D-I-TASSER O75083-D1

D-I-TASSER results for O75083-D1

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

Input Sequence in FASTA format

>O75083 (224 residues)
MPYEIKKVFASLPQVERGVSKIIGGDPKGNNFLYTNGKCVILRNIDNPALADIYTEHAHQ
VVVAKYAPSGFYIASGDVSGKLRIWDTTQKEHLLKYEYQPFAGKIKDIAWTEDSKRIAVV
GEGREKFGAVFLWDSGSSVGEITGHNKGHHAKIVCLAWSPDNEHFASGGMDMMVYVWTLS
DPETRVKIQDAHRLHHVSSLAWLDEHTLVTTSHDASVKEWTITY

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPYEIKKVFASLPQVERGVSKIIGGDPKGNNFLYTNGKCVILRNIDNPALADIYTEHAHQVVVAKYAPSGFYIASGDVSGKLRIWDTTQKEHLLKYEYQPFAGKIKDIAWTEDSKRIAVVGEGREKFGAVFLWDSGSSVGEITGHNKGHHAKIVCLAWSPDNEHFASGGMDMMVYVWTLSDPETRVKIQDAHRLHHVSSLAWLDEHTLVTTSHDASVKEWTITY
Prediction	CCCCHHHHHHCCCCCCCCCSSSSSSCCCCCSSSSSCCCSSSSSSCCCCCSSSSSCCCCCCSSSSSSCCCCCSSSSSSCCCSSSSSSCCCCCSSSSSSSCCCCCCSSSSSSCCCCCSSSSSSCCCCCCCSSSSSSCCCCCCSSSSSCCCCCCCSSSSSSCCCCCSSSSSSCCCSSSSSSCCCCCSSSSSCCCCCCCSSSSSSSCCCCSSSSSCCCCSSSSSSCCC
Confidence	99310133302677545756999994999989994899799997999936686758999889999989999899980899199987899926645750266798889999899998999968989998899997899985266451688898899999899998999928990999888999486781588879959999918999799981899299981679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MPYEIKKVFASLPQVERGVSKIIGGDPKGNNFLYTNGKCVILRNIDNPALADIYTEHAHQVVVAKYAPSGFYIASGDVSGKLRIWDTTQKEHLLKYEYQPFAGKIKDIAWTEDSKRIAVVGEGREKFGAVFLWDSGSSVGEITGHNKGHHAKIVCLAWSPDNEHFASGGMDMMVYVWTLSDPETRVKIQDAHRLHHVSSLAWLDEHTLVTTSHDASVKEWTITY
Prediction	65352551143144325130300040362320000233000001073462343040254412021102434240102343101322173444025240401544320000026342400012145441002022273441533330610543440404034332101023441432120634633240251145300000001444340001363034046246
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCHHHHHHCCCCCCCCCSSSSSSCCCCCSSSSSCCCSSSSSSCCCCCSSSSSCCCCCCSSSSSSCCCCCSSSSSSCCCSSSSSSCCCCCSSSSSSSCCCCCCSSSSSSCCCCCSSSSSSCCCCCCCSSSSSSCCCCCCSSSSSCCCCCCCSSSSSSCCCCCSSSSSSCCCSSSSSSCCCCCSSSSSCCCCCCCSSSSSSSCCCCSSSSSCCCCSSSSSSCCC
MPYEIKKVFASLPQVERGVSKIIGGDPKGNNFLYTNGKCVILRNIDNPALADIYTEHAHQVVVAKYAPSGFYIASGDVSGKLRIWDTTQKEHLLKYEYQPFAGKIKDIAWTEDSKRIAVVGEGREKFGAVFLWDSGSSVGEITGHNKGHHAKIVCLAWSPDNEHFASGGMDMMVYVWTLSDPETRVKIQDAHRLHHVSSLAWLDEHTLVTTSHDASVKEWTITY

5nrlH

0.19

0.18

5.90

1.33

DEthreader

RTELMALELSIVTGSGGKIGAIDWHPDSNNQMISCAEDLIKNFQYSELRLLGDLVGHERRISDVKYHPSGKFIGSASHDMTWRLWDASTHQE-LLLQE-GHDKGVFSLSFQCDGSLVCSGGMD----SLSMLWDIRS--GSKVMTLAGHSKPIYTVAWSPNGYQVATGGGDGIINVWDIRKRGQLNQILA-H-RNIVTQVRFSKGKKLVSCGYDNLINVYSSDT

