D-I-TASSER P19447-D2

D-I-TASSER results for P19447-D2

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

Input Sequence in FASTA format

>P19447 (206 residues)
YDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAA
CTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLG
HTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVRED
DKIVDLNFLIGPKLYEANWMELQNNG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| YDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCSSSSSCCHHHHHHHHHHHHHHHCCCCCSSSSSSCCCSCCCCCCCSSSSSHHHHHHHCCCCCHHHHHHHHCCCCCCCSSSSSCCCCCCCHHHHHHHHHCCCCSSSSSCCCCCCCCCCCHHHHHHCCCSSSSSCHHHHHHCC
Confidence	98535666899875304677568899999999998399870699908999889999999999599999997859999999999999729996518999578321479997999964676542124420789999748665538999645478828999999948777489961457556897055898649746971699998637
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| YDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNG
Prediction	75345464567370605461422511230042016445532000000143400100010024164300000235300520262047217155540020216445444614000000110133355454245116404763010000000310316303400640534110000000415463343024102421161416402758
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCSSSSSCCCCCCHHHHHHHHHHHHCCCSSSSSCCHHHHHHHHHHHHHHHCCCCCSSSSSSCCCSCCCCCCCSSSSSHHHHHHHCCCCCHHHHHHHHCCCCCCCSSSSSCCCCCCCHHHHHHHHHCCCCSSSSSCCCCCCCCCCCHHHHHHCCCSSSSSCHHHHHHCC
YDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNG

2ocaA

0.17

0.16

5.13

1.33

DEthreader

FQINEKEELSDFWLLEIYRIEPHWYQKDAVFEGLV---NRRRILNLPTSAGRSLIQALLARYYLYKILIIVPTTALTTQMADDFVDYRLFSHAMIKKIGGGADKYKNDAPVVVGTWQTVV-K------QP--KEWFS--QFGMMMNDECHLATGKSISSIISGLNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTELKIATYV

5tnuA1

0.24

0.21

6.67

1.49

SPARKS-K

IEVEENVIDSLPFPLIKDKIELRDYQAEAVKAWLKEK---RGIIVLPTGAGKTQVALKIVSIMKVATLIVVPTIDLITQWKERINKYLDFD---PGIIGGGEDSLK---GITVITYDSAYTRAEELG-----------NKFPLLIFDEVHHLPSEGYSIMAQLFASPYRLGLTATPERDDGKHELYPILVGPIVYRKSVEELAGK-

2gxsB

0.15

0.13

4.24

0.55

MapAlign

------MEFKDFPLKILEALTPTPIQAAALPLAL---EGKDLIGQARTGTGKTLAFALPIAERLPRALVLTPTRELALQVASELTAVAPL---KVVAVYGQKEALLRGADAVVATPGRALD----------YLVLLS--RVEVAVLDEADEMLEEEVEALLSATPSRQTLLFSATLPSW--AKRLAERYMKPVLINV---------

4kbfA1

0.14

0.13

4.45

0.34

CEthreader

--MEFKDFPLKPEILEALLTTPTPIQAAALPLALE---GKDLIGQARTGTGKTLAFALPIAERKPRALVLTPTRELALQVASELTAVAPH--LKVVAVYGGTEALLRGADAVVATPGRALDYLRQG--------VLDLSRVEVAVLDEADEMLEEEVEALLSATPPRQTLLFSATLPSWAKRLAERY-MKNPVLINVIKDEPVT--

5ivwV

1.00

28.00

1.49

MUSTER

YDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNG

2fwrA

0.29

0.26

7.98

1.24

HHsearch

IEFVDNAADPIPTPYFDAEISLRDYQEKALERWLV---DKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGE---EYVGEFSGRIK---ELKPLTVSTYDSAYVNA----------EKLG-NRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLA-GK

5fmf11

0.64

0.61

17.47

2.33

FFAS-3D

YDFRNDHRNPDLDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLQWCTLQPENCAVFTSDNKEMFQTESLVVSTYSMVANTRNRSHDSQKVMDFLTGREWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLYEA---------

6gym71

0.55

0.47

13.42

0.60

EigenThreader

----------------------RPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGITAACTIKKSVIVLCTSSVSVMQWRQQFLGGGGGGGGGGGGGGGGGGGGGGGGGLVVSTYSMVANGGGGGGGGGGGGGGGGGGGWGFIILDEVHVVPAAMFRRVVSTIAAHAKLGLTATLVREDDKIGDLNFLIGPKLY-----------

5ivwV

1.00

28.00

1.51

CNFpred

YDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNG

6vz4K

0.18

0.17

5.39

1.33

DEthreader

LAVRQQNIKEKIQPSILVGGTLKEYQLRGLEWMVSLNNHLNGILADEMGLGKTIQSISLITYLDIGFLVIVPL-STITNWTLEFEKWAPSL--NTIIYKGPRHLQIGNFDVLLTTYEYIIK------DKSLLSK-HD---WAHMIIDEGHRMNASLSFTISHYYRTRNRLILTGTPLQNNPELWALLNFVLPFLLRRLKKEVEKDI

