D-I-TASSER O15229-D1

D-I-TASSER results for O15229-D1

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

Input Sequence in FASTA format

>O15229 (250 residues)
MDSSVIQRKKVAVIGGGLVGSLQACFLAKRNFQIDVYEAREDTRVATFTRGRSINLALSH
RGRQALKAVGLEDQIVSQGIPILSVSRENLNKDLLTAAEKYPNVKMHFNHRLLKCNPEEG
MITVLGSDKVPKDVTCDLIVGCDGAYSTVRSHLMKKPRFDYMISVKCSSFHFKSHCVLLG
DAAHAIVPFFGQGMNAGFEDCLVFDELMDKFSNDLSLCLPVFSRLRIPDDHAISDLSMYN
YIEMRAHVNS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MDSSVIQRKKVAVIGGGLVGSLQACFLAKRNFQIDVYEAREDTRVATFTRGRSINLALSHRGRQALKAVGLEDQIVSQGIPILSVSRENLNKDLLTAAEKYPNVKMHFNHRLLKCNPEEGMITVLGSDKVPKDVTCDLIVGCDGAYSTVRSHLMKKPRFDYMISVKCSSFHFKSHCVLLGDAAHAIVPFFGQGMNAGFEDCLVFDELMDKFSNDLSLCLPVFSRLRIPDDHAISDLSMYNYIEMRAHVNS
Prediction	CCCCCCCCCCSSSSCCCHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCCSSSSSSCHHHHHHHHHCCHHHHHHHHCCCCSSCCHHHHHHHHHHHHHHCCCCSSSSSSSSCCCCCCCCSSSSSSCCCCSSSSSSCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence	9999899886899858899999999999809959999515776657666673478765575899999819189998738742101179999999999996799489996530345667745899965996168852100011231123222102333333222123455322223222688654579976542001142199999999973899999999999985079999999999988987424899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MDSSVIQRKKVAVIGGGLVGSLQACFLAKRNFQIDVYEAREDTRVATFTRGRSINLALSHRGRQALKAVGLEDQIVSQGIPILSVSRENLNKDLLTAAEKYPNVKMHFNHRLLKCNPEEGMITVLGSDKVPKDVTCDLIVGCDGAYSTVRSHLMKKPRFDYMISVKCSSFHFKSHCVLLGDAAHAIVPFFGQGMNAGFEDCLVFDELMDKFSNDLSLCLPVFSRLRIPDDHAISDLSMYNYIEMRAHVNS
Prediction	5756646533000000110000002102536040201032442344524331000000031013003303024302420111112213401420142047233020201232343325422022223444323033322220342232033223333222222222223222323222222010031221100000002013001300552663145005312721362042003003500320244168
	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                  80                 100                 120                 140                 160                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCSSSSCCCHHHHHHHHHHHHCCCSSSSSSCCCCCCCCCCCCCCSSSSSSCHHHHHHHHHCCHHHHHHHHCCCCSSCCHHHHHHHHHHHHHHCCCCSSSSSSSSCCCCCCCCSSSSSSCCCCSSSSSSCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
MDSSVIQRKKVAVIGGGLVGSLQACFLAKRNFQIDVYEAREDTRVATFTRGRSINLALSHRGRQALKAVGLEDQIVSQGIPILSVSRENLNKDLLTAAEKYPNVKMHFNHRLLKCNPEEGMITVLGSDKVPKDVTCDLIVGCDGAYSTVRSHLMKKPRFDYMISVKCSSFHFKSHCVLLGDAAHAIVPFFGQGMNAGFEDCLVFDELMDKFSNDLSLCLPVFSRLRIPDDHAISDLSMYNYIEMRAHVNS

6u0pA

0.18

5.71

1.50

DEthreader

---APDIRVPVLIVGGGPAGLTAALALSRYGVPHLLVNRHHGTA-H--T---PRAHLLNQRTGEIFRDLGIADRVEAHATPGCNLPQHLLEPLLVEAVQEACVGQLRFGHEFVSLEQDGVTSRITDRTGRDYTVRSDYLIGADGARSRVLAQLGIALDGTGINSAVAPRYASG-RVFCVGDAVHQNPPTNGLGLNSAVADSFNLCWKLKLALGAGPGLLDTYHDERQPVGRQIVDRAFRSMVDLIGIPQA

