D-I-TASSER O15037-D5

D-I-TASSER results for O15037-D5

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

Input Sequence in FASTA format

>O15037 (310 residues)
HCGDRGDCGDRGDVGDRGDKQQGMARGRGPQWKRGARGGNLVTGTQRFKEALQDPFTLCL
ANVPGQPDLRHIVIDGSNVAMVHGLQHYFSSRGIAIAVQYFWDRGHRDITVFVPQWRFSK
DAKVRESHFLQKLYSLSLLSLTPSRVMDGKRISSYDDRFMVKLAEETDGIIVSNDQFRDL
AEESEKWMAIIRERLLPFTFVGNLFMVPDDPLGRNGPTLDEFLKKPARTQGSSKAQHPSR
GFAEHGKQQQGREEEKGSGGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQ
LSEALLSLNF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| HCGDRGDCGDRGDVGDRGDKQQGMARGRGPQWKRGARGGNLVTGTQRFKEALQDPFTLCLANVPGQPDLRHIVIDGSNVAMVHGLQHYFSSRGIAIAVQYFWDRGHRDITVFVPQWRFSKDAKVRESHFLQKLYSLSLLSLTPSRVMDGKRISSYDDRFMVKLAEETDGIIVSNDQFRDLAEESEKWMAIIRERLLPFTFVGNLFMVPDDPLGRNGPTLDEFLKKPARTQGSSKAQHPSRGFAEHGKQQQGREEEKGSGGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCSSSSCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCSSSSCCHHHHHCCCCCCHHHHHHHHHHCCCSSSCCCCCCCCCCCCCCCHHHHHHHHHHHCCSSSSCHHHHHHHHHCHHHHHHHHHCSCCSSSCCCSSCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCHHHHHHHHHCCCC
Confidence	9876444421235688765444556788888776667888778631011013576556656789987775188633687888578965578999999999999199628998424663178997448999999980989984786547844555416999999998098999571379999728999999996303437518854279887788899988876157788888889999899887766667777566887768868999999999973555551166776238754658899998631579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| HCGDRGDCGDRGDVGDRGDKQQGMARGRGPQWKRGARGGNLVTGTQRFKEALQDPFTLCLANVPGQPDLRHIVIDGSNVAMVHGLQHYFSSRGIAIAVQYFWDRGHRDITVFVPQWRFSKDAKVRESHFLQKLYSLSLLSLTPSRVMDGKRISSYDDRFMVKLAEETDGIIVSNDQFRDLAEESEKWMAIIRERLLPFTFVGNLFMVPDDPLGRNGPTLDEFLKKPARTQGSSKAQHPSRGFAEHGKQQQGREEEKGSGGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF
Prediction	7145475146326414575555436666445445464565414454435443644251526644556512100000000022245542020400210041027341420000002023446552544510440363400000104415454323200200030036340000002302411553640251046200100013321113634234512504511535353564553321344415334614354575445544435315503530262147443303300434123532330141135167
	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                 260                 280                 300

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

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCSSSSCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCSSSSCCHHHHHCCCCCCHHHHHHHHHHCCCSSSCCCCCCCCCCCCCCCHHHHHHHHHHHCCSSSSCHHHHHHHHHCHHHHHHHHHCSCCSSSCCCSSCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCHHHHHHHHHCCCC
HCGDRGDCGDRGDVGDRGDKQQGMARGRGPQWKRGARGGNLVTGTQRFKEALQDPFTLCLANVPGQPDLRHIVIDGSNVAMVHGLQHYFSSRGIAIAVQYFWDRGHRDITVFVPQWRFSKDAKVRESHFLQKLYSLSLLSLTPSRVMDGKRISSYDDRFMVKLAEETDGIIVSNDQFRDLAEESEKWMAIIRERLLPFTFVGNLFMVPDDPLGRNGPTLDEFLKKPARTQGSSKAQHPSRGFAEHGKQQQGREEEKGSGGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF

7dl2A

0.07

0.05

2.04

0.67

DEthreader

LVERCAQPLLLISRAQSIHPAKWIQNL-ALMEFFRVDVSFLLQLVDLAEGHHFNSLDIEVMARSLSPP-----V-LLVILQTKLYTLAHATRVYEMLVSHIQLHYKHSYRALLR-HRL----PY--S--V----------PYS------------LLFRVLLQCLKQESDKVLKLVLGRLPELL-AL--M-------------------------------------ERLSRTLHQGLILKLTHSAISLITLTETCDMRTAVPRTLVTVVRSFNKPILL-PNESFERSVQLLDIRLHIKRLRQRIC----

2n5mA

1.00

0.17

4.70

2.45

HHsearch

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGIRKTRETERLRRQLLEVFWGQDHKVDFILQREPYCRDINQLSEALLSLNF

3v32B

0.56

0.28

7.98

1.51

SPARKS-K

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPITDQHILRELEKKKILVFTPSRRCY-------DDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKP-----------------------------------------------------------------------------------

3v32B

0.58

0.28

8.15

1.21

MapAlign

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKRPDVPITDQHILRELEKKKILVFTPSRR-------CYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRK-------------------------------------------------------------------------------------

3v32B

0.57

0.28

8.07

1.08

CEthreader

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPVPITDQHILRELEKKKILVFTPSRR-------CYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKP-----------------------------------------------------------------------------------

3v32B

0.58

0.28

8.16

1.31

MUSTER

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEPDVPITDQHILRELEKKKILVFTPSRR-------CYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKP-----------------------------------------------------------------------------------

3v32B

0.57

0.28

8.07

5.99

HHsearch

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPVPITDQHILRELEKKKILVFTPSRR-------CYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKP-----------------------------------------------------------------------------------

3v32B

0.57

0.28

8.07

1.93

FFAS-3D

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVDQHILRELEKKKILVFTPSRR-------CYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKP-----------------------------------------------------------------------------------

4g23A

0.15

0.10

3.49

0.92

EigenThreader

GVKKWDVSGGGGWHGQGWLGTGKTEDENGVCKCCKEKLVCIDINPVETETFAASLTRLACEREVERHGPFDAVIDGANG---LVNQRSFSFFQLNNTVQRCQQISPSLPLVILHKSRVNGGPATYNRALLEKWKNAGALYATPPG--------SNDDWYWLYAAVSCKCLLVTNDELFQLLGN---SFFPRWKEKHQVRIEDGLKLNPPPYSIVIQED------GTSVEDDLQTSRQK------------------------------------------------------------------------

3v33A

0.56

0.29

8.35

2.01

CNFpred

-------------------------------------------------------------------DLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKP-----------------------------------------------------------------------------------

(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	0.5618

(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	3v32B	0.49	0.96	0.562	0.493	model1_3v32B.pdb.gz
2	6npsA	0.47	6.00	0.048	0.752	model1_6npsA.pdb.gz
3	2zkmX	0.47	6.01	0.036	0.755	model1_2zkmX.pdb.gz
4	3qr0A	0.47	6.29	0.042	0.777	model1_3qr0A.pdb.gz
5	6pbcA	0.47	6.40	0.068	0.781	model1_6pbcA.pdb.gz
6	3ohmB	0.46	6.28	0.072	0.777	model1_3ohmB.pdb.gz
7	4dg5A	0.30	6.42	0.066	0.516	model1_4dg5A.pdb.gz
8	1djiB3	0.30	6.46	0.064	0.523	model1_1djiB3.pdb.gz
9	3ecmA	0.29	6.50	0.048	0.484	model1_3ecmA.pdb.gz
10	2ahuA	0.29	6.86	0.067	0.526	model1_2ahuA.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	0.78	catalytic activity
GO:0016787	0.72	hydrolase activity
GO:1901363	0.71	heterocyclic compound binding
GO:0097159	0.71	organic cyclic compound binding
GO:0004518	0.70	nuclease activity
GO:0004521	0.68	endoribonuclease activity
GO:0044822	0.67	poly(A) RNA binding
GO:0003729	0.64	mRNA binding
GO:0004527	0.63	exonuclease activity
GO:0035925	0.61	mRNA 3'-UTR AU-rich region binding
GO:0035613	0.61	RNA stem-loop binding
GO:0035198	0.61	miRNA binding
GO:0004532	0.61	exoribonuclease activity
GO:0003682	0.61	chromatin binding
GO:0003677	0.61	DNA binding
GO:0070011	0.56	peptidase activity, acting on L-amino acid peptides
GO:0036459	0.52	thiol-dependent ubiquitinyl hydrolase 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:0080090	0.98	regulation of primary metabolic process
GO:0060255	0.98	regulation of macromolecule metabolic process
GO:0031323	0.98	regulation of cellular metabolic process
GO:0032269	0.96	negative regulation of cellular protein metabolic process
GO:0031329	0.85	regulation of cellular catabolic process
GO:0031399	0.82	regulation of protein modification process
GO:0009987	0.80	cellular process
GO:0031400	0.78	negative regulation of protein modification process
GO:1903320	0.74	regulation of protein modification by small protein conjugation or removal
GO:0030162	0.74	regulation of proteolysis
GO:0008152	0.68	metabolic process
GO:0044237	0.63	cellular metabolic process
GO:0050896	0.62	response to stimulus
GO:0043170	0.62	macromolecule metabolic process
GO:0044260	0.59	cellular macromolecule metabolic process
GO:0044238	0.59	primary metabolic process
GO:0051716	0.58	cellular response to stimulus
GO:0051171	0.56	regulation of nitrogen compound metabolic process
GO:0031326	0.56	regulation of cellular biosynthetic process
GO:0010556	0.56	regulation of macromolecule biosynthetic process
GO:0032435	0.55	negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0031397	0.55	negative regulation of protein ubiquitination
GO:0016070	0.55	RNA metabolic process
GO:0080134	0.54	regulation of response to stress
GO:0061158	0.54	3'-UTR-mediated mRNA destabilization
GO:0048518	0.53	positive regulation of biological process
GO:0031347	0.52	regulation of defense response

