D-I-TASSER O75534-D3

D-I-TASSER results for O75534-D3

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

Input Sequence in FASTA format

>O75534 (83 residues)
FEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGD
HVRFNISTDRRDKLERATNIEVL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| FEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVL
Prediction	CCCCCCCSSSSSSSSSCCCCCCCCCCCCCCCSSSSSCCCCSSSCCCCCCCCCCSSSSCCCSSSSSSSSCCCCCCSSSSSSSSC
Confidence	97555506889998660378776668888957999549943841554455685131048299999863256762443577869
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| FEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVL
Prediction	76635663143303421553466457542323031427664414134525636131344430403032354653531350536
	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 AttentionPotential. 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

CCCCCCCSSSSSSSSSCCCCCCCCCCCCCCCSSSSSCCCCSSSCCCCCCCCCCSSSSCCCSSSSSSSSCCCCCCSSSSSSSSC
FEDISIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLLEGDHVRFNISTDRRDKLERATNIEVL

6y6mA2

0.31

0.29

8.73

1.17

DEthreader

EVVLSEERVTGTVTTELRTLNS---SET-TGRISYENGECFFLPYTDDV-EGNVNLRAGDKVSFQIATNQR-GNLGACHIRLE

6y6eA1

0.48

0.43

12.61

2.22

SPARKS-K

--AVDSTVYKGQVLKSLDR------NDPLPGRIRYRDYSEVEVPFGDKDQKGDFTLRHGDWVQFLLATDRRDQLQRATSIALL

6y6eA

0.29

0.28

8.43

0.63

MapAlign

FETLVASNIEGCVTREAP-KSIKSQDRVEGGVITYE-HVKKTIMYFLKDC--EKPPRIGERVRFDIYMVKRNKECIAVNVQQV

5ytsA

0.17

0.14

4.76

0.54

CEthreader

-KKVIATKVLGTVKWFNV--------RNGYGFINRNDT-KEDVFVHQTAIKYLRSVGDGETVEFDVVEGE--KGAEAANVTGP

2ytvA

0.24

0.20

6.40

1.22

MUSTER

GSSGSSGLRRATVEC-----------KDQFGFINYEVGDSKKLFFHVKEVQDGIELQAGDEVEFSVILNQRTGKCSACNVWRV

3i2zA

0.23

0.19

6.05

1.47

HHsearch

---SHMSKIKGNVKWF--------NESKGFGFITPEDSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAK-G-PSAANVTAL

6y6eA1

0.49

0.43

12.60

1.45

FFAS-3D

---VDSTVYKGQVLKSLDR------NDPLPGRIRYRAYSEVEVPFGDKDQKGDFTLRHGDWVQFLLATDRRDQLQRATSIALL

3kf8A

0.07

2.95

0.62

EigenThreader

PNLLRHINIFGKIVEQYKEKEFNGVEESYVILVISDGIDSKIRVRLSQEQFKEVGLTLDKIVELEYNWYDSINVRELKVTVLS

6y6eA

0.47

0.42

12.29

1.49

CNFpred

--AVDSTVYKGQVLKSLDRN------DPLPGRIRYRAYSEVEVPFGDKDQKGDFTLRHGDWVQFLLATDRRDQLQRATSIALL

6y6mA

0.31

0.29

8.73

1.17

DEthreader

EVVLSEERVTGTVTTELRTLNS---SET-TGRISYENGECFFLPYTDDV-EGNVNLRAGDKVSFQIATNQR-GNLGACHIRLE

(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	0.7747

(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 AttentionPotential, 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	6y6eA	0.83	1.63	0.291	0.952	model1_6y6eA.pdb.gz
2	6y6mA	0.75	2.41	0.300	0.964	model1_6y6mA.pdb.gz
3	5ytsA	0.74	1.50	0.155	0.855	model1_5ytsA.pdb.gz
4	3aqqA	0.74	1.71	0.123	0.879	model1_3aqqA.pdb.gz
5	1wfqA	0.70	1.80	0.222	0.819	model1_1wfqA.pdb.gz
6	2lssA	0.70	1.52	0.191	0.819	model1_2lssA.pdb.gz
7	1mjcA	0.69	1.88	0.239	0.807	model1_1mjcA.pdb.gz
8	3trzA	0.68	2.02	0.143	0.843	model1_3trzA.pdb.gz
9	2ytvA	0.67	2.35	0.247	0.807	model1_2ytvA.pdb.gz
10	4qqbX	0.67	1.88	0.214	0.807	model1_4qqbX.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:0044822	1.00	poly(A) RNA binding
GO:0003729	0.52	mRNA binding
GO:0003730	0.50	mRNA 3'-UTR 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	1.00	cellular process
GO:0044699	0.80	single-organism process
GO:0008152	0.72	metabolic process
GO:0071704	0.70	organic substance metabolic process
GO:0044237	0.70	cellular metabolic process
