D-I-TASSER P22301-D1

D-I-TASSER results for P22301-D1

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

Input Sequence in FASTA format

>P22301 (178 residues)
MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQ
LDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLR
LRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN
Prediction	CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCSSCCHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHCHHHHHHHHHHHHHHHHHHCHHCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence	9721899999999986311344555578865456753367999999999999874113764322046367875267764269999999999997223234575501124579999999999999715124788734899999999996140256787888999999999999976339
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN
Prediction	4513010200001100322434534467524434440343043035104403631466251333024651264045442020132005110540044145744633540540352054036304503631617544531530352055257420220121221003104510444478
	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                 100                 120                 140                 160

                   |                   |                   |                   |                   |                   |                   |                   |

SS
Seq

CCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCSSCCHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHCHHHHHHHHHHHHHHHHHHCHHCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
MHSSALLCCLVLLTGVRASPGQGTQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN

4dohA

0.24

0.20

6.12

1.17

DEthreader

--------------A--L---K-TLN-GSCVIA---T--NLQEIRNGFSEIRGSVQAKDGNIIRILRRTESLQDTKPNRCCLLRHLLRLYLDRVFKNY-QTPHYTLRKISSLANSFLTIKKDLRLCHMTCHCGEAMKKYSQILSHFEKLEQAAVVKALGELDILLQWMEET--E----

4dohA

0.28

0.23

7.04

1.67

SPARKS-K

--------------------ALKTLNLGSC-----VIATNLQEIRNGFSEIRGSVQAKDNIDIRILRRTSLQDTKPANRCCLLRHLLRLYLDRVFKNYQTPDHYTLRKISSLANSFLTIKKDLRLCHATCHCEEAMKKYSQILSHFEKLPQAAVVKALGELDILLQWMEETE------

1n1fA

0.18

0.15

4.75

1.21

MapAlign

-----------------------------LRRC---LISTMHHIEESFQEIKRAIQAKDTFNVTILSTLELQIIKPLDVCCVTKNLLAFYVDRVFKDHQEPNPKILRKISSIANSFLYMQKTLRQCQQCHCRQEATNATRVIHDNYDQLVHAAAIKSLGELDVFLAWINKNHEVMS--

1n1fA

0.17

0.15

4.79

1.00

CEthreader

-----------------------NHGLRRCL-----ISTDMHHIEESFQEIKRAIQAKDTFNVTILSLETLQIIKPLDVCCVTKNLLAFYVDRVFKDHQEPNPKILRKISSIANSFLYMQKTLRQCQQCHCRQEATNATRVIHDNYDQLVHAAAIKSLGELDVFLAWINKNHEVMSSA

2ilkA

1.00

0.87

24.38

1.95

MUSTER

-----------------------TQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN

2ilkA

1.00

0.87

24.38

4.56

HHsearch

-----------------------TQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN

2ilkA

1.00

0.87

24.38

2.10

FFAS-3D

-----------------------TQSENSCTHFPGNLPNMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCENKSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMKIRN

1n1fA

0.17

0.14

4.62

1.20

EigenThreader

--------------------------NHGLRRCLIST--DMHHIEESFQEIKRAIQAKDTFPNVTILSTLETIIKPLDVCCVTKNLLAFYVDRVFKDHQEPNPKILRKISSIANSFLYMQKTLRQCQQCHCRQEATNATRVIHDNYDQLVHAAAIKSLGELDVFLAWINKNH---EVM

1lk3A

1.00

0.76

21.39

1.35

CNFpred

--------------------------------------NMLRDLRDAFSRVKTFFQMKDQLDNLLLKESLLEDFKGYLGCQALSEMIQFYLEEVMPQAENQDPDIKAHVNSLGENLKTLRLRLRRCHRFLPCE-KSKAVEQVKNAFNKLQEKGIYKAMSEFDIFINYIEAYMTMK---

1n1fA

0.17

0.13

4.46

1.17

DEthreader

-------------------------NHGLRRCLI-ST-D-MHHIEESFQEIKRAIQAKDTFPVTILSTLETLQIIKLDVCCVTKNLLAFYVDRVFKDHQEPNPKILRKISSIANSFLYMQKTLRQCQQ-CHCRQATNATRVIHDNYDQLEHAAAIKSLGELDVFLAWINKNHEV----

