D-I-TASSER P41595-D2

D-I-TASSER results for P41595-D2

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

Input Sequence in FASTA format

>P41595 (97 residues)
KTFRDAFGRYITCNYRATKSVKTLRKRSSKIYFRNPMAENSKFFKKHGIRNGINPAMYQS
PMRLRSSTIQSSSIILLDTLLLTENEGDKTEEQVSYV

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| KTFRDAFGRYITCNYRATKSVKTLRKRSSKIYFRNPMAENSKFFKKHGIRNGINPAMYQSPMRLRSSTIQSSSIILLDTLLLTENEGDKTEEQVSYV
Prediction	CHHHHHHHHSSSSCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHCHHCCCCHHHHCCCHHHCCCCCCCCHHHHHHHHHSSCCCCCCCCCCSCCC
Confidence	7178874211453256777637888740552257841134577777501128984552284332277544212221111102126798602202149
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| KTFRDAFGRYITCNYRATKSVKTLRKRSSKIYFRNPMAENSKFFKKHGIRNGINPAMYQSPMRLRSSTIQSSSIILLDTLLLTENEGDKTEEQVSYV
Prediction	8524521342030325435425304514540325442354242134432444244432422342444624332113122111343764546642536
	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

CHHHHHHHHSSSSCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHCHHCCCCHHHHCCCHHHCCCCCCCCHHHHHHHHHSSCCCCCCCCCCSCCC
KTFRDAFGRYITCNYRATKSVKTLRKRSSKIYFRNPMAENSKFFKKHGIRNGINPAMYQSPMRLRSSTIQSSSIILLDTLLLTENEGDKTEEQVSYV

