D-I-TASSER P49789-D1

D-I-TASSER results for P49789-D1

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

Input Sequence in FASTA format

>P49789 (147 residues)
MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQ
TTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGDFHRNDSIYEELQKH
DKEDFPASWRSEEEMAAEAAALRVYFQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGDFHRNDSIYEELQKHDKEDFPASWRSEEEMAAEAAALRVYFQ
Prediction	CCCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCSSSSCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCCSSSSSSSCCCCCCCCCCCHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence	998226652465359986798999976888999729996634069923499999999999999999999998599926999707745483015589998468789876653145654021166777541489999999999999829
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGDFHRNDSIYEELQKHDKEDFPASWRSEEEMAAEAAALRVYFQ
Prediction	871421624355122002343000002232314100000034315424704460043024004301410464170631100112354040303021000001354244534513551475346425532543631462055027438
	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

CCCCCCCCCCCCCSSSSSCCCSSSSSCCCCCCCCCSSSSCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCSSSSSSCCCCCCCCCCSSSSSSSCCCCCCCCCCCHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHC
MSFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGDFHRNDSIYEELQKHDKEDFPASWRSEEEMAAEAAALRVYFQ

2fitA

0.98

0.85

23.83

1.33

DEthreader

S-FRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFS-QDGPEAGQTVKHVHVHVLPRKAGD--FH--------------FPASWRSEEE-AAEAAALRVYFQ

2fitA

0.99

0.86

24.20

2.09

SPARKS-K

-SFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFS-QDGPEAGQTVKHVHVHVLPRKAGDFHF----------------PASWRSEEE-AAEAAALRVYFQ

1emsA

0.46

0.39

11.32

1.05

MapAlign

GGLKFARFNIPADHIFYSTPHSFVFVNLKPVTDGHVLVSPKRVVPRLTDLTDAETADLFIVAKKVQAMLEKHHNVTSTTICVQDGKDAGQTVPHVHIHILPRR---------------------AGDFPRSNEQMAEEAVVYRNLM-

1emsA2

0.48

0.41

11.87

0.87

CEthreader

GGLKFARFNIPADHIFYSTPHSFVFVNLKPVTDGHVLVSPKRVVPRLTDLTDAETADLFIVAKKVQAMLEKHHNVTSTTICVQDGKDAGQTVPHVHIHILPRRAGD---------------------FPRSNEQMAEEAVVYRNLM-

2fitA

0.98

0.86

24.01

2.09

MUSTER

-SFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSQ-DGPEAGQTVKHVHVHVLPRKAGDFHF----------------PASWRSEEE-AAEAAALRVYFQ

2fitA

0.98

0.85

23.83

2.13

HHsearch

-SFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFS-QDGPEAGQTVKHVHVHVLPRKAGDFHFPA----------------SWRSEEE-AAEAAALRVYFQ

2fitA

0.93

0.81

22.73

2.12

FFAS-3D

-SFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTF-SQDGPEAGQTVKHVHVHVLPRKAGDFHFP-----------------ASWRSEEEAAEAAALRVYFQ

1emsA2

0.47

0.40

11.69

1.00

EigenThreader

ETGGLKRFNIPADHIFYSTPHSFVFVNLKPVTDGHVLVSPKRVVPRLTDLTDAETADLFIVAKKVQAMLEKHHNVTSTTICVQDGKDAGQTVPHVHIHILPRRAGD---------------------FPRSNEQMAEEAVVYRNLM-

1fhiA

1.00

0.85

23.81

1.49

CNFpred

-SFRFGQHLIKPSVVFLKTELSFALVNRKPVVPGHVLVCPLRPVERFHDLRPDEVADLFQTTQRVGTVVEKHFHGTSLTFSMQDGPEAGQTVKHVHVHVLPRKAGD---------------------SWRSEEEMAAEAAALRVYFQ

1emsA2

0.48

0.41

11.87

1.33

DEthreader

GGLKFARFNIPADHIFYSTPHSFVFVNLKPVTDGHVLVSPKRVVPRLTDLTDAETADLFIVAKKVQAMLEKHHNVTSTTICVQDGKDAGQTVPHVHIHILPRRAGD------F---------------PRSNEQMAEEAVVYRNLM-

