D-I-TASSER Q5SXH7-D1

D-I-TASSER results for Q5SXH7-D1

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

Input Sequence in FASTA format

>Q5SXH7 (137 residues)
MAGGKQFTFSYENEVCKQDYFIKSPPSQLFSSVTSWKKRFFILSKAGEKSFSLSYYKDHH
HRGSIEIDQNSSVEVGISSQEKMQSVQKMFKCHPDEVMSIRTTNREYFLIGHDREKIKDW
VSFMSSFRQDIKATQQN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAGGKQFTFSYENEVCKQDYFIKSPPSQLFSSVTSWKKRFFILSKAGEKSFSLSYYKDHHHRGSIEIDQNSSVEVGISSQEKMQSVQKMFKCHPDEVMSIRTTNREYFLIGHDREKIKDWVSFMSSFRQDIKATQQN
Prediction	CCCCCCCCCCCCCCSSSSSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCCSSSSSSCCCCCCCSSSCCCCSSSSSSCCCCCCCCCCCSSSCCCCCCSSSSSCCCSSSSSSSCCHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	99865566657896799999785588777754355332699995289971699996898755156255314898504556666542112314777168986199189999299999999999999999974776429
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MAGGKQFTFSYENEVCKQDYFIKSPPSQLFSSVTSWKKRFFILSKAGEKSFSLSYYKDHHHRGSIEIDQNSSVEVGISSQEKMQSVQKMFKCHPDEVMSIRTTNREYFLIGHDREKIKDWVSFMSSFRQDIKATQQN
Prediction	85545623354744001201021345653244344432000002556644110201437545240405514414131645753542442151445220404155210101043671155215102400563465568
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCCCCCCCSSSSSSSSSCCCCCCCCCCCCSSSSSSSSSCCCCCCSSSSSSCCCCCCCSSSCCCCSSSSSSCCCCCCCCCCCSSSCCCCCCSSSSSCCCSSSSSSSCCHHHHHHHHHHHHHHHHHHHHHHCC
MAGGKQFTFSYENEVCKQDYFIKSPPSQLFSSVTSWKKRFFILSKAGEKSFSLSYYKDHHHRGSIEIDQNSSVEVGISSQEKMQSVQKMFKCHPDEVMSIRTTNREYFLIGHDREKIKDWVSFMSSFRQDIKATQQN

2otxA

0.23

0.18

5.74

1.17

DEthreader

----PIAAQDLP-FVIKAGYLEKRRKDHSFLGF-EWQKRWCALSK-----TVFYYYGSDDQKGEFAIDGY-DVRMNN--T--L--RKD--GK-KDCCFEICAPDRIYQFTAASPKDAEEWVQQLKFILQDLG-----

1unqA

0.14

0.11

3.75

1.65

SPARKS-K

--------SMSDVAIVKEGWLHKRGEYI-----KTWRPRYFLLKND----GTFIGYKERAPLNNFSVAQCQLMKTERPR-----PNTFIIRCLQWT------TVIERTFHVETPEEREEWTTAIQTVADGLKKQEEE

1wg7A

0.21

0.18

5.55

0.58

MapAlign

--------GSQKGGITKHGWLYKGNMNSAISVTMRFKRRFFHLIQLGDGSYNLNFYKDEEPKGSIFLDSCMGVVQNN--------------KVRRFAFELKMQDSSYLLAADSEVEMEEWITILNKILQLNFEA---

1wg7A

0.20

0.18

5.82

0.54

CEthreader

GSSGAASLGSQKGGITKHGWLYKGNMNSAIVTMRSFKRRFFHLIQLGDGSYNLNFYKDKEPKGSIFLDSCMGVVQNN--------------KVRRFAFELKMQDSSYLLAADSEVEMEEWITILNKILQLNFEAAMQ

1v5uA

0.21

0.18

5.56

1.56

MUSTER

-------GSSGSSGRSYEGILYKKGAF-----MKPWKARWFVLDKTKH---QLRYYDHRMDKGVIDLAEVEAVAPGTPTIGAPKTV------DEKAFFDVKTTRRVYNFCAQDVPSAQQWVDRIQSCLSSGPSSG--