5lqwX5

0.12

0.08

2.93

0.56

CEthreader

-----------------------------SIKSQIVSDSPLSIATKHFTNNKIGVCSISSSGRLNIGRVSNFPTLDNWFHVHERPRTFPNNPKSILF

3j4aA

0.04

2.11

0.67

EigenThreader

GAKSVYERLKNDRAPYETRAQNCAQYTIPSLFPKDRLTISEYEAKQLLSDPDGLAKVDEGLSMVERIIMNYIESNSYRVTLFEALKQLVVAGNVLLY

5myjAC

0.16

0.14

4.77

0.25

FFAS-3D

-AFRRAQKQAIQRAMRAGAK-----GIKTQVSGRLNGADIAR---AEGYSEGVPLHTLRADIDYAWEEADTTYGKLGVKVWIYRGEVLPTKKSV---

6iqtA

0.16

0.15

5.12

0.73

SPARKS-K

AVVDSATSKFVSFGY----SKNSLRDRKDQLQY-CDVSFQTQARFNENIRQFVDKVRAEAIISSQREKVKNSPLTRLTTIKITPDTENITKKQVTIY

2fmlA

0.25

0.05

1.60

0.38

CNFpred

--------------------------------------------------------------------------LTVDMVLLCYNK---EADQLKVL

5jajA

0.02

1.40

0.83

DEthreader

YQWLPTLTASP-GTGGE------TQVYN-LLNDTNPRLSKLEEILQEHFQGSSRGLLFVRYGLMTRELNSL--LMEIRAVQAMPERKYRKIL-----

2pffA1

0.05

2.39

0.84

MapAlign

GGGGGGGGGGGGGGGGGGGGVTFKDKYVLITGAGKGSIGAEVLQGLLQGGAKVYGAKGSTLIVVPFNQGSKQDVEALIEFIYDTEKNGGLGWDLDAI

3hgfC

0.12

0.10

3.66

0.60

MUSTER

KKIENIVT-------KIDKKKYIYKKLLNEIAEIEKDKTSLEEVKNINMGKSLNKLFLEKIKKKSENMIKSMEKYIKDLDEIKEQSPKAEMN-----

6tpkA

0.14

0.13

4.55

0.66

HHsearch

GHLFHGIDSFWNESYLTGSRD-ERKKSLL---SKFGMDEGV-TFMFIGRDRGQKGV--DVLLKSSKKEFQEMRFIIIGKGDPEEGWARSLEEKHGNV

4avfA

0.14

4.90

0.44

CEthreader

SQEALTFDDVLGYSEVLPKDVSLKTRLTRGIELNIPMAQEGGIGIIHKLRVGAAVVVVVDTAHGHSKGVIERGNIATAEAAKALAEAGADAVKVGIG

(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	0.4063

(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	3ahcA1	0.49	3.84	0.076	0.825	model1_3ahcA1.pdb.gz
2	3cmuA	0.46	4.60	0.052	0.814	model1_3cmuA.pdb.gz
3	5mpbZ4	0.45	4.39	0.058	0.814	model1_5mpbZ4.pdb.gz
4	1itzA	0.45	4.47	0.042	0.814	model1_1itzA.pdb.gz
5	5vrbA	0.45	4.55	0.052	0.845	model1_5vrbA.pdb.gz
6	5l4kZ3	0.45	4.34	0.011	0.825	model1_5l4kZ3.pdb.gz
7	4xjnA	0.44	4.44	0.043	0.783	model1_4xjnA.pdb.gz
8	4uftB	0.39	3.95	0.071	0.660	model1_4uftB.pdb.gz
9	2e6kA2	0.39	4.31	0.065	0.701	model1_2e6kA2.pdb.gz
10	4co6A1	0.38	4.10	0.011	0.649	model1_4co6A1.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:0004993	1.00	G-protein coupled serotonin receptor activity
GO:1901363	0.92	heterocyclic compound binding
GO:0097159	0.92	organic cyclic compound binding
GO:0005096	0.92	GTPase activator activity
GO:0051378	0.91	serotonin binding
GO:0008144	0.91	drug binding
GO:0001965	0.91	G-protein alpha-subunit 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:0065008	1.00	regulation of biological quality
GO:0051649	1.00	establishment of localization in cell
GO:0048598	1.00	embryonic morphogenesis
GO:0044765	1.00	single-organism transport
GO:0050789	0.96	regulation of biological process
GO:0050794	0.95	regulation of cellular process
GO:0007165	0.94	signal transduction
GO:0044763	0.93	single-organism cellular process
GO:0007186	0.93	G-protein coupled receptor signaling pathway
GO:1901564	0.92	organonitrogen compound metabolic process
GO:1901360	0.92	organic cyclic compound metabolic process
GO:0070374	0.92	positive regulation of ERK1 and ERK2 cascade
GO:0055085	0.92	transmembrane transport
GO:0051240	0.92	positive regulation of multicellular organismal process
GO:0051046	0.92	regulation of secretion
GO:0050790	0.92	regulation of catalytic activity
GO:0048523	0.92	negative regulation of cellular process
GO:0044281	0.92	small molecule metabolic process
GO:0044260	0.92	cellular macromolecule metabolic process
GO:0044238	0.92	primary metabolic process
GO:0042221	0.92	response to chemical
GO:0034641	0.92	cellular nitrogen compound metabolic process
GO:0031328	0.92	positive regulation of cellular biosynthetic process
GO:0019932	0.92	second-messenger-mediated signaling
GO:0009628	0.92	response to abiotic stimulus
GO:0007204	0.92	positive regulation of cytosolic calcium ion concentration
GO:0006811	0.92	ion transport
GO:0006725	0.92	cellular aromatic compound metabolic process
GO:0003018	0.92	vascular process in circulatory system
GO:0071502	0.91	cellular response to temperature stimulus
GO:0070528	0.91	protein kinase C signaling
GO:0070371	0.91	ERK1 and ERK2 cascade
GO:0051781	0.91	positive regulation of cell division
GO:0051209	0.91	release of sequestered calcium ion into cytosol
GO:0051000	0.91	positive regulation of nitric-oxide synthase activity
GO:0050715	0.91	positive regulation of cytokine secretion
GO:0043123	0.91	positive regulation of I-kappaB kinase/NF-kappaB signaling
GO:0043066	0.91	negative regulation of apoptotic process
GO:0042493	0.91	response to drug
GO:0042310	0.91	vasoconstriction
GO:0019722	0.91	calcium-mediated signaling
GO:0014827	0.91	intestine smooth muscle contraction
GO:0014065	0.91	phosphatidylinositol 3-kinase signaling
GO:0014033	0.91	neural crest cell differentiation
GO:0010513	0.91	positive regulation of phosphatidylinositol biosynthetic process
GO:0010507	0.91	negative regulation of autophagy
GO:0007210	0.91	serotonin receptor signaling pathway
GO:0007205	0.91	protein kinase C-activating G-protein coupled receptor signaling pathway
GO:0006182	0.91	cGMP biosynthetic process
GO:0003300	0.91	cardiac muscle hypertrophy
GO:0003007	0.91	heart morphogenesis
GO:0001938	0.91	positive regulation of endothelial cell proliferation
GO:0001755	0.91	neural crest cell migration
GO:0050795	0.52	regulation of behavior

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:0044424	1.00	intracellular part
GO:0016020	0.95	membrane
GO:0005886	0.94	plasma membrane
GO:0005737	0.91	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	0.060	1xqzA	0.414	3.81	0.104	0.691	2.7.11.1 2.7.1.37	NA
2	0.060	1pz2A	0.421	4.40	0.075	0.742	3.2.1.55	NA
3	0.060	1occA	0.418	4.93	0.055	0.845	1.9.3.1	NA
4	0.060	1dwaM	0.414	4.34	0.052	0.742	3.2.1.147	NA
5	0.060	2wpnB	0.421	4.73	0.059	0.825	1.12.7.2	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:

No Binding sites was predicted

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

	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.