D-I-TASSER Q5QJ74-D2

D-I-TASSER results for Q5QJ74-D2

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

Input Sequence in FASTA format

>Q5QJ74 (88 residues)
DLRPQSSAKVEVHFNDQVEEMSIRLDQTVAELKKQLKTLVQLPTSNMLLYYFDHEAPFGP
EEMKYSSRALHSFGIRDGDKIYVESKTK

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| DLRPQSSAKVEVHFNDQVEEMSIRLDQTVAELKKQLKTLVQLPTSNMLLYYFDHEAPFGPEEMKYSSRALHSFGIRDGDKIYVESKTK
Prediction	CCCCCCSSSSSSSSCCSSSSSSSSHHHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCSSSSSSCCC
Confidence	9999707999999898678999844551999999999986999501499997588887871004687452774478897899996269
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| DLRPQSSAKVEVHFNDQVEEMSIRLDQTVAELKKQLKTLVQLPTSNMLLYYFDHEAPFGPEEMKYSSRALHSFGIRDGDKIYVESKTK
Prediction	8463654030203046544525041442054026304621704344120110267353445314246441332416432402035558
	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

                   |                   |                   |                   |

SS
Seq

CCCCCCSSSSSSSSCCSSSSSSSSHHHHHHHHHHHHHHHHCCCCCCSSSSSSCCCCCCCCCCCCCCCCCCSSSCCCCCCSSSSSSCCC
DLRPQSSAKVEVHFNDQVEEMSIRLDQTVAELKKQLKTLVQLPTSNMLLYYFDHEAPFGPEEMKYSSRALHSFGIRDGDKIYVESKTK

2kanA

0.25

0.23

7.06

1.33

DEthreader

SHAAVRKIHVTVKFPSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYS-------GIELADDYRNLNEYGITEFSEIVVFLKSN

6jh0D2

0.17

0.15

4.88

1.96

SPARKS-K

--NSNDPLSILVRNKGRSIAYEVWLTQTVAELKQQVCQQEHVQADLFWLTFEGKPME--------DKHQLGEYGLTPQCTVFMNLRLR

1t0yA

0.23

0.22

6.77

0.58

MapAlign

----TEVYDLEITTNATPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFD-GDDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTG

1t0yA

0.23

0.22

6.78

0.38

CEthreader

---MTEVYDLEITTNATPMEKKYPAGMSLNDLKKKLELVVGTTVDSMRIQLFDG-DDQLKGELTDGAKSLKDLGVRDGYRIHAVDVTG

1wjnA

0.20

6.52

1.64

MUSTER

SGSSGQLLTLKIKCSNQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRWSGP

6px3C

0.11

0.09

3.28

1.04

HHsearch

-------MQIFVKTTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQ-------LED-GRTLSDYNIQKESTLHLVLRLR

2kanA

0.25

0.23

7.03

1.21

FFAS-3D

--AAVRKIHVTVKFPSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYSGI-------ELADDYRNLNEYGITEFSEIVVFLKSI

1wjnA

0.20

6.52

0.73

EigenThreader

SGSSGQLLTLKIKCSNQILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSKMPGREIELENDLQPLQFYSVENGDCLLVRWSGP

2bweS

0.19

0.16

5.12

1.40

CNFpred

------SLNIHIKSGQDKWEVNVAPESTVLQFKEAINKANGIPVANQRLIYS-------GKILKD-DQTVESYHIQDGHSVHLVKSQ-

1wjnA

0.19

0.18

5.89

1.33

DEthreader

-GSSGQLLTLKIKCQPRILEKQLPDSMTVQKVKGLLSRLLKVPVSELLLSYESSMPG-REIELENDLQPLQFYSVENGDCLLVRWSGP

(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	0.8931

(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	1wjnA	0.86	1.50	0.193	0.977	model1_1wjnA.pdb.gz
2	1t0yA	0.84	1.42	0.238	0.955	model1_1t0yA.pdb.gz
3	2kanA	0.82	1.41	0.247	0.909	model1_2kanA.pdb.gz
4	3jyuA	0.81	1.79	0.143	0.955	model1_3jyuA.pdb.gz
5	4melA	0.81	2.24	0.081	0.966	model1_4melA.pdb.gz
6	5v6rA	0.80	2.03	0.106	0.943	model1_5v6rA.pdb.gz
7	3ppaA	0.80	2.11	0.095	0.955	model1_3ppaA.pdb.gz
8	1v5oA	0.78	1.43	0.148	0.875	model1_1v5oA.pdb.gz
9	2bwfA	0.74	1.87	0.169	0.875	model1_2bwfA.pdb.gz
10	5c1zA	0.74	1.73	0.123	0.830	model1_5c1zA.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:0005198	0.49	structural molecule activity
GO:0097159	0.47	organic cyclic compound binding
GO:1901363	0.46	heterocyclic compound binding
GO:0003735	0.45	structural constituent of ribosome

