D-I-TASSER P08588-D3

D-I-TASSER results for P08588-D3

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

Input Sequence in FASTA format

>P08588 (90 residues)
QRLLCCARRAARRRHATHGDRPRASGCLARPGPPPSPGAASDDDDDDVVGATPPARLLEP
WAGCNGGAAADSDSSLDEPCRPGFASESKV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| QRLLCCARRAARRRHATHGDRPRASGCLARPGPPPSPGAASDDDDDDVVGATPPARLLEPWAGCNGGAAADSDSSLDEPCRPGFASESKV
Prediction	CCCSCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	950115003211112456888888888778889999876655666455678888644576667788656788777446888886531369
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| QRLLCCARRAARRRHATHGDRPRASGCLARPGPPPSPGAASDDDDDDVVGATPPARLLEPWAGCNGGAAADSDSSLDEPCRPGFASESKV
Prediction	843321244374533346452562643345644574454456464564355445342342134243444655544256545644445667
	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

                   |                   |                   |                   |

SS
Seq

CCCSCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
QRLLCCARRAARRRHATHGDRPRASGCLARPGPPPSPGAASDDDDDDVVGATPPARLLEPWAGCNGGAAADSDSSLDEPCRPGFASESKV

5xgsA2

0.07

2.80

0.64

CEthreader

VSLPLDRPQETRVLQVSCGRLVLTDREGVFSMGNNSYGQCGRKVVENEIYSESHRVHRMQDFDGQFLTDKGEVYSCGWGADGQTGLGHYN

2h8oA2

0.07

2.80

0.62

EigenThreader

GMAGGQALDLAAEKKAPDEDGIITLQAMKTGALLRFACEAGAIIAGSNRQRLRLFGEKIGLSFQLADDLLDLTLVALRGEAWAREKLQEQ

2xkyI

0.14

0.11

3.82

0.31

FFAS-3D

---LCSARDLAEKKYILSNANSFCYENEVALTSKEEEEDSENGVPESTSTDSPP----------GIDLHNQASVPLEPRPLR---RESEI

3bogA

0.11

0.09

3.20

1.27

SPARKS-K

------------------CKGADGAHGVGCPGTAGAAGSVGGPGCDGGHGGNGGCAGGVGGAGGASGGTGVGGRGGKGGSGTPKGADGAP

2egmA

0.24

0.06

1.73

0.44

CNFpred

--EAICVVCRESRSHKQHSVVPL-------------------------------------------------------------------

4nreA2

0.11

0.09

3.22

0.83

DEthreader

IFA-FSHELTHLHSHPTCSKHAVSAGQFCAWMPPPSMQLPP-PTSKGLATEGFILPPVNATCDVIL-ALWLLSK---VSI----------

2i0qA

0.05

0.04

2.18

0.74

MapAlign

--IRVHRATLRLYNGQRQFNANVFYSSSWALFSTDKRSVTQEINNQDAVSDTTPFSFSSAKILQVHELDEYTNELKLKDASGQVFYTLSL

3bogA

0.12

0.11

3.89

0.86

MUSTER

----C---KGADGAHGVGCPGT--AGAAGSVGGPGCDGGHGGNGGNGNPGCAG-GVGGAGGASGGTGVGGRGGKGGSGTPKGADGAPGAP

2g87A

0.19

0.07

2.14

0.46

HHsearch

VTTLCCGKNPLGDDEASTTV----SKT-ET--SQVAP------------------A----------------------------------

4xdzA

0.10

3.67

0.44

CEthreader

MKKGADLVFAHGFNIHFKIIEPPKDSDVYMIAPKSPGPIVRR---SYEMGGGVPALVAVYQNVSGEALQKALAIAKGIGCARAGVIESTF

(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	0.5008

(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	7cq5C1	0.44	3.98	0.077	0.778	model1_7cq5C1.pdb.gz
2	5b49A	0.43	4.57	0.048	0.833	model1_5b49A.pdb.gz
3	1cruB	0.42	4.24	0.079	0.789	model1_1cruB.pdb.gz
4	7bxuA	0.42	4.45	0.047	0.811	model1_7bxuA.pdb.gz
5	3nd0A	0.42	4.33	0.038	0.789	model1_3nd0A.pdb.gz
6	4ktpA	0.42	5.04	0.035	0.889	model1_4ktpA.pdb.gz
7	3auxA	0.42	4.47	0.057	0.822	model1_3auxA.pdb.gz
8	3dmdB1	0.42	4.50	0.050	0.778	model1_3dmdB1.pdb.gz
9	1kpkA	0.42	4.30	0.063	0.800	model1_1kpkA.pdb.gz