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:0043229	1.00	intracellular organelle
GO:0043232	0.97	intracellular non-membrane-bounded organelle
GO:0044446	0.89	intracellular organelle part
GO:0044444	0.77	cytoplasmic part
GO:0043227	0.76	membrane-bounded organelle
GO:0044428	0.74	nuclear part
GO:0043231	0.72	intracellular membrane-bounded organelle
GO:0005634	0.60	nucleus
GO:0005737	0.58	cytoplasm
GO:0032991	0.57	macromolecular complex
GO:0016605	0.56	PML body
GO:0005730	0.55	nucleolus
GO:0044425	0.54	membrane part
GO:0016020	0.54	membrane

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	3gm8A	0.401	6.68	0.051	0.697	3.2.1.-	NA
2	0.060	1gz3A	0.399	6.32	0.054	0.664	1.1.1.38	NA
3	0.060	1qbaA	0.447	6.04	0.063	0.716	3.2.1.52	NA
4	0.060	1xc6A	0.400	6.30	0.040	0.674	3.2.1.23	93,156
5	0.060	3ihyC	0.441	6.67	0.039	0.748	2.7.1.137	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	0.09	3csfA	0.433	6.73	0.052	0.752	0.23	DW2	complex1.pdb.gz	106,170,171,172,173,212
2	0.07	1e7uA	0.431	6.64	0.045	0.739	0.28	KWT	complex2.pdb.gz	103,105,107,109,170,171,172,173
3	0.07	3ml8A	0.432	6.67	0.052	0.745	0.20	ML8	complex3.pdb.gz	72,77,82,98,100
4	0.06	3ebiA	0.450	6.78	0.050	0.806	0.13	BEY	complex4.pdb.gz	76,90,94,97,98
5	0.06	3apcA	0.402	6.92	0.044	0.713	0.22	MMD	complex5.pdb.gz	74,76,79,206
6	0.05	3l17A	0.429	6.70	0.042	0.745	0.19	JZY	complex6.pdb.gz	169,170,171,172,209
7	0.05	2v4lA	0.434	6.64	0.049	0.745	0.21	ABJ	complex7.pdb.gz	76,90,94,95,133
8	0.01	3t8vA	0.444	6.88	0.066	0.806	0.15	BTJ	complex8.pdb.gz	93,100,101,106
9	0.01	2chzA	0.402	6.82	0.047	0.713	0.18	093	complex9.pdb.gz	77,93,94,131
10	0.01	3oawA	0.432	6.71	0.045	0.748	0.25	OAW	complex10.pdb.gz	58,72,75,94

	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.