I-TASSER results

I-TASSER results for job id Rv0698

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

Input Sequence in FASTA format

>protein (203 residues)
MGRRGNRRVHVDRVRLTGTERELRAENQSPPIFRPQNTLGDGANGLPLAVCTTTAHTCHT
SHTHPSRWTPNPVPATKGVPAGLVQATFIIENLDPGNNDTPTPPTPKLRLARKPGHHRRS
EYDADSVLRRKDTSRRCVQADDVRCVQLVQDPRRGRVELGGYRAELTVGRRAAVNCQRPQ
YGADGWPVRLGCGVGGAARGDQR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGRRGNRRVHVDRVRLTGTERELRAENQSPPIFRPQNTLGDGANGLPLAVCTTTAHTCHTSHTHPSRWTPNPVPATKGVPAGLVQATFIIENLDPGNNDTPTPPTPKLRLARKPGHHRRSEYDADSVLRRKDTSRRCVQADDVRCVQLVQDPRRGRVELGGYRAELTVGRRAAVNCQRPQYGADGWPVRLGCGVGGAARGDQR
Prediction	CCCCCCCEEEEEEHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCHCCCCCCCCCCCCCCHHHHHHHHCCCCCCHCCCCEEEEEEHCCCCCCEEEHCCEEEEEEHCCEEEEHCCCCCCCCCCCCEEEHCCCCCCCCCCCC
Conf.Score	98888877899876588667899987579987787767778888876567658888888888888878999988778887544566676544799999999999975334578887655556666766665564443435665677764488876688767567877544445445787778888766665566766667789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MGRRGNRRVHVDRVRLTGTERELRAENQSPPIFRPQNTLGDGANGLPLAVCTTTAHTCHTSHTHPSRWTPNPVPATKGVPAGLVQATFIIENLDPGNNDTPTPPTPKLRLARKPGHHRRSEYDADSVLRRKDTSRRCVQADDVRCVQLVQDPRRGRVELGGYRAELTVGRRAAVNCQRPQYGADGWPVRLGCGVGGAARGDQR
Prediction	85554644131441426445441445255431132413235314112001224333334243433441446334445412111130201043144466643433434131254435444562415421444634431252542302411443552414134231412234412240643523264120201012123344578
	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                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCEEEEEEHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCCCCCCCCCCCCCCHCCCCCCCCCCCCCCHHHHHHHHCCCCCCHCCCCEEEEEEHCCCCCCEEEHCCEEEEEEHCCEEEEHCCCCCCCCCCCCEEEHCCCCCCCCCCCC
MGRRGNRRVHVDRVRLTGTERELRAENQSPPIFRPQNTLGDGANGLPLAVCTTTAHTCHTSHTHPSRWTPNPVPATKGVPAGLVQATFIIENLDPGNNDTPTPPTPKLRLARKPGHHRRSEYDADSVLRRKDTSRRCVQADDVRCVQLVQDPRRGRVELGGYRAELTVGRRAAVNCQRPQYGADGWPVRLGCGVGGAARGDQR

4kfvA

0.18

0.16

0.87

0.67

MUSTER

----GGEGFHLHGVQENSAQQALEPYFGHSRLNKENKALLKANVEKPVKLEV---FNMKTMRVREVEVVPSNMWGGQGLLGASVRFCSFRRASEHVWHLDVEPSSP----AALAGLRPYTDY-----IVGSDQILQ--ESEDF--FTLIES-HEGKLKL--YNSESDSCREVTVTPNA-AWGGEG---SLGCGIGGYPSSQYK

2kfuA

0.16

0.12

0.72

0.63

dPPAS

-----------------------------VTDMNPDIEKDQTSDEVTVETSVFRADFLSELDAPAQAGTESAVSGVEGLPPG--SALLVVKR-GPNAGSRFLLDQAITSAGRHPDDVTVSRRHA--EFRLENNSLNGTYVNREPVDSAVLAN-GDEVQIGKFRLVFLTGPK-----QGEDDGSTGGP----------------

2kb4A

0.20

0.12

0.62

0.48

wdPPAS

-------------------------------------MSDNNGTPEPQVETTSVFRADLLKEMESSTGTAPASTGAENLPAG--SALLVVKR---GPNAGAR-DQPTTTAGRHP--------ESDIFL--DDVSRR-INEGEFEVVDV--GSLNG-TYVNREP------NAQVM--------QTGDEIQIG--LAGPAE----

