D-I-TASSER Q68D91-D1

D-I-TASSER results for Q68D91-D1

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

Input Sequence in FASTA format

>Q68D91 (149 residues)
MSALEWYAHKSLGDGIFWIQERFYESGNRANIWLVRGSEQDVVIDTGLGLRSLPEYLYSS
GLLQDREAKEDAARRPLLAVATHVHFDHSGGLYQFDRVAVHHAEAEALARGDNFETVTWL
SDSEVVRTPSPGWRARQFRVQAVQPTLIL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSALEWYAHKSLGDGIFWIQERFYESGNRANIWLVRGSEQDVVIDTGLGLRSLPEYLYSSGLLQDREAKEDAARRPLLAVATHVHFDHSGGLYQFDRVAVHHAEAEALARGDNFETVTWLSDSEVVRTPSPGWRARQFRVQAVQPTLIL
Prediction	CCCCCCSSSSSSCCCSSSSSCCCCCCCCCCSSSSSSCCCSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCSSSSSCCCCCCCCCCHHHCCCSSSCHHHHHHHHCCCCHHHHHHHHCCSSCCCCCCCCCCCCSSSCCCCCCSCC
Confidence	98666658999749979995688788874189999839938999399997412667765345667876531268975999658880115751442704438999999976972256888626611038999988122254378875009
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSALEWYAHKSLGDGIFWIQERFYESGNRANIWLVRGSEQDVVIDTGLGLRSLPEYLYSSGLLQDREAKEDAARRPLLAVATHVHFDHSGGLYQFDRVAVHHAEAEALARGDNFETVTWLSDSEVVRTPSPGWRARQFRVQAVQPTLIL
Prediction	86675213245147300102043354343000000337731000001223440452145442443453155145220100000112001000430351101442262056355441133136441552446614365042471424346
	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

                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCSSSSSSCCCSSSSSCCCCCCCCCCSSSSSSCCCSSSSSSCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCSSSSSCCCCCCCCCCHHHCCCSSSCHHHHHHHHCCCCHHHHHHHHCCSSCCCCCCCCCCCCSSSCCCCCCSCC
MSALEWYAHKSLGDGIFWIQERFYESGNRANIWLVRGSEQDVVIDTGLGLRSLPEYLYSSGLLQDREAKEDAARRPLLAVATHVHFDHSGGLYQFDRVAVHHAEAEALARGDNFETVTWLSDSEVVRTPSPGWRARQFRVQAVQPTLIL

1a7tA

0.12

0.10

3.58

1.17

DEthreader

-KISDDISITQLSDKVYTYVSLAEIWGVPSNGMIVINNHQAALLDTPINDAQTEMLVNW--VTDS--H--AK---VTTFIPNHWHGDCIGGLGYLQQSYANQMTIDLAKEK---FTDSLTVSLQCYYLGGGHTDN-IVVWLP-------

1bvtA

0.16

0.15

4.93

1.74

SPARKS-K

KNETGTISISQLNKNVWVHTELGSFEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQ--------KRVTDVIITHAHADRIGGIKTLKEAHSTALTAELAKKNGYEETNLKFGNMKVETFYGKGHTEDNIVVWLPQYNILV

6lipA

0.15

0.13

4.51

0.71

MapAlign

DQRFGDLVFRQLAPNVWQHTSYLDFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNW--IKQ------EINLPVALAVVTHAHQDKMGGMDALIATYANALSNQLASLTFAANGWVNFGPLKVFYPGPGHTSD-NITVG--------

6e0sA

0.16

0.14

4.70

0.52

CEthreader

-DWNDPQEPFAVFGSTYYVGV------RGLSAVLIASPQGHILIDGGSSAPQIAQHIRQLGFK---------LEDVKLILNSHEHFDHAGGISELQTVLASVQGEKVLRSGQPSGEVVKLGPLAVTARYTPGHTQGGVSWTWRATENGK

2zo4A

0.22

0.20

6.34

1.07

MUSTER

----------ALLPGLYLLPVPIPYPLKTVNLYLLQGAGEVALVDTALGTRAARGALELH-----LAELGLCFQDVKTILLTHHHPDHYGLSGFFERVFLHEEEFARGHREPEAFAEASWRLFLDHGTPEETVEKTRERVHPPQNPLPL

5i0pA

0.14

0.13

4.56

1.14

HHsearch

DTLPAAGDTFEVAPGVRWLRMPLPFSLDHINLWLLRDEAGWTIVDCGISSEAIRTHWEQIFLDG---------LPVLRVLVTHCHPDHFGLANWLCELWMTLGEYMFGCLMAAPYDAVKIGARTWRVVTGYGHSPEHCALHSE-ADGVL

6uxuA1

0.18

0.15

4.83

1.32

FFAS-3D

------MRSQQLAPGVYAHLPADKGGVAGTSGGLIVGTRGAMLIETMLNRRLFDQVQA-------LAKKEALGLPLLYAVNTSYHGDHSYGNMYLKAVIQSTKTRDYVDGPPGGRVSVDLGGKTVEIIDFFAQTGGDL-----------

