D-I-TASSER Q2Q1W2-D1

D-I-TASSER results for Q2Q1W2-D1

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

Input Sequence in FASTA format

>Q2Q1W2 (166 residues)
MASFPETDFQICLLCKEMCGSPAPLSSNSSASSSSSQTSTSSGGGGGGPGAAARRLHVLP
CLHAFCRPCLEAHRLPAAGGGAAGEPLKLRCPVCDQKVVLAEAAGMDALPSSAFLLSNLL
DAVVATADEPPPKNGRAGAPAGAGGHSNHRHHAHHAHPRASASAPP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MASFPETDFQICLLCKEMCGSPAPLSSNSSASSSSSQTSTSSGGGGGGPGAAARRLHVLPCLHAFCRPCLEAHRLPAAGGGAAGEPLKLRCPVCDQKVVLAEAAGMDALPSSAFLLSNLLDAVVATADEPPPKNGRAGAPAGAGGHSNHRHHAHHAHPRASASAPP
Prediction	CCCCCCCCSSSSSHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCHHHHHHHHHHHHHCCCCCCCCCCCSSSCCCCCSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	9988866614541124331798765578777776544444456777654333589653188665569999868763245666788657869987869878998861106876999999999999742357887665566666543211121124567665456889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MASFPETDFQICLLCKEMCGSPAPLSSNSSASSSSSQTSTSSGGGGGGPGAAARRLHVLPCLHAFCRPCLEAHRLPAAGGGAAGEPLKLRCPVCDQKVVLAEAAGMDALPSSAFLLSNLLDAVVATADEPPPKNGRAGAPAGAGGHSNHRHHAHHAHPRASASAPP
Prediction	7552475513102013414644443445454444454444465243442464345030315220463742652344444454455544045235445150455510620351230042024114544755566656454653364266454157444554566658
	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

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCCCCCCSSSSSHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCSSCCCCHHHHHHHHHHHHHCCCCCCCCCCCSSSCCCCCSSSSCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MASFPETDFQICLLCKEMCGSPAPLSSNSSASSSSSQTSTSSGGGGGGPGAAARRLHVLPCLHAFCRPCLEAHRLPAAGGGAAGEPLKLRCPVCDQKVVLAEAAGMDALPSSAFLLSNLLDAVVATADEPPPKNGRAGAPAGAGGHSNHRHHAHHAHPRASASAPP

6y22A1

0.22

0.10

3.23

1.56

SPARKS-K

TEELKVPPDEDCIICMEKLSTASGYSDVTDSKAIGSL----------------AVGHLTKCSHAFHLLCLLAMYCNG------NKDGSLQCPSCKTIYG-------------------------------------------------------------------

1z6uA

0.21

0.09

2.88

1.56

CNFpred

--------SFMCVCCQELVY----------------------------------QPVTTECFHNVCKDCLQRSFKA----------QVFSCPACRHDLGQNY------IMIPNEILQTLLDLFFPGYSKGR-----------------------------------

7bbdB

0.26

0.12

3.72

1.27

HHsearch

MASTMMWEEVTCPICLDPF----------------------------------VEPVSIECGHSFCQECISQVGK----------GGGSVCPVCRQRFLLKN------L-RPNRQLANMVNNLKEISQE-------------------------------------

5vzvA

0.25

0.11

3.55

0.72

CEthreader

--------VLECGVCEDVF-----------------------------SLQGDKVPRLLLCGHTVCHDCLTRLPL---------HGRAIRCPFDRQVTDLGDS-GVWGLKKNFALLELLERLQN------------------------------------------

4k7dA

0.08

3.10

0.65

EigenThreader

VLIPNRMSGECQSPDCPGTRAHPTSDKDTSVALNLITN--NSRSIPCIACTDVRNPVLFQCRHVICLDCFHLYCVTRLNDRQFQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQAEECVLQMLGCGFDCKEAYHEGECDRVDPRCNVPQPQCKLCGCEWNR