6f3tA

0.23

0.22

6.86

1.68

SPARKS-K

MDEKTASELKILYGHSGPV-YGASFSPDRNYLLSSSDGTVRLWSLQTFTCLVGYKGHNYPVWDTQFSPYGYYFVSGGHDRVARLWATDHYQPLR--IFAGHLADVNCTRFHPNSNYVATGSAD----RTVRLWDVLN--GNCVRIFTGHKGPIHSLTFSPNGRFLATGATDGRVLLWDIGHG-LMVGELKGHT-DTVCSLRFRDGEILASGSMDNTVRLWDAIK

5mzhA

0.14

0.12

4.26

0.37

MapAlign

--------------GHQTEIVCLSFNPQSTIIATGSMNTAKLWDVETGQERATLAGHRAEIVSLGFNTGGDLIVTGSFDHDSRLWDVRTGQCVHVLSG--HRGEVSSTQFNYAGTLVVSGSID----CTSRLWDVR--SGRCLSVKQGHTDEVLDVAFDAAGTKMVSASADGSARLYHTLTGVCQHTL-VGH-EGEISKVAFNQGTRLITASSDKTCRLWDCD-

5mzhA

0.15

0.14

4.81

0.23

CEthreader

WDVETGQERATLAGHRAEIVSLGFNTGGDLIVTGSFDHDSRLWDVRTGQCVHVLSGHRGEVSSTQFNYAGTLVVSGSIDCTSRLWDVRSGRCLSVKQ--GHTDEVLDVAFDAAGTKMVSASAD----GSARLYHTLT--GVCQHTLVGHEGEISKVAFNPQGTRLITASSDKTCRLWDCDTGECLQVLEGHT--DEIFSCAFNYGDFIITGSKDNTCRIWKALT

2ce8A1

0.14

0.13

4.41

1.44

MUSTER

------DYFQGA--MGSKPAYSFHVTADGQMQPVFPPDALIGPGIPRHARQINTLNHGEVVCAVTISNPTRHVYTGG-KGCVKVWDISHPGNSPVSQLDCLN-RDNSLGYCPTGEWLAVGMES----SNVEVLHVNKPD---KYQLHLHESCVLSLKFAYCGKWFVSTGKDNLLNAWRTPYGASIFQS--KESSSVLSCDISVDDKYIVTGSGDKKATVYEVIY

6t9iD

0.18

0.17

5.54

0.67

HHsearch

LDKDEDPTCKTLVGHSGTV-YSTSFSPDNKYLLSSEDKTVRLWSMDTHTALVSYKGHNHPVWDVSFSPLGHYFATASHDQTARLWSCDHIYPLRI--FAGHLNDVDCVSFHPNGCYVFTGSSD----KTCRMWDVSTG--DSVRLFLGHTAPVISIAVCPDGRWLSTGSEDGIINVWDIGTGKRLKQM-RGHGKNAIYSLSYSEGNVLISGGADHTVRVWDLKK

7k36B

0.14

0.13

4.57

1.99

FFAS-3D

-TWNPKYTL----RSHFDGVRALAFHPVEPVLVTASDHTLKLWNLDVEP-IYTFRAHIGPVLSLAISSNGEQCFSGGIDATIQWWNMPSPSVDLAGTLVGHTDAVWGLAYSGIKNQLLSCSADGTVRLWNHIKFFDNKTGKMIHSMVAHLDAVTSLAVDPNGIYLMSGSHDCSIRLWNLDSKTCVQEI-TAHRESIYDVAFHSSKAYIASAGADALAKVF----

7apxE

0.10

3.61

0.50

EigenThreader

SKGNTSH---IEDITPNEILSLKFHVSGSSMAYSRMDGSLTVWFIKDASFDVEVYIPDCCATDLSWNPTSNQIAVVSNSSEISLLLIKSLTAKLRTLSLGSKTKVNTCLYDPLGNWLLAATKSE----KIYLFDVKKDHSSVCSLNQEDNDVVYSLAWSNGGSHIFIGFKSGYLAILKAKHG-ILETKIKAH-TGPITEIKMDPGRNFITGSIDGNCYVWNMKS

5m23A

0.14

0.12

4.30

2.67

CNFpred

-------LKFTLAGHT-KAVSSVKFSPNGEWLASSSAKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKG--HSNYVFCCNFNPQSNLIVSGSFD----ESVRIWDVK--TGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDD-DNPPVSFVKFSPGKYILAATLDNTLKLWDYSK

1sq9A

0.14

4.84

1.33

DEthreader

FIATANAFTVLVTTSSGSFWALKWGASNSHRLVATDVKTTYIWKFHTLELQGTVESPSQFATSVDISER-GLIATGFNNGTVQISELSTLRPLYNFESQHNSNSIRSVKFSPQGSLLAIAHDS-NSFGCITLYETE-FGERIGSLSFAHSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDLPGVFDVKFLKKESLCCVCLDRSIRWFREAG