(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	0.892

(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	2ocaA	0.80	2.72	0.198	0.932	model1_2ocaA.pdb.gz
2	6gym7	0.80	1.93	0.568	0.888	model1_6gym7.pdb.gz
3	6vz4K	0.80	2.76	0.171	0.932	model1_6vz4K.pdb.gz
4	6ryrW	0.79	2.33	0.187	0.903	model1_6ryrW.pdb.gz
5	3mwyW	0.79	2.56	0.124	0.922	model1_3mwyW.pdb.gz
6	5x0xO	0.78	2.89	0.187	0.927	model1_5x0xO.pdb.gz
7	1wp9A1	0.78	2.20	0.204	0.879	model1_1wp9A1.pdb.gz
8	6tdaS	0.78	2.92	0.161	0.922	model1_6tdaS.pdb.gz
9	1z3iX	0.78	2.72	0.175	0.903	model1_1z3iX.pdb.gz
10	3ewsA	0.75	3.12	0.148	0.898	model1_3ewsA.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	0.97	catalytic activity
GO:0017111	0.96	nucleoside-triphosphatase activity
GO:0042623	0.91	ATPase activity, coupled
GO:0004386	0.88	helicase activity
GO:0008094	0.83	DNA-dependent ATPase activity
GO:0003678	0.74	DNA helicase activity
GO:0016772	0.72	transferase activity, transferring phosphorus-containing groups
GO:0004674	0.70	protein serine/threonine kinase activity
GO:0008353	0.69	RNA polymerase II carboxy-terminal domain kinase activity
GO:1901363	0.60	heterocyclic compound binding
GO:0097159	0.60	organic cyclic compound binding
GO:0043138	0.60	3'-5' DNA helicase 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	0.96	cellular process
GO:0008152	0.94	metabolic process
GO:0090304	0.93	nucleic acid metabolic process
GO:0044260	0.93	cellular macromolecule metabolic process
GO:0016070	0.92	RNA metabolic process
GO:0050896	0.90	response to stimulus
GO:0044271	0.86	cellular nitrogen compound biosynthetic process
GO:0009059	0.86	macromolecule biosynthetic process
GO:0032774	0.85	RNA biosynthetic process
GO:0006950	0.81	response to stress
GO:0006351	0.80	transcription, DNA-templated
GO:0006366	0.78	transcription from RNA polymerase II promoter
GO:0006259	0.74	DNA metabolic process
GO:0006974	0.73	cellular response to DNA damage stimulus
GO:0006281	0.72	DNA repair
GO:0009628	0.70	response to abiotic stimulus
GO:0065007	0.64	biological regulation
GO:0050789	0.64	regulation of biological process
GO:0050794	0.63	regulation of cellular process
GO:0006289	0.63	nucleotide-excision repair
GO:0044699	0.62	single-organism process
GO:0009314	0.62	response to radiation
GO:0016043	0.61	cellular component organization
GO:0009411	0.60	response to UV
GO:0060255	0.58	regulation of macromolecule metabolic process
GO:0031323	0.58	regulation of cellular metabolic process
GO:0080090	0.57	regulation of primary metabolic process
GO:0019219	0.56	regulation of nucleobase-containing compound metabolic process
GO:0010468	0.56	regulation of gene expression
GO:0051252	0.55	regulation of RNA metabolic process
GO:0006996	0.53	organelle organization
GO:0044763	0.52	single-organism cellular process
GO:0071103	0.51	DNA conformation change
GO:0006283	0.51	transcription-coupled nucleotide-excision repair
GO:0031326	0.50	regulation of cellular biosynthetic process
GO:0010556	0.50	regulation of macromolecule 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:0044424	1.00	intracellular part
GO:0044446	0.90	intracellular organelle part
GO:0044428	0.88	nuclear part
GO:0032991	0.88	macromolecular complex
GO:0043234	0.87	protein complex
GO:0044451	0.85	nucleoplasm part
GO:1990234	0.84	transferase complex
GO:0005667	0.84	transcription factor complex
GO:1902554	0.83	serine/threonine protein kinase complex
GO:0090575	0.83	RNA polymerase II transcription factor complex
GO:0005675	0.82	holo TFIIH complex
GO:0043226	0.60	organelle
GO:0043229	0.59	intracellular organelle
GO:0043227	0.56	membrane-bounded organelle
GO:0043231	0.55	intracellular 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	0.067	1em8A	0.508	3.14	0.100	0.626	2.7.7.7	NA
2	0.066	2kbfA	0.548	3.58	0.072	0.699	3.6.4.13	115
3	0.066	1jr6A	0.464	3.13	0.083	0.568	3.6.1.15	115
4	0.060	8ohmA	0.558	3.33	0.177	0.699	2.7.7.48	148,150
5	0.060	3iuyA	0.719	2.70	0.142	0.850	3.6.4.13	51,115,174

	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	0.45	2fwrC	0.775	2.45	0.277	0.864	1.70	PO4	complex1.pdb.gz	47,49,50,51,52,53
	2	0.26	3b7gA	0.737	2.39	0.150	0.850	1.05	ANP	complex2.pdb.gz	21,26,48,49,50,51,52,53,54

	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.