D-I-TASSER P09603-D3

D-I-TASSER results for P09603-D3

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

Input Sequence in FASTA format

>P09603 (71 residues)
QSEGSFSPQLQESVFHLLVPSVILVLLAVGGLLFYRWRRRSHQEPQRADSPLEQPEGSPL
TQDDRQVELPV

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| QSEGSFSPQLQESVFHLLVPSVILVLLAVGGLLFYRWRRRSHQEPQRADSPLEQPEGSPLTQDDRQVELPV
Prediction	CCCCCCCCCCCCSSSSSSHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCSCCCCC
Confidence	99899998898335533155799999985221111244563138655678666889998886553103799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| QSEGSFSPQLQESVFHLLVPSVILVLLAVGGLLFYRWRRRSHQEPQRADSPLEQPEGSPLTQDDRQVELPV
Prediction	88665564524320233333332233233211211334445465354364426437755146755536258
	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

                   |                   |                   |

SS
Seq

CCCCCCCCCCCCSSSSSSHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCSCCCCC
QSEGSFSPQLQESVFHLLVPSVILVLLAVGGLLFYRWRRRSHQEPQRADSPLEQPEGSPLTQDDRQVELPV

3vemA

0.01

1.35

1.33

DEthreader

NDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEHNTRTTKIE--KDKNLVIN

3jacA

0.05

0.04

2.07

0.54

CEthreader

-----GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

6m97A

0.06

2.52

0.47

EigenThreader

VIEAAQVKDALTKMRAAALDAQKALLQTVLHVIQVVVSYFLMLVFMTYNAYLCMAVAAGAGLGYFLFSWKK

2m20A

0.22

0.17

5.34

0.48

FFAS-3D

-----------PSIATGLVGALLLLLVVALGIGLFIRRRHIVRKRTLRRLLQERELVEPLTPSGEK-----

6efnA1

0.14

4.79

0.82

SPARKS-K

-PELAVHLQPHGAVMIDLSGRGAQLAFLLSKNTARIWEIMKKEEMSADQLKSAHPFTEAWTEGLLDQPLHV

3k07A

0.06

0.03

1.20

0.55

CNFpred

-------------IMSLGGIAIAVGAMVDAAIVMIENAHKRLEE---------------------------

6h9lA

0.07

2.87

1.33

DEthreader

KIEALRKATKEDIEDLREATKEDIEALRKATKEDIEALREDIEALRKATKEEKLEAELKSYV-DA-RVIES

3l72R

0.06

2.52

0.92

MapAlign

DVMDATTSSQTSSEDRKGFSYLVTATACVATAYAAKNVVTCVPIANSGDFGGYYCPCHGSHYDASGRIRKG

2kluA

0.21

0.20

6.25

0.96

MUSTER

---GPLVP--RGSMALIVLGGVAGLLLFIGLGIFFSVRSRHRRRQAERMSQIKRLLSEKKTQSPHRFQKPI

2m20A

0.20

0.17

5.39

0.92

HHsearch

---------KIPSIATGLVGALLLLLVVALGIGLFIRRRHIVRKRTLRRLLQERELVEPLTPSEKLWS---

(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	0.5772

(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	4e40A	0.68	2.99	0.015	0.958	model1_4e40A.pdb.gz
2	3i9wA	0.67	3.05	0.119	0.944	model1_3i9wA.pdb.gz
3	2j69A1	0.67	3.16	0.087	0.944	model1_2j69A1.pdb.gz
4	1st6A	0.67	2.68	0.058	0.915	model1_1st6A.pdb.gz
5	6z9lA	0.67	3.15	0.090	0.930	model1_6z9lA.pdb.gz
6	3u0cA	0.66	2.74	0.047	0.901	model1_3u0cA.pdb.gz
7	6jfkA	0.66	2.47	0.094	0.901	model1_6jfkA.pdb.gz
8	5fwlE	0.66	2.67	0.062	0.915	model1_5fwlE.pdb.gz
9	6h7wB	0.66	3.03	0.061	0.930	model1_6h7wB.pdb.gz
10	2d4cB	0.66	2.97	0.062	0.915	model1_2d4cB.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:0042803	1.00	protein homodimerization activity
GO:0005102	0.80	receptor binding
GO:0005126	0.77	cytokine receptor binding
GO:0008083	0.76	growth factor activity
GO:0005125	0.76	cytokine activity
GO:0005157	0.75	macrophage colony-stimulating factor 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:0044767	1.00	single-organism developmental process
GO:0030316	1.00	osteoclast differentiation
GO:0008283	1.00	cell proliferation
GO:0065007	0.88	biological regulation
GO:0050789	0.87	regulation of biological process
GO:0050794	0.85	regulation of cellular process
GO:0048518	0.81	positive regulation of biological process