5vzvA

0.25

0.11

3.54

0.88

FFAS-3D

---------------------------------------LECGVCEDVFSQGDKVPRLLLCGHTVCHDCLTRLPLH---------GRAIRCPFDRQVTDLGD-SGVWGLKKN-FALLELLERLQN-----------------------------------------

5o6cA1

0.18

0.14

4.51

1.45

SPARKS-K

ATSLKQDADDMCMICFTEALSAAPA-------------------------------IQLDCSHIFHLQCCRRVLENRWLGPRITFG-FISCPICKNKIN------HIVLKDLLDPIKELYEDVRRKALMEYEGLHKSEAITTPGVRFYNDPAGYAMNRYAYYVCYK

3fl2A

0.19

0.08

2.72

1.50

CNFpred

--------TFQCICCQELV----------------------------------FRPITTVCQHNVCKDCLDRSFRA----------QVFSCPACRYDLGRSY------AMQVNQPLQTVLNQLFPGYGNGR-----------------------------------

6f0kC

0.05

0.04

1.73

0.83

DEthreader

VNFVFWV--G------GHAGTLISAILFLFRQ-----RWR----------TSINRAE---IVVFWYVGLIPDLATLRDRLMG-----GFF------ALGWCGANHWRNYVYLLGLATPLVLSVHSVSFDFRITITLHDYFVP---TWVDVLTLGSGLFFTLFLLLR

5vzvA

0.25

0.11

3.55

0.76

MapAlign

--------VLECGVCEDVF-----------------------------SLQGDKVPRLLLCGHTVCHDCLTRLPLH---------GRAIRCPFDRQVTDLG-DSGVWGLKKNFALLELLERLQ-------------------------------------------

(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	0.6005

(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	6f0kC	0.49	4.53	0.043	0.747	model1_6f0kC.pdb.gz
2	1dgkN	0.47	5.31	0.072	0.831	model1_1dgkN.pdb.gz
3	2uvcG	0.46	5.21	0.052	0.783	model1_2uvcG.pdb.gz
4	5nd1B	0.45	4.94	0.063	0.747	model1_5nd1B.pdb.gz
5	3hmjG	0.45	5.19	0.065	0.789	model1_3hmjG.pdb.gz
6	1m1cA	0.45	5.25	0.074	0.789	model1_1m1cA.pdb.gz
7	2dcuA	0.39	5.37	0.053	0.693	model1_2dcuA.pdb.gz
8	2c2nA	0.38	5.92	0.065	0.729	model1_2c2nA.pdb.gz
9	1hkgA	0.36	5.04	0.022	0.608	model1_1hkgA.pdb.gz
10	3b8aX1	0.33	5.60	0.024	0.602	model1_3b8aX1.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:1901363	0.76	heterocyclic compound binding
GO:0097159	0.76	organic cyclic compound binding
GO:0003824	0.76	catalytic activity
GO:0016740	0.75	transferase activity
GO:0004842	0.74	ubiquitin-protein transferase activity
GO:0003676	0.71	nucleic acid binding
GO:0003723	0.69	RNA binding
GO:0035198	0.57	miRNA 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:0009987	0.87	cellular process
GO:0065007	0.86	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0050794	0.84	regulation of cellular process
GO:0044699	0.82	single-organism process
GO:0032502	0.79	developmental process
GO:0044767	0.77	single-organism developmental process
GO:0008152	0.70	metabolic process
GO:0071704	0.68	organic substance metabolic process
GO:0048519	0.68	negative regulation of biological process
GO:0019222	0.68	regulation of metabolic process
GO:0048523	0.67	negative regulation of cellular process
GO:0044238	0.67	primary metabolic process
GO:0044237	0.67	cellular metabolic process
GO:0043170	0.67	macromolecule metabolic process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0044260	0.66	cellular macromolecule metabolic process
GO:0009892	0.64	negative regulation of metabolic process
GO:0080090	0.63	regulation of primary metabolic process
GO:0060255	0.63	regulation of macromolecule metabolic process
GO:0034641	0.63	cellular nitrogen compound metabolic process
GO:0031324	0.63	negative regulation of cellular metabolic process
GO:0048856	0.62	anatomical structure development
GO:0016070	0.61	RNA metabolic process
GO:0032268	0.60	regulation of cellular protein metabolic process
GO:0019538	0.59	protein metabolic process
GO:0007165	0.59	signal transduction
GO:0051171	0.58	regulation of nitrogen compound metabolic process
GO:0044267	0.58	cellular protein metabolic process
GO:0032269	0.58	negative regulation of cellular protein metabolic process
GO:2000112	0.57	regulation of cellular macromolecule biosynthetic process
GO:0010468	0.57	regulation of gene expression
GO:0006464	0.57	cellular protein modification process
GO:0016567	0.56	protein ubiquitination
GO:0006417	0.56	regulation of translation
GO:1903047	0.55	mitotic cell cycle process
GO:0060964	0.55	regulation of gene silencing by miRNA
GO:0034660	0.55	ncRNA metabolic process
GO:0010629	0.55	negative regulation of gene expression
GO:2000177	0.54	regulation of neural precursor cell proliferation
GO:0072089	0.54	stem cell proliferation
GO:0051865	0.54	protein autoubiquitination
GO:0035278	0.54	miRNA mediated inhibition of translation
GO:0021915	0.54	neural tube development
GO:0010586	0.54	miRNA metabolic process
GO:0008543	0.54	fibroblast growth factor receptor signaling pathway
GO:0000082	0.54	G1/S 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:0043226	0.86	organelle
GO:0043229	0.85	intracellular organelle
GO:0032991	0.85	macromolecular complex
GO:0043232	0.81	intracellular non-membrane-bounded organelle
GO:0044444	0.77	cytoplasmic part
GO:0030529	0.67	intracellular ribonucleoprotein complex
GO:0036464	0.63	cytoplasmic ribonucleoprotein granule
GO:0000932	0.62	cytoplasmic mRNA processing body