1w0sA

0.20

0.18

0.87

0.62

wMUSTER

CHG-GPHEPKETRSRKCS---------APEPSQKPP---GKPCPGLAYEQRRCTGLPPCPVAGGWGPWGPSPCPVTCGL--GQTMEQRTCNHPVPQHGGPFCADATRTHICNTPVDGEWDSWGEWSPCIRKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDI-----RHCYSIQHPLKGSSEWT----CGPNPTAR--QR

4kfvA

0.24

0.18

0.74

0.49

wPPAS

----GGEGFHLHGVQEN-----------SP--LEPY---FDTIGHSRLN-VKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASVRFCWHVLDVEPS---SP---------AALAG----RPYT-D-YIVGSDQILQ--ESEDF--FTLIES-HEGKLKL--YNSESDSCREVTVT---PNAGGEG---SLGCGIGGYPSSQYK

2kfuA

0.16

0.12

0.72

0.64

dPPAS2

--------------------------VTDMN---PDIEKDQTSDEVTVETSVFRADFLSELDAPAQAGTESAVSGVEGLPPG--SALLVVKR-GPNAGSRFLLDQAITSAGRHPDDVTVSRRHA--EFRLENNSLNGTYVNREPVDSAVLAN--GEVQIGKFRLVFLTGPKQG-----EDDGSTGGP----------------

4pkdB

0.22

0.20

0.94

0.61

PPAS

--TRPNHTIYINNLNEKIKKDELKKSLYA-QILDSRSLKMRGMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVEETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKARVNYDTESKLRRE-----FEVYGPIKRIHMVYSKRSGK-PRGAYEMHKKIGRRVLVDVERGR-TVKGWPRRLGGGLGGTRRG---

3gasA2

0.21

0.15

0.72

0.69

Env-PPAS

---------DLKGVEE--EVKAFKEGFDSVCLA----TL--HPNGHVVCSYAPLSYYIYVSHFAGLKNNPH-------N------VEVFLE--DES--KAKSAIRKRLRYTRFIE--RGAEFDFDSFIEKTAGGIKTIRAQDFHLIALD--FKEGRFVKGGQAYDILGDKIAYVGDKGPHNFAH-------------------

3dpaA

0.15

0.14

0.90

0.66

MUSTER

LDRRSEKSMTL-DISNDNKQLPYQEKIITGPVIPPVQRLDPGAKSVRL---STTPDISKLPQDRESYFNLREIPPRSEKANVLLQTKIKLFYRPAAIKTRPEVWQDQLILNKVSGGENPTPYYV-IGLGGSEKQAEEGEFET-----VMLSPRSEQVKSAN-YNTPYL---SYIN----DYGGR-PVLSFICN-GSRCSVKKE

2kb4A

0.19

0.13

0.68

0.57

dPPAS

-------------------------------------MSDNNGTPEPQVETTSVFRADLLKEMESSTGTAPASTGAENLPAG--SALLVVKR-GPNAGARFLLDQPTTTAGRHP--------ESDIFLDDVTVSRRH--------AEFRINEGEFEVVDVGSLNGTYVNREPR----NAQVMQTGDEIQIGKFLAGPAE----

(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=-4.75

Estimated TM-score = 0.23±0.06

Estimated RMSD = 17.2±2.7Å

Download Model 2

C-score=-4.54

Download Model 3

C-score=-4.99

Download Model 4

C-score=-5.00

Download Model 5

C-score=-5.00

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	4kfvA	0.555	4.40	0.088	0.803
2	3rleA	0.468	5.18	0.076	0.778
3	3i8bA	0.421	5.50	0.068	0.739
4	1d0nA	0.415	5.63	0.060	0.734
5	3hz6A	0.415	5.93	0.069	0.763
6	3gbtA	0.415	5.88	0.057	0.759
7	5e04A	0.413	5.58	0.048	0.714
8	3poyA	0.411	5.58	0.051	0.719
9	2wgqB2	0.407	5.42	0.069	0.680
10	2x2hA	0.406	5.34	0.016	0.685

(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	0.07	4	4qkoB	MG	Rep, Mult	10,92
2	0.05	3	2b4fA	XYP	Rep, Mult	92,96
3	0.05	3	1ykpA	DHB	Rep, Mult	38,40,47
4	0.03	2	2z48A	NGA	Rep, Mult	10,11,12,13,32
5	0.03	2	2z48A	NGA	Rep, Mult	10,11,33,36
6	0.03	2	1siwA	SF4	Rep, Mult	10,31,32,34,82,83
7	0.03	2	3e22C	MG	Rep, Mult	41,44,79
8	0.03	2	3de8A	CA	Rep, Mult	22,26
9	0.02	1	2nvqB	DUT	Rep, Mult	66,67
10	0.02	1	1le5E	NUC	Rep, Mult	24,34,43
11	0.02	1	2x88A	CU	Rep, Mult	56,59
12	0.02	1	1cq1B	CA	Rep, Mult	45,47
13	0.02	1	1ev6F	III	Rep, Mult	88,89
14	0.02	1	1h1vG	CA	Rep, Mult	94,194,195
15	0.02	1	3cg8A	O	Rep, Mult	62,64,116
16	0.02	1	2hv8B	2ME	Rep, Mult	21,24
17	0.02	1	2e75G	OPC	Rep, Mult	89,93