5fn0A1

0.36

0.34

10.25

1.96

SPARKS-K

------NARQVTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAGLEREVLADSEVIWSINRDRLNRILLDGAEAAG-ASIHFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDLGLEATLRLTTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSA-ADNASALAAFTAQRQPDALAIQAMALENYVEMSSKV--

6u0pA

0.18

0.17

5.47

0.63

MapAlign

----PDIRVPVLIVGGGPAGLTAALALSRYGVPHLLVNRHHGTAHT------PRAHLLNQRTGEIFRDLGIADRVEAHATGLCNLPQHLLEPLLVEAVQEACVGQLRFGHEFVSLEQHGVTSRITDRRGRDYTVRSDYLIGADGARSRVLAQLIALDSAWEVNSAVAPRYAS-GRVFCVGDAVHQNPPTNGLGLNSAVADSFNLCWKLKLAGLAGPGLLDTYHDERQPVGRQIVDRAFRSMVDL------

5fn0A

0.36

0.35

10.36

0.52

CEthreader

------NARQVTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAGLEREVLAEAVMIWSINRDRLNRILLDGAEAA-GASIHFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDTGKLATLRLTTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSAA-DNASALAAFTAQRQPDALAIQAMALENYVEMSSKVAS

5fn0A1

0.36

0.34

10.25

1.58

MUSTER

------NARQVTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAGLEREVLAEAEVIWSINRDRLNRILLDGAEAA-GASIHFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDLGLEATLRLTTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSA-ADNASALAAFTAQRQPDALAIQAMALENYVEMSSKV--

5fn0A

0.36

0.34

10.26

1.08

HHsearch

------NARQVTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAGLEREVLAEAVMIWSINRDRLNRILLDGAEAA-GASIHFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDLGALATLRLTTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSAADN-ASALAAFTAQRQPDALAIQAMALENYVEMSSKVAS

5fn0A1

0.36

0.34

10.25

2.30

FFAS-3D

------NARQVTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAGLEREVLAEAVVIWSINRDRLNRILLDGAEAAG-ASIHFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDLGEHLELRLTTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQS-AADNASALAAFTAQRQPDALAIQAMALENYVEMSSKV--

3c96A

0.21

0.20

6.34

0.70

EigenThreader

-------PIDILIAGAGIGGLSCALALHQAIGKVTLLESSSEIRPLGV-----GINIQ-PAAVEALAELGLGPALAATAYPQYSIHRGELQMILLAAVRERQAVRTG--LGVERIEEGRVLIGARDGHGKPQALGADVLVGADGIHSAVRAHLHPDQRPLQYPMVDRLPHWGRGRITLLGDAAHLMYPMGANGASQAILDGIELAAALARN-ADVAAALREYEEARRPTANKIILANREREKEEWAAASR

6lkeA

0.82

0.77

21.78

1.68

CNFpred

------EGKRVVVIGGGLVGALNACFLAKRNFQVDVYEAREDIRVA-----RSINLALSYRGRQALKAVGLEDQIVSKGQYILSISREKLNKDLLTAVESYPNAKVHFGHKLSKC-----ILTMLGPNKVPRDITCDLIVGCDGAYSTVRAHLMKKPPAQPMISVKCSPFHLKSRCVLMGDAAHAIVPFFGQGMNAGFEDCLVFDELMDKFNNDLSVCLPEFSRFRIPDDHAISDLSMYNYIEMRAHVNS

6pvfA1

0.21

0.20

6.34

1.50

DEthreader

------EEVQVIIVGLGIVGLAAAIECREKGHSVHAFEKS-NILKS--I--GD-CIGLQSNATRIIKRWGVHEALR-PWIVNYLLPRSELIRVMYEHALKIG-VEISLGVEVCEPSEDGASVVALTRDGERQIVRGDFIICSDGVHSKMRKAIMPQPVEPRLNHKPLDHWVSSHRLILIGDAAHPLSPAAGQGASQGIEDANVLATSLSLAGQRVSLALHVAERIRYARASAVQLISHRVNEGWRNQDWD