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	0.97	cellular process
GO:0065007	0.88	biological regulation
GO:0050789	0.88	regulation of biological process
GO:0044699	0.88	single-organism process
GO:0050794	0.87	regulation of cellular process
GO:0044763	0.83	single-organism cellular process
GO:0048518	0.74	positive regulation of biological process
GO:0048522	0.73	positive regulation of cellular process
GO:0016043	0.69	cellular component organization
GO:0008152	0.66	metabolic process
GO:0071704	0.65	organic substance metabolic process
GO:0044260	0.64	cellular macromolecule metabolic process
GO:0044238	0.64	primary metabolic process
GO:0048519	0.62	negative regulation of biological process
GO:0019538	0.62	protein metabolic process
GO:0006996	0.62	organelle organization
GO:0048523	0.61	negative regulation of cellular process
GO:0032502	0.61	developmental process
GO:0022607	0.61	cellular component assembly
GO:0006464	0.61	cellular protein modification process
GO:0080090	0.60	regulation of primary metabolic process
GO:0060255	0.60	regulation of macromolecule metabolic process
GO:0050896	0.60	response to stimulus
GO:0044767	0.60	single-organism developmental process
GO:0031323	0.60	regulation of cellular metabolic process
GO:0022402	0.60	cell cycle process
GO:0051246	0.59	regulation of protein metabolic process
GO:0051234	0.59	establishment of localization
GO:0007165	0.59	signal transduction
GO:0042981	0.58	regulation of apoptotic process
GO:0032268	0.58	regulation of cellular protein metabolic process
GO:0006950	0.58	response to stress
GO:0006511	0.58	ubiquitin-dependent protein catabolic process
GO:0065008	0.57	regulation of biological quality
GO:0051716	0.57	cellular response to stimulus
GO:0051248	0.57	negative regulation of protein metabolic process
GO:0048856	0.57	anatomical structure development
GO:0042176	0.56	regulation of protein catabolic process
GO:0035556	0.56	intracellular signal transduction
GO:0032269	0.56	negative regulation of cellular protein metabolic process
GO:1903050	0.55	regulation of proteolysis involved in cellular protein catabolic process
GO:0072331	0.55	signal transduction by p53 class mediator
GO:0051276	0.55	chromosome organization
GO:0032446	0.55	protein modification by small protein conjugation
GO:0006974	0.55	cellular response to DNA damage stimulus
GO:0065003	0.54	macromolecular complex assembly
GO:0043066	0.54	negative regulation of apoptotic process
GO:0016567	0.54	protein ubiquitination
GO:0006810	0.54	transport
GO:0048583	0.53	regulation of response to stimulus
GO:0044702	0.53	single organism reproductive process
GO:0034622	0.53	cellular macromolecular complex assembly
GO:0031399	0.53	regulation of protein modification process
GO:0019220	0.53	regulation of phosphate metabolic process
GO:0002376	0.53	immune system process
GO:0051649	0.52	establishment of localization in cell
GO:0050790	0.52	regulation of catalytic activity
GO:0048869	0.52	cellular developmental process
GO:0044710	0.52	single-organism metabolic process
GO:0044271	0.52	cellular nitrogen compound biosynthetic process
GO:0034645	0.52	cellular macromolecule biosynthetic process
GO:0010604	0.52	positive regulation of macromolecule metabolic process
GO:0007219	0.52	Notch signaling pathway
GO:0001932	0.52	regulation of protein phosphorylation
GO:1903047	0.51	mitotic cell cycle process
GO:0080134	0.51	regulation of response to stress
GO:0051726	0.51	regulation of cell cycle
GO:0051239	0.51	regulation of multicellular organismal process
GO:0048584	0.51	positive regulation of response to stimulus
GO:0046907	0.51	intracellular transport
GO:0045937	0.51	positive regulation of phosphate metabolic process
GO:0045935	0.51	positive regulation of nucleobase-containing compound metabolic process
GO:0045859	0.51	regulation of protein kinase activity
GO:0045732	0.51	positive regulation of protein catabolic process
GO:0044765	0.51	single-organism transport
GO:0043408	0.51	regulation of MAPK cascade
GO:0043086	0.51	negative regulation of catalytic activity
GO:0043085	0.51	positive regulation of catalytic activity
GO:0031400	0.51	negative regulation of protein modification process
GO:0031328	0.51	positive regulation of cellular biosynthetic process
GO:0016032	0.51	viral process
GO:0009968	0.51	negative regulation of signal transduction
GO:0006355	0.51	regulation of transcription, DNA-templated
GO:0006259	0.51	DNA metabolic process
GO:1901796	0.50	regulation of signal transduction by p53 class mediator
GO:0090263	0.50	positive regulation of canonical Wnt signaling pathway
GO:0090090	0.50	negative regulation of canonical Wnt signaling pathway
GO:0075733	0.50	intracellular transport of virus
GO:0070987	0.50	error-free translesion synthesis
GO:0070911	0.50	global genome nucleotide-excision repair
GO:0070423	0.50	nucleotide-binding oligomerization domain containing signaling pathway
GO:0061418	0.50	regulation of transcription from RNA polymerase II promoter in response to hypoxia
GO:0060071	0.50	Wnt signaling pathway, planar cell polarity pathway
GO:0051437	0.50	positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
GO:0051436	0.50	negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
GO:0051092	0.50	positive regulation of NF-kappaB transcription factor activity
GO:0050852	0.50	T cell receptor signaling pathway
GO:0045944	0.50	positive regulation of transcription from RNA polymerase II promoter
GO:0045742	0.50	positive regulation of epidermal growth factor receptor signaling pathway
GO:0043488	0.50	regulation of mRNA stability
GO:0043123	0.50	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043065	0.50	positive regulation of apoptotic process
GO:0042769	0.50	DNA damage response, detection of DNA damage
GO:0042276	0.50	error-prone translesion synthesis
GO:0042059	0.50	negative regulation of epidermal growth factor receptor signaling pathway
GO:0038128	0.50	ERBB2 signaling pathway
GO:0038095	0.50	Fc-epsilon receptor signaling pathway
GO:0038061	0.50	NIK/NF-kappaB signaling
GO:0036297	0.50	interstrand cross-link repair
GO:0035666	0.50	TRIF-dependent toll-like receptor signaling pathway
GO:0034220	0.50	ion transmembrane transport
GO:0032480	0.50	negative regulation of type I interferon production
GO:0031145	0.50	anaphase-promoting complex-dependent catabolic process
GO:0030512	0.50	negative regulation of transforming growth factor beta receptor signaling pathway
GO:0019068	0.50	virion assembly
GO:0016197	0.50	endosomal transport
GO:0010939	0.50	regulation of necrotic cell death
GO:0010803	0.50	regulation of tumor necrosis factor-mediated signaling pathway
GO:0008543	0.50	fibroblast growth factor receptor signaling pathway
GO:0007254	0.50	JNK cascade
GO:0006977	0.50	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0006297	0.50	nucleotide-excision repair, DNA gap filling
GO:0006296	0.50	nucleotide-excision repair, DNA incision, 5'-to lesion
GO:0006294	0.50	nucleotide-excision repair, preincision complex assembly
GO:0006283	0.50	transcription-coupled nucleotide-excision repair
GO:0005978	0.50	glycogen biosynthetic process
GO:0002755	0.50	MyD88-dependent toll-like receptor signaling pathway
GO:0002223	0.50	stimulatory C-type lectin receptor signaling pathway
GO:0000717	0.50	nucleotide-excision repair, DNA duplex unwinding
GO:0000715	0.50	nucleotide-excision repair, DNA damage recognition
GO:0000209	0.50	protein polyubiquitination
GO:0000187	0.50	activation of MAPK activity
GO:0000122	0.50	negative regulation of transcription from RNA polymerase II promoter
GO:0000086	0.50	G2/M transition of mitotic cell cycle