GO:0048522	0.80	positive regulation of cellular process
GO:0080090	0.79	regulation of primary metabolic process
GO:0060255	0.79	regulation of macromolecule metabolic process
GO:0031323	0.79	regulation of cellular metabolic process
GO:0048583	0.78	regulation of response to stimulus
GO:0032268	0.78	regulation of cellular protein metabolic process
GO:0031325	0.78	positive regulation of cellular metabolic process
GO:0019220	0.78	regulation of phosphate metabolic process
GO:0010604	0.78	positive regulation of macromolecule metabolic process
GO:0051240	0.77	positive regulation of multicellular organismal process
GO:0048584	0.77	positive regulation of response to stimulus
GO:0009966	0.77	regulation of signal transduction
GO:0007165	0.77	signal transduction
GO:0001934	0.77	positive regulation of protein phosphorylation
GO:2000026	0.76	regulation of multicellular organismal development
GO:0051094	0.76	positive regulation of developmental process
GO:0050790	0.76	regulation of catalytic activity
GO:0048856	0.76	anatomical structure development
GO:0045597	0.76	positive regulation of cell differentiation
GO:0042127	0.76	regulation of cell proliferation
GO:0032879	0.76	regulation of localization
GO:0032101	0.76	regulation of response to external stimulus
GO:0010628	0.76	positive regulation of gene expression
GO:0009967	0.76	positive regulation of signal transduction
GO:0007166	0.76	cell surface receptor signaling pathway
GO:0002684	0.76	positive regulation of immune system process
GO:1904141	0.75	positive regulation of microglial cell migration
GO:1902228	0.75	positive regulation of macrophage colony-stimulating factor signaling pathway
GO:0045860	0.75	positive regulation of protein kinase activity
GO:0045672	0.75	positive regulation of osteoclast differentiation
GO:0045657	0.75	positive regulation of monocyte differentiation
GO:0045651	0.75	positive regulation of macrophage differentiation
GO:0032946	0.75	positive regulation of mononuclear cell proliferation
GO:0010759	0.75	positive regulation of macrophage chemotaxis
GO:0010744	0.75	positive regulation of macrophage derived foam cell differentiation
GO:0007169	0.75	transmembrane receptor protein tyrosine kinase signaling pathway
GO:0003006	0.75	developmental process involved in reproduction
GO:0001954	0.75	positive regulation of cell-matrix adhesion
GO:0030225	0.69	macrophage differentiation
GO:0009653	0.58	anatomical structure morphogenesis
GO:0044707	0.57	single-multicellular organism 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:0005615	1.00	extracellular space
GO:0044464	0.91	cell part
GO:0044424	0.87	intracellular part
GO:0044444	0.82	cytoplasmic part
GO:0043227	0.80	membrane-bounded organelle
GO:0032991	0.79	macromolecular complex
GO:0043234	0.78	protein complex
GO:1990682	0.75	CSF1-CSF1R complex
GO:0070062	0.75	extracellular exosome
GO:0048471	0.75	perinuclear region of cytoplasm
GO:0016020	0.54	membrane

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	0.067	2h8nA	0.549	2.21	0.048	0.690	3.5.1.98	NA
2	0.067	3e7kH	0.539	1.96	0.077	0.662	2.7.11.1	NA
3	0.067	1wt6B	0.565	2.31	0.089	0.690	2.7.11.1	NA
4	0.060	1q5nA	0.586	2.70	0.088	0.887	5.5.1.2	NA
5	0.060	1i0aA	0.584	2.83	0.101	0.901	4.3.2.1	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:

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	0.03	1ujw1	0.630	3.18	0.132	0.944	0.69	III	complex1.pdb.gz	33,37,39,40,59,60,68,69

	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.