(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	0.857

(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	6f3tA	0.89	1.70	0.225	0.951	model1_6f3tA.pdb.gz
2	3ow8A	0.89	1.68	0.189	0.946	model1_3ow8A.pdb.gz
3	3fm0A	0.89	1.83	0.176	0.964	model1_3fm0A.pdb.gz
4	1vyhT	0.89	1.73	0.150	0.946	model1_1vyhT.pdb.gz
5	4lg8A	0.88	1.94	0.150	0.955	model1_4lg8A.pdb.gz
6	6t9iD	0.88	1.85	0.187	0.955	model1_6t9iD.pdb.gz
7	6tblE	0.88	2.11	0.120	0.964	model1_6tblE.pdb.gz
8	4d6vA	0.88	1.94	0.165	0.946	model1_4d6vA.pdb.gz
9	2ymuA	0.88	1.56	0.230	0.933	model1_2ymuA.pdb.gz
10	6iamA	0.88	1.85	0.201	0.955	model1_6iamA.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:0003676	0.29	nucleic acid binding
GO:0003723	0.27	RNA binding
GO:0003824	0.25	catalytic activity
GO:0044877	0.22	macromolecular complex binding
GO:0032403	0.20	protein complex binding
GO:0016740	0.20	transferase activity
GO:0008092	0.19	cytoskeletal protein binding
GO:0003779	0.17	actin binding
GO:0051015	0.16	actin filament binding
GO:0042393	0.16	histone binding
GO:0019899	0.16	enzyme binding
GO:0000989	0.15	transcription factor activity, transcription factor binding
GO:0030515	0.14	snoRNA binding
GO:0016787	0.14	hydrolase activity
GO:0042802	0.13	identical protein binding
GO:0017111	0.13	nucleoside-triphosphatase activity
GO:0004402	0.13	histone acetyltransferase activity
GO:0003712	0.13	transcription cofactor activity
GO:0046972	0.12	histone acetyltransferase activity (H4-K16 specific)
GO:0043996	0.12	histone acetyltransferase activity (H4-K8 specific)
GO:0043995	0.12	histone acetyltransferase activity (H4-K5 specific)
GO:0042803	0.12	protein homodimerization activity
GO:0042800	0.12	histone methyltransferase activity (H3-K4 specific)
GO:0016887	0.12	ATPase activity
GO:0003682	0.12	chromatin binding
GO:0070615	0.11	nucleosome-dependent ATPase activity
GO:0046976	0.11	histone methyltransferase activity (H3-K27 specific)
GO:0046974	0.11	histone methyltransferase activity (H3-K9 specific)
GO:0042826	0.11	histone deacetylase binding
GO:0035064	0.11	methylated histone binding
GO:0035035	0.11	histone acetyltransferase binding
GO:0031491	0.11	nucleosome binding
GO:0003714	0.11	transcription corepressor 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	0.85	cellular process
GO:0071840	0.61	cellular component organization or biogenesis
GO:0044237	0.60	cellular metabolic process
GO:0044238	0.58	primary metabolic process
GO:0043170	0.58	macromolecule metabolic process
GO:0044260	0.57	cellular macromolecule metabolic process
GO:0016043	0.56	cellular component organization

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:0044424	0.99	intracellular part
GO:0032991	0.83	macromolecular complex
GO:0044446	0.80	intracellular organelle part
GO:0044428	0.66	nuclear part
GO:0043234	0.64	protein complex
GO:0043226	0.62	organelle
GO:0043229	0.59	intracellular organelle
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	0.108	1ri6A	0.826	2.30	0.098	0.942	3.1.1.31	NA
2	0.104	3dr2A	0.735	3.23	0.087	0.911	3.1.1.17	NA
3	0.088	2fpcA	0.760	3.13	0.114	0.933	4.3.3.2	NA
4	0.087	1v04A	0.749	3.16	0.090	0.929	3.1.1.2 3.1.8.1	NA
5	0.071	1vcuB	0.768	3.56	0.077	0.991	3.2.1.18	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	0.20	3p4fA	0.879	1.88	0.201	0.955	0.77	III	complex1.pdb.gz	18,20,37,60,61,62,78,104,106,122
2	0.18	2ce8A	0.867	1.96	0.170	0.942	0.86	III	complex2.pdb.gz	19,21,61,63,78,107,121,151,154,170,198
3	0.17	3smrC	0.867	2.25	0.150	0.955	0.73	NP7	complex3.pdb.gz	20,21,61,62,63,106,152,154,170
4	0.07	2xl2A	0.879	1.88	0.201	0.955	1.17	III	complex4.pdb.gz	27,68,69,71,72,94,110,112,136
5	0.04	1a0rB	0.857	2.36	0.131	0.955	0.71	FAR	complex5.pdb.gz	188,197,210,212,214,216,218,220

	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.