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	0.060	3ikmC	0.371	5.57	0.065	0.693	2.7.7.7	NA
2	0.060	1bqgA	0.289	5.83	0.033	0.548	4.2.1.40	NA
3	0.060	3czoB	0.363	5.52	0.013	0.669	4.3.1.3	NA
4	0.060	1galA	0.423	5.65	0.047	0.801	1.1.3.4	28
5	0.060	1qhaA	0.480	5.25	0.060	0.831	2.7.1.1	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	0.04	1ntzC	0.400	5.01	0.074	0.693	0.18	HEM	complex1.pdb.gz	25,37,38,43,46
2	0.03	1l0lC	0.433	4.89	0.067	0.759	0.13	FMX	complex2.pdb.gz	51,52,53,54,66,67,106
3	0.03	1qhaB	0.482	5.26	0.054	0.831	0.16	ANP	complex3.pdb.gz	47,66,67,70
4	0.03	3h1iC	0.436	4.90	0.047	0.771	0.20	HEM	complex4.pdb.gz	51,54,70,71,107
5	0.01	1be3C	0.433	5.00	0.053	0.765	0.11	HEM	complex5.pdb.gz	39,40,46,68
6	0.01	3bccC	0.359	5.42	0.046	0.681	0.11	SIG	complex6.pdb.gz	99,101,105,109
7	0.01	3h1jP	0.438	5.06	0.068	0.771	0.17	SMA	complex7.pdb.gz	69,91,94,106
8	0.01	1ntkC	0.400	5.27	0.066	0.717	0.12	AY1	complex8.pdb.gz	16,23,51
9	0.01	3l75C	0.374	5.76	0.043	0.717	0.22	HEM	complex9.pdb.gz	20,23,24,26,52
10	0.01	3l73C	0.370	5.80	0.035	0.711	0.20	HEM	complex10.pdb.gz	42,44,50,51

	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.