2lulA

0.15

0.13

4.45

1.29

HHsearch

MGHHHHHHSHMNFNTILEEILIKRSQQKKKTSPLNYKERLFVLT-----KSMLTYYEGRAKKGFIDVSKIKCVEIVKNDDVIPCQNKYPF--------QVVHDANTLYIFAPSPQSRDLWVKKLKEEIKNNNNIMIK

1wg7A

0.21

0.19

6.02

1.57

FFAS-3D

-SSGAASLGSQKGGITKHGWLYKGNMNSAISVMRSFKRRFFHLIQLGDGSYNLNFYKDEKIKGSIFLDSCMGVVQNNK-------------VRRFAFELKMQDKSSYLLAADSEVEMEEWITILNKILQLNFEAAMQ

2lulA

0.15

0.14

4.66

0.78

EigenThreader

MGHHHHHHSHMNFNTILEEILIKRSQQKKKTSPLNYKERLFVLTK-----SMLTYYEGRAEKGFIDVSKIKCVEIVKNDD-------GVIPCQNKYPFQVVHDANTLYIFAPSPQSRDLWVKKLKEEIKNNNNIMIK

2lulA

0.15

0.12

4.15

1.56

CNFpred

--------------TILEEILIKRSQQKKKTSPLNYKERLFVLTK-----SMLTYYEGRYRKGFIDVSKIKCVEIVKNDDGVIPC--------NKYPFQVVHDANTLYIFAPSPQSRDLWVKKLKEEIKNNNNIMIK

2lulA

0.15

0.12

4.19

1.17

DEthreader

--HHHHSHMNF--NTILEEILIKRSQQKK-TSPLNYKERLFVLTK-----SMLTYYEGRARKGFIDVSKIKCVEIVKN-DD--GV-IPCQNK---YPFQVVHDANTLYIFAPSPQSRDLWVKKLKEEIKNNN-----

