akmA

0.27

0.21

6.46

1.98

MUSTER

GIYQVLNGSRLCIKAEMGIQLIVQDKSPRRYFNIDPNATQASGNCGTRKSNLLLNF-QGGFVNLTFTK-DEESYYISEVGAYLTVSDPTVYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDECS-----------------------------------------

6xbws

0.19

0.18

5.76

4.43

HHsearch

VPVSYNDSYDTRILFWAQN-FSVAYGEHSRTFGVQ-DLNLTGSFWNDTVARLVLTYDSLVTFKFILANSSARHWTLENLEIHSNGSV-AYFN-----ASQVTGPSIYSFHCEHVSSENEPSLWQMTFRDFQIQAFNVTDKKFSYASDCAGF---FSPGIWMGLLTSL-FMLFIFTYGLHMILSLDRFD--

5gv0A

0.35

0.27

8.18

1.98

FFAS-3D

SKYNVTGNNGTCLLASMALQLNITYKTVTRAFNISPND-TSSGSCGINLVTLKVENKNRALELQFGMNASSSLFFLQGVRLNMTLPDVPTFSISNHSLKALQATVGNSYKCNTEEHIFVSKMLSLNVFSVQVQAFKVDSDRFGSVEECVQD---------------------------------------

6xbws

0.18

0.17

5.63

1.33

EigenThreader

NVPVSYNSYDTRILFWANFSVAYG----EHWEDLTSRTFLTGSFWNDTVARLVLTYDTMVTFKFILANSVSARHWFTLENLEIHSNGSVAYFNA----SQVTGPSIYSFHCEHVSSLVPDSLWQMTFRDFQIQAFNVTDKKFSYASDC---AGFFSPGIWMGLLTSLFMLFIFTYGLHMILSLKTMDRFD

5gv0A

0.36

0.28

8.46

2.31

CNFpred

SKYNVTGNNGTCLLASMALQLNITYLTVTRAFNISPN-DTSSGSCGINLVTLKVENK-NRALELQFGMNASSLFFLQGVRLNMTLPDAPTFSISNHSLKALQATVGNSYKCNTEEHIFVSKMLSLNVFSVQVQAFKVDSDRFGSVEECVQDG--------------------------------------

4akmA

0.27

0.21

6.32

1.17

DEthreader

GIYQVLNGSRLCIKAEMGIQLIVQDKEPRRYFNIDPNATQASGNCGTRKSNLLLNFQ-GGFVNLTFTKD-EESYYISEVGAYLTVSPETVYQGIKHAVVMFQTAVGHSFKCVSEQSLQLSAHLQVKTTDVQLQAFDFEDDHFGNVDEC-S----------------------------------------

(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	0.7238

(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	6xbws	0.77	2.40	0.206	0.900	model1_6xbws.pdb.gz
2	5gv0A	0.75	1.28	0.353	0.789	model1_5gv0A.pdb.gz
3	4akmA	0.73	1.33	0.265	0.774	model1_4akmA.pdb.gz
4	5gv3A	0.68	2.00	0.166	0.763	model1_5gv3A.pdb.gz
5	3holA	0.50	5.31	0.050	0.821	model1_3holA.pdb.gz
6	3pquA	0.49	5.21	0.046	0.795	model1_3pquA.pdb.gz
7	3pqsA	0.49	5.26	0.051	0.795	model1_3pqsA.pdb.gz
8	4qq1A2	0.45	3.84	0.088	0.626	model1_4qq1A2.pdb.gz
9	3v8uA2	0.44	4.14	0.039	0.642	model1_3v8uA2.pdb.gz
10	2lfuA	0.37	4.36	0.041	0.542	model1_2lfuA.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:0019899	0.77	enzyme 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:0065007	0.91	biological regulation
GO:0065008	0.81	regulation of biological quality
GO:0050821	0.80	protein stabilization
GO:0009987	0.71	cellular process
GO:0044699	0.63	single-organism process
GO:0006810	0.58	transport
GO:0045184	0.54	establishment of protein localization
GO:0044763	0.50	single-organism cellular 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:0016020	0.95	membrane
GO:0044464	0.94	cell part
GO:0044424	0.91	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0044446	0.82	intracellular organelle part
GO:0098805	0.78	whole membrane
GO:0098588	0.78	bounding membrane of organelle
GO:0043229	0.76	intracellular organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0005774	0.75	vacuolar membrane
GO:0005765	0.74	lysosomal membrane
GO:0005773	0.71	vacuole
GO:0005764	0.61	lysosome
GO:0010008	0.59	endosome membrane
GO:0005768	0.59	endosome
GO:0005886	0.56	plasma membrane
GO:0031982	0.54	vesicle
GO:0044425	0.53	membrane 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	1gweA	0.421	4.84	0.038	0.674	1.11.1.6	NA
2	0.060	1qwlA	0.416	5.12	0.032	0.684	1.11.1.6	NA
3	0.060	1oacB	0.408	3.92	0.058	0.568	1.4.3.21 1.4.3.6	102
4	0.060	3ej6A	0.428	5.47	0.040	0.747	1.11.1.6	NA
5	0.060	2wgqB	0.411	4.01	0.058	0.574	1.4.3.21	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	0.04	1ggjD	0.443	5.18	0.061	0.753	0.10	HDD	complex1.pdb.gz	43,44,50,51,63
2	0.01	1sy7A	0.463	4.99	0.027	0.758	0.14	HEM	complex2.pdb.gz	43,50,51,52,101,108
3	0.01	1ye9F	0.251	6.28	0.023	0.505	0.28	HDD	complex3.pdb.gz	105,143,145
4	0.01	3ibrA	0.400	6.00	0.065	0.742	0.11	BLA	complex4.pdb.gz	45,65,67
5	0.01	1cf9A	0.450	5.27	0.059	0.758	0.12	HEM	complex5.pdb.gz	43,49,50,51,107
6	0.01	3fidA	0.431	4.74	0.065	0.679	0.16	CXE	complex6.pdb.gz	50,52,132
7	0.01	3p9qB	0.440	5.35	0.049	0.763	0.15	UUU	complex7.pdb.gz	6,43,50,51,52
8	0.01	3fidB	0.430	4.84	0.052	0.684	0.23	CXE	complex8.pdb.gz	43,45,50,51,52,66
9	0.01	3nbxX	0.420	5.15	0.042	0.674	0.18	ADP	complex9.pdb.gz	3,5,54
10	0.01	3c2wD	0.400	5.58	0.068	0.711	0.13	BLA	complex10.pdb.gz	43,64,66

	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.