10	2ismB	0.42	3.91	0.083	0.744	model1_2ismB.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:0004871	1.00	signal transducer activity
GO:0004872	0.94	receptor activity
GO:0004930	0.93	G-protein coupled receptor activity
GO:0004940	0.92	beta1-adrenergic receptor activity
GO:0097159	0.90	organic cyclic compound binding
GO:0051380	0.88	norepinephrine binding
GO:0051379	0.88	epinephrine binding
GO:0098772	0.78	molecular function regulator
GO:0005088	0.77	Ras guanyl-nucleotide exchange factor activity
GO:0005057	0.77	receptor signaling protein 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:0071880	1.00	adenylate cyclase-activating adrenergic receptor signaling pathway
GO:0048518	1.00	positive regulation of biological process
GO:0044699	0.94	single-organism process
GO:0009987	0.94	cellular process
GO:0044763	0.93	single-organism cellular process
GO:0002025	0.92	vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure
GO:0001996	0.92	positive regulation of heart rate by epinephrine-norepinephrine
GO:0001659	0.92	temperature homeostasis
GO:0007267	0.83	cell-cell signaling
GO:0080090	0.82	regulation of primary metabolic process
GO:0031325	0.82	positive regulation of cellular metabolic process
GO:1902531	0.81	regulation of intracellular signal transduction
GO:0048584	0.81	positive regulation of response to stimulus
GO:0043085	0.81	positive regulation of catalytic activity
GO:0030819	0.81	positive regulation of cAMP biosynthetic process
GO:0043950	0.80	positive regulation of cAMP-mediated signaling
GO:0043547	0.80	positive regulation of GTPase 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 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:0031224	0.93	intrinsic component of membrane
GO:0005887	0.92	integral component of plasma membrane
GO:0044424	0.87	intracellular part
GO:0016020	0.86	membrane
GO:0044444	0.83	cytoplasmic part
GO:0043226	0.82	organelle
GO:0043231	0.81	intracellular membrane-bounded organelle
GO:0005886	0.81	plasma membrane
GO:0005768	0.78	endosome
GO:0005769	0.77	early endosome

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	1qgjA	0.410	4.46	0.026	0.800	1.11.1.7	NA
2	0.060	1o4zB	0.400	4.18	0.026	0.744	3.2.1.81	23
3	0.060	2akjA	0.402	4.15	0.012	0.733	1.7.7.1	NA
4	0.060	1o0uB	0.412	4.79	0.058	0.833	2.7.1.31	NA
5	0.060	1e2tA	0.404	4.53	0.024	0.789	2.3.1.118	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	0.01	1q16A	0.421	4.24	0.110	0.789	0.22	SF4	complex1.pdb.gz	19,20,21,29,30
2	0.01	1eccA	0.420	4.15	0.062	0.789	0.22	PCP	complex2.pdb.gz	18,25,26,27,28
3	0.01	1ecgA	0.410	4.66	0.036	0.833	0.19	PIN	complex3.pdb.gz	20,21,23,24,28
4	0.01	3av0B	0.385	4.87	0.057	0.811	0.11	AGS	complex4.pdb.gz	7,8,20,21,23,24,25
5	0.01	1c9uA	0.422	4.06	0.068	0.778	0.11	PQQ	complex5.pdb.gz	61,63,76,84,86
6	0.01	3ir5A	0.419	4.22	0.110	0.789	0.29	SF4	complex6.pdb.gz	58,60,62,69,79
7	0.01	1ecbA	0.407	4.44	0.025	0.789	0.17	5GP	complex7.pdb.gz	12,14,15

	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.