6h0cA1

0.13

0.12

4.17

0.80

EigenThreader

--PAKDVQICPIAVDTTVFRSFEIEYGLTANSYLISAD-KIALFDPPSFTDNFVGTLIQRLDLNS----------LDYVILGHVNANRAHTLKLLATIICSNPAAQNLEKLLANPIQVMKGNDTFIPTPSPRYPGQLCTYDPRTEILFT

1dxkA

0.15

0.14

4.74

1.63

CNFpred

KNETGTISISQLNKNVWVHTELGSFNAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMV--------EKKFQKRVTDVIITHAHADRIGGIKTLKKAHSTALTAELAKKN-QTVTNLKFGNMKVETFYPKGHTEDNIVVWLPQYNILV

6cqsA

0.14

0.12

4.12

1.17

DEthreader

-RLNDELEVREILPNAFVITHKFP---WGGNSLVVLIGKYAVFVDTPYTPEATENVLDW--INKQ-YG--NR--QF-IEINTGYHVDNLGGNDALLPIIGSDKTVSLLRERG-QLTEGYHFTIEVFFPGETHPDN-IVVYFP-------

(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	0.7475

(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	1a7tA	0.80	2.39	0.121	0.919	model1_1a7tA.pdb.gz
2	6tt8A	0.78	2.61	0.177	0.919	model1_6tt8A.pdb.gz
3	2yntA	0.78	2.41	0.145	0.913	model1_2yntA.pdb.gz
4	1jjeB	0.78	2.54	0.158	0.919	model1_1jjeB.pdb.gz
5	4wd6A	0.78	2.38	0.159	0.913	model1_4wd6A.pdb.gz
6	1bvtA	0.78	2.51	0.149	0.919	model1_1bvtA.pdb.gz
7	5mmdE	0.78	2.41	0.159	0.913	model1_5mmdE.pdb.gz
8	6t5kC	0.78	2.44	0.171	0.913	model1_6t5kC.pdb.gz
9	6t5lA	0.77	2.54	0.184	0.919	model1_6t5lA.pdb.gz
10	6jv4A	0.77	2.56	0.158	0.913	model1_6jv4A.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	0.87	catalytic activity
GO:0016787	0.86	hydrolase activity
GO:0046872	0.82	metal ion binding
GO:0008270	0.73	zinc ion binding
GO:0016788	0.67	hydrolase activity, acting on ester bonds
GO:0008800	0.67	beta-lactamase activity
GO:1901363	0.54	heterocyclic compound binding
GO:0097159	0.54	organic cyclic compound binding
GO:0003676	0.51	nucleic acid binding

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:0008152	0.96	metabolic process
GO:0009987	0.95	cellular process
GO:0044237	0.93	cellular metabolic process
GO:0071704	0.81	organic substance metabolic process
GO:1901360	0.75	organic cyclic compound metabolic process
GO:0034641	0.74	cellular nitrogen compound metabolic process
GO:0044238	0.73	primary metabolic process
GO:0046483	0.72	heterocycle metabolic process
GO:0006725	0.72	cellular aromatic compound metabolic process
GO:0044260	0.71	cellular macromolecule metabolic process
GO:0006139	0.69	nucleobase-containing compound metabolic process
GO:0090304	0.68	nucleic acid metabolic process
GO:0016070	0.67	RNA metabolic process
GO:0009058	0.67	biosynthetic process
GO:0044248	0.66	cellular catabolic process
GO:1901576	0.64	organic substance biosynthetic process
GO:0044249	0.63	cellular biosynthetic process
GO:0017001	0.62	antibiotic catabolic process
GO:1901362	0.61	organic cyclic compound biosynthetic process
GO:0019438	0.61	aromatic compound biosynthetic process
GO:0044271	0.60	cellular nitrogen compound biosynthetic process
GO:0009059	0.60	macromolecule biosynthetic process
GO:0034645	0.59	cellular macromolecule biosynthetic process
GO:0006351	0.58	transcription, DNA-templated
GO:0050896	0.51	response to stimulus
GO:0042221	0.50	response to chemical

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:0070062	1.00	extracellular exosome
GO:0044464	0.95	cell part
GO:0044424	0.92	intracellular part
GO:0043229	0.76	intracellular organelle
GO:0043231	0.74	intracellular membrane-bounded organelle
GO:0005634	0.69	nucleus

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	0.388	1m2xA	0.747	2.71	0.184	0.899	3.5.2.6	87
2	0.082	1jjeB	0.778	2.54	0.158	0.919	3.5.2.6	87
3	0.066	3hnnA	0.669	3.26	0.118	0.886	1.-.-.-	NA
4	0.060	1qh5A	0.609	2.77	0.134	0.745	3.1.2.6	49
5	0.060	1ycfA	0.696	2.82	0.174	0.873	1.7.99.7	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:

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	0.23	1znbA	0.787	2.47	0.121	0.919	1.03	NA	complex1.pdb.gz	30,31,45,46,87,88
	2	0.19	1hlkA	0.793	2.43	0.113	0.919	0.71	NA	complex2.pdb.gz	19,30,31,45,46,87

	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.