I-TASSER results

I-TASSER results for job id Rv3437

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (158 residues)
MVGRAVPSPNRRYRRVWPPRTKGQHLSNPYAQHQLKLIRHTGALILWQQRTYVVSGTREQ
CEAAYKSAQTYNLLVGWWSLVSLLAMNWIALISNFNAIRRVRAAADGASVPHGPHAIAHP
AVPRGPIPAGWYPDPSGAGLRYWDGATWTHWTHPPRHR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MVGRAVPSPNRRYRRVWPPRTKGQHLSNPYAQHQLKLIRHTGALILWQQRTYVVSGTREQCEAAYKSAQTYNLLVGWWSLVSLLAMNWIALISNFNAIRRVRAAADGASVPHGPHAIAHPAVPRGPIPAGWYPDPSGAGLRYWDGATWTHWTHPPRHR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCCEEEEEEHCCCEEHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC
Conf.Score	98888899876545678998899988998875899999756478998766756744499999999999887677778899999999999999999999999998668899999989888999998999888889999876666765444567887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MVGRAVPSPNRRYRRVWPPRTKGQHLSNPYAQHQLKLIRHTGALILWQQRTYVVSGTREQCEAAYKSAQTYNLLVGWWSLVSLLAMNWIALISNFNAIRRVRAAADGASVPHGPHAIAHPAVPRGPIPAGWYPDPSGAGLRYWDGATWTHWTHPPRHR
Prediction	74454335565425433454565543642323130303522100000224534131214304400450432100223223200332231111333431440451277653444654444444464533522143274433321314403734536678
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHCCEEEEEEHCCCEEHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC
MVGRAVPSPNRRYRRVWPPRTKGQHLSNPYAQHQLKLIRHTGALILWQQRTYVVSGTREQCEAAYKSAQTYNLLVGWWSLVSLLAMNWIALISNFNAIRRVRAAADGASVPHGPHAIAHPAVPRGPIPAGWYPDPSGAGLRYWDGATWTHWTHPPRHR

1jvrA

0.15

0.12

0.82

1.14

dPPAS2

-------HMGQIHGLSPTPIPKAPRGLST----------HHWLNFLYRLQPGPSDFDFQQLRRFLKLALKTPIWLDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

5cr4A

0.06

0.05

0.88

1.04

dPPAS2

FGHNDHRYVWRKKGEACKPKNTIPTVKHGGGSIMLWGCFAAGGTGALHKIDG--IMDAVQYVDILKQHLKTSVRKLKLGRKWVFQHDNDPKHTSKVVAKWLKDNKVKVLEWPSQSPDLNPIENLWAEL-----------------KKRVRARRPTNLT

1jvrA

0.16

0.13

0.82

0.76

MUSTER

HMGQIHGLSPTP--IPKAPRGLSTH-------HWLNFLQAA-----YRLQPGPSDFDFQQLRRFLKLALKTPIWL--YSLLASLI-GYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

1jvrA

0.13

0.11

0.84

0.80

dPPAS

-------HMGQIHGLSPTPIPKAPRGLSTHHWLNF-------LQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

1jvrA

0.16

0.13

0.77

0.89

wdPPAS

-------HMGQIHGLSPTPIPKAPRGLST----------HHWLFLQAAYRLQPGPS--DFDFQQLRRFLKLALKT-WYSLLASLI-GRVVEIINILVKNQV---SPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

1jvrA

0.21

0.16

0.76

0.88

wMUSTER

M-GQIHGLSPTP--IPKAPRGLSTH--------------HLNFL--AAYRLQPGPFDFQQLRRFLKLALKTPI---WYSLLASLI-GRVVEIINILVKN---QVSPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

1jvrA

0.21

0.16

0.74

0.84

wPPAS

M-GQIHGLSPTPI--PKAPRGLSTH--------QAAYRLQPG----------PSDFDFQQLRRFLKLALKTPI---WYSLLASLI--RVVEIINILVKNQV---SPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

2ifoA

0.09

0.03

0.29

0.98

dPPAS2

-----------------------------------------------------------SGGGGVDVGDVVSAIQGAAGPIAAIGGAVLTVMVGIKVYKWVRRAM-----------------------------------------------------

