D-I-TASSER P29274-D2

D-I-TASSER results for P29274-D2

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

Input Sequence in FASTA format

>P29274 (120 residues)
REFRQTFRKIIRSHVLRQQEPFKAAGTSARVLAAHGSDGEQVSLRLNGHPPGVWANGSAP
HPERRPNGYALGLVSGGSAQESQGNTGLPDVELLSHELKGVCPEPPGLDDPLAQDGAGVS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| REFRQTFRKIIRSHVLRQQEPFKAAGTSARVLAAHGSDGEQVSLRLNGHPPGVWANGSAPHPERRPNGYALGLVSGGSAQESQGNTGLPDVELLSHELKGVCPEPPGLDDPLAQDGAGVS
Prediction	CHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCSSSSSCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence	348999999999998615563335882134455417887625899738887413158899876588875324456885134579888886533455435545789987887655677879
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| REFRQTFRKIIRSHVLRQQEPFKAAGTSARVLAAHGSDGEQVSLRLNGHPPGVWANGSAPHPERRPNGYALGLVSGGSAQESQGNTGLPDVELLSHELKGVCPEPPGLDDPLAQDGAGVS
Prediction	863453034004521244454164644434434444454740413146234422453445535645414333135445247346544145352345645443464451744446644548
	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

                   |                   |                   |                   |                   |                   |

SS
Seq

CHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCSSSSSCCCCCCCSSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
REFRQTFRKIIRSHVLRQQEPFKAAGTSARVLAAHGSDGEQVSLRLNGHPPGVWANGSAPHPERRPNGYALGLVSGGSAQESQGNTGLPDVELLSHELKGVCPEPPGLDDPLAQDGAGVS

1vt4I3

0.13

4.60

0.59

CEthreader

GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG

2b9cB

0.07

2.77

0.45

EigenThreader

VEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARK---LVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEDKV

3jcsE

0.11

0.09

3.33

0.34

FFAS-3D

----NTTKAHVQNMITG-----VTKGYRFKVRCAYAHFPINVSVDGQNIEVRNFLGEKRVRRQLVPSSVKVSQTD--------PSKVKDEIIFDGNDLEQVSREAAVLHQMCLVKKKDIR

7jjvA

0.07

2.71

1.08

SPARKS-K

----MQCDGLDGADGTSNGQAGASGLAGGKGGKGAPGVGTAGGAGGVGGAGGNGGAGGSGGNSDVAAGGAGAAGGAAGGTGGTGGNGGAGKPGGGGAGTPAGSAGSPGQTTVL-------

4ew8A

0.17

0.04

1.37

0.42

CNFpred

KRLAQTLDHLVENALRQTP-------------------GGRVTLSARR------------------------------------------------------------------------

1e6vA1

0.08

0.07

2.68

0.83

DEthreader

-FEFQ-KLMSYVEGDDLTNNMQMWDRMPVLAV-TMYPDDPKVALEVIAAGAMLYDIWLGFTQYTAPDNILDDVYYGLE-------TH-QRAAVCAAGCSAAAHFCVHPKV-FA--FTEPR

1irxB

0.08

3.25

0.82

MapAlign

NFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRWKDYLGMPISEVPDPWGCHESYAEHIIEWDGGWKVKYKCPEGHEGWVDIRSGNVKEPAGKDHLVAGSSYDTGKEIIKEVYGKEAP