GO:0044238	0.69	primary metabolic process
GO:0043170	0.68	macromolecule metabolic process
GO:0044260	0.67	cellular macromolecule metabolic process
GO:0034641	0.65	cellular nitrogen compound metabolic process
GO:0090304	0.63	nucleic acid metabolic process
GO:0065007	0.62	biological regulation
GO:0050789	0.62	regulation of biological process
GO:0016070	0.62	RNA metabolic process
GO:0050794	0.60	regulation of cellular process
GO:0060255	0.55	regulation of macromolecule metabolic process
GO:0044763	0.55	single-organism cellular process
GO:0031323	0.55	regulation of cellular metabolic process
GO:0016071	0.55	mRNA metabolic process
GO:0080090	0.54	regulation of primary metabolic process
GO:0016043	0.54	cellular component organization
GO:0010468	0.54	regulation of gene expression
GO:2000112	0.53	regulation of cellular macromolecule biosynthetic process
GO:0051171	0.53	regulation of nitrogen compound metabolic process
GO:0048519	0.53	negative regulation of biological process
GO:0048523	0.52	negative regulation of cellular process
GO:0043933	0.52	macromolecular complex subunit organization
GO:0006417	0.52	regulation of translation
GO:2000113	0.51	negative regulation of cellular macromolecule biosynthetic process
GO:0051172	0.51	negative regulation of nitrogen compound metabolic process
GO:0044265	0.51	cellular macromolecule catabolic process
GO:0034655	0.51	nucleobase-containing compound catabolic process
GO:0034622	0.51	cellular macromolecular complex assembly
GO:0032501	0.51	multicellular organismal process
GO:0032269	0.51	negative regulation of cellular protein metabolic process
GO:0010629	0.51	negative regulation of gene expression
GO:0070966	0.50	nuclear-transcribed mRNA catabolic process, no-go decay
GO:0046331	0.50	lateral inhibition
GO:0042714	0.50	dosage compensation complex assembly
GO:0019233	0.50	sensory perception of pain
GO:0017148	0.50	negative regulation of translation
GO:0009047	0.50	dosage compensation by hyperactivation of X chromosome

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:0005737	1.00	cytoplasm
GO:0044444	0.81	cytoplasmic part
GO:0043229	0.80	intracellular organelle
GO:0043227	0.78	membrane-bounded organelle
GO:0043231	0.77	intracellular membrane-bounded organelle
GO:0016020	0.75	membrane
GO:0005886	0.73	plasma membrane
GO:0005794	0.72	Golgi apparatus

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	2a1aA	0.562	2.94	0.075	0.759	2.7.11.1	27,31
2	0.060	3ej2A	0.537	2.80	0.117	0.771	3.6.1.1	NA
3	0.060	1go3E	0.615	2.37	0.200	0.783	2.7.7.6	10,63
4	0.060	2cfmA	0.565	3.56	0.049	0.868	6.5.1.1	NA
5	0.060	2id0C	0.624	2.12	0.157	0.795	3.1.13.1	26,59

	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	3pf5A	0.672	1.43	0.234	0.771	0.75	RQA	complex1.pdb.gz	31,45,50
2	0.04	2es2A	0.664	1.58	0.234	0.771	0.73	QNA	complex2.pdb.gz	14,15,32,43,45,47
3	0.04	3pf4A	0.672	1.43	0.234	0.771	0.53	NA	complex3.pdb.gz	31,32,46,48
4	0.03	2vw9A	0.630	3.25	0.076	0.952	1.08	QNA	complex4.pdb.gz	12,13,14,34,42,58,59
5	0.02	1z9f0	0.628	3.14	0.128	0.916	0.53	III	complex5.pdb.gz	10,11,12,34,35,36,38,40,41,42,43,60,69
6	0.02	1eygC	0.608	3.49	0.110	0.964	0.52	QNA	complex6.pdb.gz	5,12,13,14,15,30,31,32,34,40,41,42,43,45,58,59,61,67,69,75,77
7	0.02	1eygB	0.609	3.49	0.099	0.964	0.52	QNA	complex7.pdb.gz	12,13,14,15,32,34,36,40,42,43,44,58,59,68,70,73,74,75
8	0.01	2fmm8	0.379	3.03	0.063	0.554	0.53	III	complex8.pdb.gz	14,16,32,40,44

	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.