(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	0.7539

(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	4dohA	0.76	1.77	0.247	0.820	model1_4dohA.pdb.gz
2	1n1fA	0.74	2.02	0.161	0.815	model1_1n1fA.pdb.gz
3	6df3C	0.74	2.01	0.199	0.820	model1_6df3C.pdb.gz
4	1m4rA	0.67	2.43	0.179	0.786	model1_1m4rA.pdb.gz
5	3oq3A	0.66	2.95	0.096	0.820	model1_3oq3A.pdb.gz
6	3pivA	0.65	2.79	0.085	0.798	model1_3pivA.pdb.gz
7	1wu3I	0.65	3.16	0.088	0.826	model1_1wu3I.pdb.gz
8	3hhcB	0.63	3.31	0.130	0.820	model1_3hhcB.pdb.gz
9	4o6kA	0.63	2.58	0.129	0.742	model1_4o6kA.pdb.gz
10	1itfA	0.63	3.02	0.096	0.798	model1_1itfA.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:0005102	0.97	receptor binding
GO:0005125	0.87	cytokine activity
GO:0005126	0.66	cytokine receptor binding
GO:0070851	0.51	growth factor receptor binding
GO:0005141	0.50	interleukin-10 receptor 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:0065007	1.00	biological regulation
GO:0050789	1.00	regulation of biological process
GO:0050794	0.96	regulation of cellular process
GO:0050896	0.90	response to stimulus
GO:0048518	0.90	positive regulation of biological process
GO:0048583	0.89	regulation of response to stimulus
GO:0048522	0.89	positive regulation of cellular process
GO:0006954	0.87	inflammatory response
GO:0051239	0.77	regulation of multicellular organismal process
GO:0048519	0.76	negative regulation of biological process
GO:0001817	0.74	regulation of cytokine production
GO:0051241	0.73	negative regulation of multicellular organismal process
GO:0009987	0.72	cellular process
GO:0001818	0.72	negative regulation of cytokine production
GO:0048523	0.69	negative regulation of cellular process
GO:0032715	0.68	negative regulation of interleukin-6 production
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:0051246	0.65	regulation of protein metabolic process
GO:0051240	0.64	positive regulation of multicellular organismal process
GO:0032879	0.64	regulation of localization
GO:0031325	0.64	positive regulation of cellular metabolic process
GO:0010604	0.64	positive regulation of macromolecule metabolic process
GO:0008152	0.64	metabolic process
GO:0071704	0.63	organic substance metabolic process
GO:0051171	0.63	regulation of nitrogen compound metabolic process
GO:0050707	0.63	regulation of cytokine secretion
GO:0044237	0.63	cellular metabolic process
GO:0042981	0.63	regulation of apoptotic process
GO:0032268	0.63	regulation of cellular protein metabolic process
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0010556	0.63	regulation of macromolecule biosynthetic process
GO:0010033	0.63	response to organic substance
GO:0051248	0.62	negative regulation of protein metabolic process
GO:0051173	0.62	positive regulation of nitrogen compound metabolic process
GO:0050710	0.62	negative regulation of cytokine secretion
GO:0043207	0.62	response to external biotic stimulus
GO:0043170	0.62	macromolecule metabolic process
GO:0033993	0.62	response to lipid
GO:0031328	0.62	positive regulation of cellular biosynthetic process
GO:0031324	0.62	negative regulation of cellular metabolic process
GO:0010557	0.62	positive regulation of macromolecule biosynthetic process
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0002682	0.62	regulation of immune system process
GO:0001819	0.62	positive regulation of cytokine production
GO:1901576	0.61	organic substance biosynthetic process
GO:0065009	0.61	regulation of molecular function
GO:0050776	0.61	regulation of immune response
GO:0048585	0.61	negative regulation of response to stimulus
GO:0045893	0.61	positive regulation of transcription, DNA-templated
GO:0044260	0.61	cellular macromolecule metabolic process
GO:0042127	0.61	regulation of cell proliferation
GO:0014070	0.61	response to organic cyclic compound
GO:0009719	0.61	response to endogenous stimulus
GO:0002683	0.61	negative regulation of immune system process
GO:0051384	0.60	response to glucocorticoid
GO:0051249	0.60	regulation of lymphocyte activation
GO:0050777	0.60	negative regulation of immune response
GO:0050715	0.60	positive regulation of cytokine secretion
GO:0045861	0.60	negative regulation of proteolysis
GO:0044093	0.60	positive regulation of molecular function
GO:0043065	0.60	positive regulation of apoptotic process
GO:0009059	0.60	macromolecule biosynthetic process
GO:0008285	0.60	negative regulation of cell proliferation
GO:0002697	0.60	regulation of immune effector process
GO:0002237	0.60	response to molecule of bacterial origin
GO:0051091	0.59	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0051045	0.59	negative regulation of membrane protein ectodomain proteolysis
GO:0032800	0.59	receptor biosynthetic process
GO:0030889	0.59	negative regulation of B cell proliferation
GO:0002904	0.59	positive regulation of B cell apoptotic process
GO:0002740	0.59	negative regulation of cytokine secretion involved in immune response
GO:0048584	0.53	positive regulation of response to stimulus
GO:0009966	0.53	regulation of signal transduction
GO:0002376	0.53	immune system process
GO:1902533	0.52	positive regulation of intracellular signal transduction
GO:0046427	0.51	positive regulation of JAK-STAT cascade
GO:0006955	0.51	immune response

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:0005615	1.00	extracellular space
GO:0044464	0.60	cell part

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	1jqoA	0.493	4.99	0.055	0.803	4.1.1.31	NA
2	0.060	1jtnA	0.250	6.07	0.028	0.466	3.2.1.17	NA
3	0.060	3no6A	0.494	4.51	0.090	0.764	3.5.99.2	163
4	0.060	3ee4A	0.595	4.21	0.046	0.809	1.17.4.1	NA
5	0.060	3d4sA	0.493	4.12	0.059	0.714	3.2.1.17	157

	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	0.03	1m4r0	0.669	2.43	0.179	0.786	0.38	III	complex1.pdb.gz	43,49,52
2	0.01	1xvgB	0.584	4.10	0.052	0.798	0.36	BRJ	complex2.pdb.gz	106,109,110,113
3	0.01	1azs3	0.240	3.75	0.033	0.326	0.26	III	complex3.pdb.gz	104,106,109,110,112,113,114,116,117,120,121
4	0.01	1azs1	0.240	3.75	0.033	0.326	0.34	III	complex4.pdb.gz	110,111,113,117,121
5	0.01	2avu2	0.223	3.71	0.048	0.309	0.39	III	complex5.pdb.gz	90,94,101,111,112,113,114
6	0.01	3ee4A	0.595	4.21	0.046	0.809	0.27	UUU	complex6.pdb.gz	44,47,98,101,113
7	0.01	3dhi0	0.572	4.31	0.069	0.815	0.13	III	complex7.pdb.gz	113,115,155,158,159,162
8	0.01	1xvgA	0.583	4.11	0.052	0.798	0.27	BRJ	complex8.pdb.gz	152,155,156,159,160

	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.