5wb1A

0.16

5.26

0.66

MUSTER

TKFRQELHCLLAEFRLVPRGP--RGSQVQLVESGGGLVRPGGSLRLSCAASGSIFTIYAMGWYRQAPGKQRELVARITFGGDTNYADSVKGRFTISRDNAKNAVYLQMNSLKPEDTAVYY

2ks9A

0.13

0.06

2.03

0.55

HHsearch

DRFRLGFKHAFRCCPFISAGDYEG-LEMKSTRYLQTQGSVYKVSRLETTIST-------------VVGA---------------------------------------------------

4b6cA

0.12

4.10

0.44

CEthreader

RGLHHLIWEVVDNAVDEAMAGF------ATRVDVKIHADGSVEVRDDGRGIPVPTIDVVMTQVGVSTRLEATVLRDGYEWFQYYDRSVPGKLKQGGETKETGTTIRFWADPEIFETTDYN

(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	0.4267

(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	4ix3A	0.45	4.77	0.036	0.842	model1_4ix3A.pdb.gz
2	2wb8A	0.45	4.51	0.070	0.783	model1_2wb8A.pdb.gz
3	1w96A	0.45	4.51	0.078	0.808	model1_1w96A.pdb.gz
4	1lmlA	0.45	4.36	0.062	0.775	model1_1lmlA.pdb.gz
5	2dzdA1	0.43	4.46	0.078	0.758	model1_2dzdA1.pdb.gz
6	1f0qA	0.41	4.86	0.079	0.750	model1_1f0qA.pdb.gz
7	1iowA	0.40	4.34	0.079	0.658	model1_1iowA.pdb.gz
8	1ckjA	0.39	5.01	0.049	0.767	model1_1ckjA.pdb.gz
9	2qf7A	0.38	4.88	0.061	0.758	model1_2qf7A.pdb.gz
10	1koaA1	0.37	4.81	0.047	0.658	model1_1koaA1.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:0001609	1.00	G-protein coupled adenosine receptor activity
GO:0042802	0.73	identical protein binding
GO:0019899	0.73	enzyme 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:0048518	0.96	positive regulation of biological process
GO:0065008	0.95	regulation of biological quality
GO:0050896	0.95	response to stimulus
GO:0050794	0.86	regulation of cellular process
GO:0032501	0.81	multicellular organismal process
GO:0044699	0.80	single-organism process
GO:0003013	0.80	circulatory system process
GO:0009987	0.79	cellular process
GO:0007165	0.76	signal transduction
GO:0080090	0.75	regulation of primary metabolic process
GO:0044763	0.75	single-organism cellular process
GO:0031323	0.75	regulation of cellular metabolic process
GO:0048522	0.74	positive regulation of cellular process
GO:0031326	0.74	regulation of cellular biosynthetic process
GO:0019219	0.74	regulation of nucleobase-containing compound metabolic process
GO:0009893	0.74	positive regulation of metabolic process
GO:0007186	0.74	G-protein coupled receptor signaling pathway
GO:0050790	0.73	regulation of catalytic activity
GO:0045937	0.73	positive regulation of phosphate metabolic process
GO:0045935	0.73	positive regulation of nucleobase-containing compound metabolic process
GO:0031328	0.73	positive regulation of cellular biosynthetic process
GO:0045762	0.72	positive regulation of adenylate cyclase activity
GO:0007187	0.72	G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger
GO:0007267	0.71	cell-cell signaling
GO:0007188	0.71	adenylate cyclase-modulating G-protein coupled receptor signaling pathway
GO:0006950	0.56	response to stress
GO:0032502	0.53	developmental process
GO:0050878	0.51	regulation of body fluid levels
GO:0010579	0.51	positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway

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:0044459	1.00	plasma membrane part
GO:0005886	1.00	plasma membrane
GO:0016021	0.74	integral component of membrane
GO:0005887	0.73	integral component of plasma membrane
GO:0044424	0.55	intracellular 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	3ialB	0.417	4.36	0.054	0.708	6.1.1.15	NA
2	0.060	1f0kB	0.415	4.68	0.093	0.758	2.4.1.227	NA
3	0.060	2esmA	0.426	4.86	0.049	0.792	2.7.11.1	NA
4	0.060	2h96A	0.417	4.90	0.060	0.775	2.7.11.24	NA
5	0.060	2np8A	0.401	4.63	0.076	0.708	2.7.11.1	59,71

	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	2h9vA	0.436	4.82	0.059	0.800	0.16	Y27	complex1.pdb.gz	51,52,54
2	0.01	3bi6A	0.433	4.44	0.063	0.742	0.25	396	complex2.pdb.gz	20,22,23,72,73,74,75,76,77
3	0.01	2acwA	0.428	4.76	0.052	0.775	0.13	UPG	complex3.pdb.gz	16,17,38,51,52,53,54,63,64
4	0.01	2v55A	0.431	4.76	0.061	0.767	0.18	ANP	complex4.pdb.gz	24,71,72,73,77
5	0.01	3nczB	0.372	5.28	0.080	0.758	0.23	3NC	complex5.pdb.gz	43,45,73,74,114
6	0.01	2vuwA	0.445	4.64	0.070	0.792	0.24	5ID	complex6.pdb.gz	49,51,52,53,55
7	0.01	2io6A	0.431	4.43	0.063	0.733	0.17	330	complex7.pdb.gz	44,46,70,72,73,74
8	0.01	2f2uB	0.431	4.70	0.061	0.775	0.26	M77	complex8.pdb.gz	68,71,79
9	0.01	2acv0	0.425	4.60	0.042	0.758	0.18	III	complex9.pdb.gz	16,23,24
10	0.01	2in6A	0.430	4.42	0.063	0.733	0.24	839	complex10.pdb.gz	22,23,41,74,75,117

	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.