1jvrA

0.16

0.13

0.79

0.89

PPAS

-------HMGQIHGLSPTPIPKAPRGLST----------HHWLNFLYRLQPGPSDFDFQQLRRFLKLALKTPI---WYSLLASLI-GYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPP--SPEAHVPP----------PYVEPTTTQ

2bryA3

0.07

0.06

0.91

0.72

Env-PPAS

LISAAKFVPEGFTIREMRGKLADTSMMRAESSARVQEKHGARLLLGLVGDCLVEPFGTGVARGFLAAFDAAWMVKRWAEGA-----GPLEVLAERESLYQLLSQTSPENMHRNVAQYGLD-------PATRYPNLNLRAVTPNQVQDLYDMMDKE---

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 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.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-2.84

Estimated TM-score = 0.39±0.13

Estimated RMSD = 11.3±4.5Å

Download Model 2

C-score=-3.32

Download Model 3

C-score=-3.44

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.12

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	2dhtA	0.527	4.78	0.054	0.854
2	1xgvA	0.520	4.88	0.061	0.848
3	3ecpA	0.518	4.56	0.061	0.804
4	2iv0A	0.518	4.88	0.041	0.848
5	3w5mA	0.517	4.89	0.039	0.880
6	7r1rA	0.514	4.84	0.032	0.842
7	3czjA	0.513	5.09	0.045	0.854
8	2zkmX	0.512	4.85	0.048	0.835
9	3blvH	0.508	4.79	0.111	0.817
10	3ohmB	0.508	4.55	0.054	0.810

(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 function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.05	3	2xawA	III	Rep, Mult	68,69,71,72,83,103
2	0.05	3	4z9vB	III	Rep, Mult	73,78,81,82,85
3	0.05	3	2x0xA	III	Rep, Mult	85,86,88,89,110
4	0.05	3	4ct4B	MG	Rep, Mult	57,58,59
5	0.03	2	2eh3A	MG	Rep, Mult	59,62
6	0.03	2	2r1rA	III	Rep, Mult	64,66,67,68,69,100
7	0.03	2	1brrC	ARC	Rep, Mult	64,84,88
8	0.03	2	6r1rA	III	Rep, Mult	72,73,74,75,76,105
9	0.02	1	3qv4C	UUU	Rep, Mult	77,141,145,146
10	0.02	1	2a01B	AC9	Rep, Mult	60,64
11	0.02	1	1m56B	HEA	Rep, Mult	45,128
12	0.02	1	1rwtB	CLA	Rep, Mult	140,143
13	0.02	1	2j7wA	GTP	Rep, Mult	27,58,66,147,148
14	0.02	1	3e2vA	MG	Rep, Mult	40,106
15	0.02	1	1aczA	GLC	Rep, Mult	78,148
16	0.02	1	2boqA	ZN	Rep, Mult	115,134
17	0.02	1	2wse4	CLA	Rep, Mult	99,114

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	2d1cA	0.491	4.87	0.076	0.804	1.1.1.42	NA
2	0.060	1w0dD	0.493	4.66	0.065	0.797	1.1.1.85	NA
3	0.060	1t09B	0.493	4.98	0.049	0.817	1.1.1.42	39,52
4	0.060	1w0dA	0.502	5.00	0.056	0.817	1.1.1.85	NA
5	0.060	1cnzA	0.478	4.65	0.054	0.759	1.1.1.85	59
6	0.060	3blvC	0.484	4.69	0.052	0.759	1.1.1.41	NA
7	0.060	1ug9A	0.486	4.96	0.076	0.829	3.2.1.70	62
8	0.060	2hi1A	0.484	5.27	0.057	0.829	1.1.1.262	40,72,97,105
9	0.060	1ayqB	0.496	4.94	0.082	0.817	1.1.1.85	NA
10	0.060	1dr0A	0.504	5.04	0.083	0.829	1.1.1.85	NA
11	0.060	3blvH	0.508	4.79	0.111	0.817	1.1.1.41	NA
12	0.060	2cvtA	0.494	4.24	0.032	0.747	1.17.4.1	72
13	0.060	1bglA	0.489	4.77	0.032	0.791	3.2.1.23	NA
14	0.060	1t09A	0.493	5.02	0.067	0.823	1.1.1.42	NA
15	0.060	1zyzA	0.483	4.19	0.034	0.734	1.17.4.1	72
16	0.060	5r1rA	0.515	4.85	0.032	0.848	1.17.4.1	NA
17	0.060	2iv0A	0.518	4.88	0.041	0.848	1.1.1.42	NA
18	0.060	1a05A	0.484	5.00	0.090	0.817	1.1.1.85	NA
19	0.060	2dhtA	0.527	4.78	0.054	0.854	1.1.1.42	NA