(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	0.9154

(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	5fn0A	0.91	1.90	0.360	0.964	model1_5fn0A.pdb.gz
2	6u0pA	0.90	1.82	0.174	0.960	model1_6u0pA.pdb.gz
3	4cy6A1	0.88	1.89	0.169	0.948	model1_4cy6A1.pdb.gz
4	4j2wA	0.88	2.04	0.382	0.960	model1_4j2wA.pdb.gz
5	6pvfA	0.87	1.99	0.202	0.944	model1_6pvfA.pdb.gz
6	1pn0C	0.87	2.20	0.206	0.968	model1_1pn0C.pdb.gz
7	6lkdA	0.87	1.87	0.803	0.924	model1_6lkdA.pdb.gz
8	3c96A	0.86	2.12	0.213	0.940	model1_3c96A.pdb.gz
9	2r0gA1	0.86	2.04	0.221	0.940	model1_2r0gA1.pdb.gz
10	4bjyA	0.86	1.95	0.176	0.920	model1_4bjyA.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	1.00	catalytic activity
GO:0016491	0.99	oxidoreductase activity
GO:0004497	0.94	monooxygenase activity
GO:0050660	0.90	flavin adenine dinucleotide binding
GO:0071949	0.80	FAD binding
GO:0016709	0.76	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
GO:0004502	0.75	kynurenine 3-monooxygenase activity
GO:0016651	0.66	oxidoreductase activity, acting on NAD(P)H
GO:0016174	0.64	NAD(P)H oxidase 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:0008152	1.00	metabolic process
GO:0044710	0.99	single-organism metabolic process
GO:0044711	0.93	single-organism biosynthetic process
GO:0044550	0.90	secondary metabolite biosynthetic process
GO:0009987	0.83	cellular process
GO:0071704	0.82	organic substance metabolic process
GO:0055114	0.82	oxidation-reduction process
GO:0044237	0.82	cellular metabolic process
GO:0044763	0.81	single-organism cellular process
GO:0044281	0.81	small molecule metabolic process
GO:0044238	0.79	primary metabolic process
GO:1901564	0.78	organonitrogen compound metabolic process
GO:1901605	0.77	alpha-amino acid metabolic process
GO:1901360	0.77	organic cyclic compound metabolic process
GO:0006733	0.77	oxidoreduction coenzyme metabolic process
GO:0019674	0.76	NAD metabolic process
GO:0042180	0.68	cellular ketone metabolic process
GO:0070189	0.64	kynurenine metabolic process
GO:1901576	0.57	organic substance biosynthetic process
GO:0044249	0.57	cellular biosynthetic process
GO:0044283	0.55	small molecule biosynthetic process
GO:1901566	0.54	organonitrogen compound biosynthetic process
GO:1901565	0.54	organonitrogen compound catabolic process
GO:0044282	0.54	small molecule catabolic process
GO:0044248	0.54	cellular catabolic process
GO:0006568	0.54	tryptophan metabolic process
GO:1901362	0.53	organic cyclic compound biosynthetic process
GO:0043650	0.53	dicarboxylic acid biosynthetic process
GO:0019438	0.53	aromatic compound biosynthetic process
GO:0018130	0.53	heterocycle biosynthetic process
GO:0009108	0.53	coenzyme biosynthetic process
GO:0006569	0.53	tryptophan catabolic process
GO:0034354	0.52	'de novo' NAD biosynthetic process from tryptophan
GO:0032787	0.52	monocarboxylic acid metabolic process
GO:0043420	0.51	anthranilate metabolic process
GO:0019805	0.51	quinolinate biosynthetic 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:0044464	1.00	cell part
GO:0016020	1.00	membrane
GO:0044424	0.94	intracellular part
GO:0044444	0.77	cytoplasmic part
GO:0044446	0.71	intracellular organelle part
GO:0031090	0.70	organelle membrane
GO:0005741	0.69	mitochondrial outer membrane
GO:0043227	0.52	membrane-bounded organelle

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	0.243	1dodA	0.853	2.36	0.186	0.944	1.14.13.2	14,142,144,181,186
2	0.060	1kfyA	0.704	3.31	0.062	0.852	1.3.99.1	NA
3	0.060	1qo8D	0.691	3.18	0.111	0.828	1.3.99.1	NA
4	0.060	1pn0C	0.874	2.20	0.206	0.968	1.14.13.7	181,188,194
5	0.060	1zovA	0.668	3.22	0.132	0.800	1.5.3.1	30

	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.76	3fmwC	0.859	2.05	0.235	0.936	1.01	FAD	complex1.pdb.gz	14,15,17,18,19,37,38,39,40,54,55,56,57,87,112,143,144,148,180,181,188,191,193,194,195

	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.