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	0.87	intracellular organelle part
GO:0043226	0.87	organelle
GO:0043229	0.86	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005634	0.74	nucleus
GO:0044444	0.70	cytoplasmic part
GO:0005737	0.66	cytoplasm
GO:0044430	0.62	cytoskeletal part
GO:0005829	0.60	cytosol
GO:0044428	0.50	nuclear 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	0.067	2jrhA	0.652	2.53	0.132	0.864	2.7.11.25	31
2	0.067	2o2vA	0.637	2.56	0.055	0.830	2.7.12.2	NA
3	0.060	2idyA	0.528	3.03	0.083	0.761	2.7.7.48	31,76
4	0.060	1dgjA	0.557	2.69	0.043	0.784	1.2.-.-	NA
5	0.060	1zxiA	0.510	3.16	0.091	0.750	1.2.99.2	74

	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	0.05	2ayo1	0.739	1.49	0.110	0.830	0.86	III	complex1.pdb.gz	41,43,46,48,50,60,61,62,78,82,84,85,86
2	0.05	3a9kB	0.727	1.76	0.110	0.830	0.64	III	complex2.pdb.gz	51,52,53,59
3	0.03	2d3gA	0.731	1.18	0.113	0.807	0.66	III	complex3.pdb.gz	14,49,51,52,53,59,61,79,81,83
4	0.03	1yd80	0.724	1.31	0.111	0.818	0.69	III	complex4.pdb.gz	11,13,51,53,57,58,59,80
5	0.03	2c7n1	0.725	1.31	0.111	0.818	0.68	III	complex5.pdb.gz	11,12,49,51,52,60,79,81,83,84,85,86

	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.