(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	0.8504

(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	2fitA	0.85	0.77	0.992	0.871	model1_2fitA.pdb.gz
2	1emsA2	0.83	0.70	0.488	0.850	model1_1emsA2.pdb.gz
3	5cs2A	0.83	0.82	0.368	0.850	model1_5cs2A.pdb.gz
4	3lb5C	0.77	1.72	0.225	0.857	model1_3lb5C.pdb.gz
5	3anoA	0.76	2.10	0.269	0.850	model1_3anoA.pdb.gz
6	2eo4A	0.75	2.43	0.224	0.857	model1_2eo4A.pdb.gz
7	3o0mA	0.73	2.11	0.254	0.844	model1_3o0mA.pdb.gz
8	3p0tA	0.71	2.43	0.205	0.850	model1_3p0tA.pdb.gz
9	3i4sA	0.71	2.70	0.206	0.871	model1_3i4sA.pdb.gz
10	3nrdA	0.69	2.72	0.206	0.844	model1_3nrdA.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	0.93	catalytic activity
GO:0016787	0.90	hydrolase activity
GO:0016817	0.84	hydrolase activity, acting on acid anhydrides
GO:0016462	0.74	pyrophosphatase activity
GO:0004551	0.69	nucleotide diphosphatase activity
GO:0047710	0.64	bis(5'-adenosyl)-triphosphatase 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:0006139	1.00	nucleobase-containing compound metabolic process
GO:0044699	0.90	single-organism process
GO:0044763	0.88	single-organism cellular process
GO:0044281	0.87	small molecule metabolic process
GO:0055086	0.86	nucleobase-containing small molecule metabolic process
GO:1901564	0.78	organonitrogen compound metabolic process
GO:0065007	0.76	biological regulation
GO:0050789	0.75	regulation of biological process
GO:0006796	0.75	phosphate-containing compound metabolic process
GO:0050794	0.74	regulation of cellular process
GO:0009117	0.74	nucleotide metabolic process
GO:0072521	0.71	purine-containing compound metabolic process
GO:0080090	0.67	regulation of primary metabolic process
GO:0060255	0.67	regulation of macromolecule metabolic process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0048519	0.66	negative regulation of biological process
GO:0048523	0.65	negative regulation of cellular process
GO:0006163	0.65	purine nucleotide metabolic process
GO:0032268	0.64	regulation of cellular protein metabolic process
GO:0031324	0.63	negative regulation of cellular metabolic process
GO:0010605	0.63	negative regulation of macromolecule metabolic process
GO:0007165	0.63	signal transduction
GO:1903050	0.62	regulation of proteolysis involved in cellular protein catabolic process
GO:0097193	0.62	intrinsic apoptotic signaling pathway
GO:0072331	0.62	signal transduction by p53 class mediator
GO:0045861	0.62	negative regulation of proteolysis
GO:0072332	0.61	intrinsic apoptotic signaling pathway by p53 class mediator
GO:0032435	0.61	negative regulation of proteasomal ubiquitin-dependent protein catabolic process

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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0005829	0.82	cytosol
GO:0043226	0.80	organelle
GO:0043227	0.79	membrane-bounded organelle
GO:0043229	0.56	intracellular organelle
GO:0043231	0.53	intracellular membrane-bounded organelle
GO:0005737	0.53	cytoplasm

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	0.214	2fitA	0.865	0.76	0.992	0.884	3.6.1.29	NA
2	0.060	1rqiA	0.491	4.65	0.043	0.809	2.5.1.10	NA
3	0.060	1z5oA	0.476	4.84	0.071	0.823	3.2.2.9	61,74
4	0.060	2j1pB	0.497	4.61	0.059	0.816	2.5.1.1 2.5.1.10 2.5.1.29	107
5	0.060	1de5A	0.463	4.36	0.051	0.714	5.3.1.14	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	0.90	5fitA	0.842	0.62	1.000	0.857	1.57	AP2	complex1.pdb.gz	8,25,26,27,28,29,35,37,83,89,91,92,96,98
2	0.50	4fit0	0.840	0.67	1.000	0.857	2.00	III	complex2.pdb.gz	46,47,48,50,52,55,56,59,60,63,67,70,76,77,78,79,80,81,82,84,85,86,87,88,102,103,104
3	0.29	3oj7A	0.589	2.56	0.243	0.701	1.24	SO4	complex3.pdb.gz	83,89,90,91,96,98
4	0.25	3l7xA	0.647	2.41	0.216	0.742	0.90	NA	complex4.pdb.gz	85,90,94,96

	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.