(a)	Cscore^EC is the confidence score for the 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.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.07	0.494	4.78	0.06	0.79	2g4oA	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0040007 GO:0046872 GO:0051287 GO:0055114
1	0.07	0.498	5.02	0.09	0.82	4iwhA	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
2	0.07	0.518	4.88	0.04	0.85	2iv0A	GO:0000287 GO:0004450 GO:0006097 GO:0006099 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
3	0.07	0.527	4.78	0.05	0.85	2dhtA	GO:0000166 GO:0000287 GO:0004450 GO:0016491 GO:0016616 GO:0051287 GO:0055114
4	0.07	0.499	4.83	0.09	0.80	2y42D	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0042802 GO:0046872 GO:0051287 GO:0055114
5	0.07	0.499	4.94	0.07	0.82	1cm7A	GO:0000287 GO:0003862 GO:0005737 GO:0005829 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0030145 GO:0034198 GO:0046872 GO:0051287 GO:0055114
6	0.07	0.488	5.28	0.07	0.84	3ty3A	GO:0000287 GO:0005737 GO:0005739 GO:0008652 GO:0009085 GO:0016491 GO:0016616 GO:0019878 GO:0046872 GO:0047046 GO:0051287 GO:0055114
7	0.07	0.485	5.04	0.06	0.82	5j32A	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0009507 GO:0009536 GO:0009570 GO:0009941 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
8	0.07	0.493	4.83	0.07	0.80	3blvC	GO:0000287 GO:0003723 GO:0003824 GO:0004449 GO:0005739 GO:0005758 GO:0005759 GO:0005829 GO:0005962 GO:0006099 GO:0006102 GO:0006537 GO:0006626 GO:0008152 GO:0016491 GO:0016616 GO:0042645 GO:0046872 GO:0051287 GO:0055114
9	0.07	0.484	5.00	0.09	0.82	1a05A	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
10	0.07	0.490	4.82	0.06	0.79	1vlcA	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
11	0.07	0.499	4.95	0.07	0.82	3uduA	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
12	0.07	0.508	4.79	0.11	0.82	3blvH	GO:0000287 GO:0003723 GO:0003824 GO:0004449 GO:0005739 GO:0005759 GO:0005962 GO:0006099 GO:0006102 GO:0006537 GO:0008152 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
13	0.07	0.491	4.87	0.08	0.80	2d1cA	GO:0000287 GO:0004450 GO:0006097 GO:0006099 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
14	0.07	0.468	5.07	0.04	0.78	2uxqA	GO:0000166 GO:0000287 GO:0004450 GO:0006099 GO:0006102 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
15	0.07	0.491	4.83	0.09	0.78	1wpwA	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114
16	0.07	0.482	5.04	0.05	0.77	4y1pB	GO:0000287 GO:0003862 GO:0009098 GO:0016491 GO:0016616 GO:0051287 GO:0055114
17	0.07	0.493	5.13	0.05	0.84	3ah3A	GO:0000287 GO:0008652 GO:0009085 GO:0016491 GO:0016616 GO:0019878 GO:0046872 GO:0047046 GO:0051287 GO:0055114
18	0.07	0.485	5.12	0.06	0.81	3vmkA	GO:0000287 GO:0003862 GO:0005737 GO:0008652 GO:0009082 GO:0009098 GO:0016491 GO:0016616 GO:0046872 GO:0051287 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0050662	GO:0016614	GO:0046872	GO:0000166
GO-Score	0.58	0.58	0.58	0.58
Biological Processes	GO:1901566	GO:0009081	GO:0046394	GO:0006551
GO-Score	0.37	0.37	0.37	0.37
Cellular Component	GO:0044424
GO-Score	0.37

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(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.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.