(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	0.8085

(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	1wg7A	0.72	2.03	0.211	0.810	model1_1wg7A.pdb.gz
2	1k5gH	0.70	2.42	0.091	0.832	model1_1k5gH.pdb.gz
3	2otxA	0.70	1.98	0.209	0.796	model1_2otxA.pdb.gz
4	1v5mA	0.69	2.71	0.144	0.818	model1_1v5mA.pdb.gz
5	1v5uA	0.66	2.43	0.204	0.774	model1_1v5uA.pdb.gz
6	2dn6A	0.66	2.11	0.213	0.752	model1_2dn6A.pdb.gz
7	3a8nA	0.66	2.22	0.133	0.766	model1_3a8nA.pdb.gz
8	1x05A	0.66	2.84	0.193	0.803	model1_1x05A.pdb.gz
9	3wyfB	0.65	2.39	0.080	0.774	model1_3wyfB.pdb.gz
10	1u5dA	0.65	2.00	0.212	0.730	model1_1u5dA.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:0030674	0.69	protein binding, bridging
GO:0035591	0.68	signaling adaptor activity
GO:0019899	0.67	enzyme binding
GO:1901981	0.65	phosphatidylinositol phosphate binding
GO:0019900	0.65	kinase binding
GO:0019904	0.56	protein domain specific binding
GO:0005215	0.55	transporter activity
GO:0003824	0.55	catalytic activity
GO:0016773	0.52	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.52	kinase activity
GO:0022892	0.50	substrate-specific transporter 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:0065007	0.93	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0050794	0.89	regulation of cellular process
GO:0009987	0.85	cellular process
GO:0044699	0.80	single-organism process
GO:0044763	0.74	single-organism cellular process
GO:0007165	0.74	signal transduction
GO:0008152	0.67	metabolic process
GO:0071704	0.66	organic substance metabolic process
GO:0048583	0.66	regulation of response to stimulus
GO:0044238	0.66	primary metabolic process
GO:0044237	0.66	cellular metabolic process
GO:0048869	0.63	cellular developmental process
GO:0044260	0.63	cellular macromolecule metabolic process
GO:0051179	0.62	localization
GO:0048518	0.62	positive regulation of biological process
GO:0007166	0.60	cell surface receptor signaling pathway
GO:0006810	0.60	transport
GO:0050896	0.59	response to stimulus
GO:0048522	0.59	positive regulation of cellular process
GO:0032502	0.59	developmental process
GO:0016043	0.59	cellular component organization
GO:0080090	0.58	regulation of primary metabolic process
GO:0044767	0.58	single-organism developmental process
GO:0023051	0.58	regulation of signaling
GO:0010646	0.58	regulation of cell communication
GO:0006796	0.58	phosphate-containing compound metabolic process
GO:0006464	0.58	cellular protein modification process
GO:0031323	0.57	regulation of cellular metabolic process
GO:0060255	0.56	regulation of macromolecule metabolic process
GO:0048584	0.56	positive regulation of response to stimulus
GO:0044707	0.56	single-multicellular organism process
GO:0034641	0.56	cellular nitrogen compound metabolic process
GO:0009966	0.56	regulation of signal transduction
GO:1902578	0.55	single-organism localization
GO:0051641	0.55	cellular localization
GO:0050776	0.55	regulation of immune response
GO:0048856	0.55	anatomical structure development
GO:0002684	0.55	positive regulation of immune system process
GO:0050790	0.54	regulation of catalytic activity
GO:0050778	0.54	positive regulation of immune response
GO:0044765	0.54	single-organism transport
GO:1901576	0.53	organic substance biosynthetic process
GO:0065008	0.53	regulation of biological quality
GO:0046907	0.53	intracellular transport
GO:0044710	0.53	single-organism metabolic process
GO:0006950	0.53	response to stress
GO:0071702	0.52	organic substance transport
GO:0048513	0.52	animal organ development
GO:0044249	0.52	cellular biosynthetic process
GO:0009653	0.52	anatomical structure morphogenesis
GO:0006996	0.52	organelle organization
GO:0002764	0.52	immune response-regulating signaling pathway
GO:0002376	0.52	immune system process
GO:1902589	0.51	single-organism organelle organization
GO:0051336	0.51	regulation of hydrolase activity
GO:0051171	0.51	regulation of nitrogen compound metabolic process
GO:0051716	0.50	cellular response to stimulus
GO:0043087	0.50	regulation of GTPase activity
GO:0043085	0.50	positive regulation of catalytic activity
GO:0031326	0.50	regulation of cellular biosynthetic process
GO:0010556	0.50	regulation of macromolecule biosynthetic process
GO:0007275	0.50	multicellular organism development
GO:0002768	0.50	immune response-regulating cell surface receptor signaling pathway

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:0016020	0.86	membrane
GO:0005737	0.85	cytoplasm
GO:0044444	0.76	cytoplasmic part
GO:0043226	0.72	organelle
GO:0043229	0.67	intracellular organelle
GO:0043227	0.63	membrane-bounded organelle
GO:0005886	0.60	plasma membrane
GO:0043231	0.58	intracellular membrane-bounded organelle
GO:0044446	0.56	intracellular organelle part
GO:0005829	0.55	cytosol

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	0.219	2rovA	0.633	2.52	0.162	0.745	2.7.11.1	42,44,100
2	0.154	2dynA	0.587	2.28	0.140	0.693	3.6.5.5	54,56
3	0.067	2kieA	0.594	2.82	0.093	0.759	3.1.3.36	106
4	0.060	2etfB	0.412	4.88	0.056	0.730	3.4.24.69	NA
5	0.060	2ys1A	0.570	2.90	0.176	0.708	3.6.5.5	56,58,120

	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	0.06	3dxcA	0.630	2.20	0.098	0.745	0.62	III	complex1.pdb.gz	67,68,70,71,72,73,74,75,76,96,103,116,118,125,128,129,131,132,135,136
2	0.03	2p0hA	0.632	2.11	0.182	0.723	0.52	I3S	complex2.pdb.gz	37,38,40
3	0.02	1i7aA	0.608	2.31	0.062	0.708	1.01	III	complex3.pdb.gz	22,24,77,96,97

	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, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.