	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	2nztA	0.332	5.75	0.048	0.611	2.7.1.1	NA
2	0.060	3gvjA	0.396	4.95	0.072	0.630	3.2.1.129	88
3	0.060	1qhaA	0.393	5.78	0.044	0.709	2.7.1.1	NA
4	0.060	1v4tA	0.299	5.61	0.053	0.512	2.7.1.2,2.7.1.1	NA
5	0.060	3cn8B	0.276	5.80	0.039	0.502	1.5.3.17	NA
6	0.060	1bdgA	0.399	5.73	0.067	0.724	2.7.1.1	NA
7	0.060	1vncA	0.397	5.92	0.047	0.700	1.11.1.10	96,133
8	0.060	2cb1A	0.390	5.64	0.075	0.670	4.2.99.10	NA
9	0.060	3hz6A	0.415	5.93	0.069	0.763	2.7.1.17	NA
10	0.060	3bi2B	0.396	5.41	0.026	0.685	1.5.3.11	NA
11	0.060	3f9mA	0.312	6.22	0.033	0.596	2.7.1.2	NA
12	0.060	2aeyA	0.342	5.65	0.064	0.601	3.2.1.80	53
13	0.060	1y4iA	0.395	5.55	0.050	0.670	4.4.1.11	126
14	0.060	2zueA	0.388	5.23	0.017	0.645	6.1.1.19	NA
15	0.060	1szqA	0.388	5.69	0.083	0.680	4.2.1.79	NA
16	0.060	1q16A	0.332	6.01	0.054	0.621	1.7.99.4	NA
17	0.060	3cmmC	0.388	5.79	0.023	0.690	6.3.2.19	NA
18	0.060	1iq0A	0.388	5.43	0.063	0.655	6.1.1.19	10
19	0.060	2vz9B	0.392	5.97	0.058	0.719	2.3.1.85	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	0.555	4.40	0.09	0.80	4kfvA	GO:0000139 GO:0005794 GO:0006810 GO:0007030 GO:0015031 GO:0016020 GO:0050774
1	0.07	0.481	4.93	0.08	0.78	4kfwA	GO:0005794 GO:0005797 GO:0006996 GO:0007030 GO:0016020 GO:0032580
2	0.06	0.412	5.84	0.07	0.75	3kzbA	GO:0000166 GO:0004856 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
3	0.06	0.340	6.10	0.08	0.64	2dpnA	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
4	0.06	0.337	6.17	0.06	0.63	3gbtA	GO:0000166 GO:0005524 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046316
5	0.06	0.302	6.20	0.01	0.57	5cltA	GO:0003824 GO:0003844 GO:0004553 GO:0005829 GO:0005975 GO:0005977 GO:0005978 GO:0006091 GO:0016740 GO:0016757 GO:0043169 GO:0070062
6	0.06	0.341	6.24	0.05	0.66	4bc2A	GO:0000166 GO:0004856 GO:0005524 GO:0005737 GO:0005829 GO:0005975 GO:0005997 GO:0005998 GO:0006091 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019640 GO:0042732 GO:0046835 GO:0070062
7	0.06	0.426	5.87	0.07	0.78	4e1jC	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
8	0.06	0.372	5.87	0.04	0.67	5bsmA	GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0009698 GO:0016207 GO:0016874
9	0.06	0.338	6.06	0.04	0.61	3qbxB	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
10	0.06	0.414	5.90	0.08	0.77	3h3nO	GO:0000166 GO:0004370 GO:0005524 GO:0005975 GO:0006071 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019563
11	0.06	0.425	5.41	0.06	0.74	3i8bA	GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046872
12	0.06	0.329	6.01	0.03	0.61	2itmA	GO:0000166 GO:0004856 GO:0005524 GO:0005737 GO:0005975 GO:0005997 GO:0005998 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0042732 GO:0042843 GO:0046835
13	0.06	0.330	5.98	0.05	0.60	3ifrA	GO:0004856 GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
14	0.06	0.250	6.16	0.02	0.45	3ch8A	GO:0005102 GO:0005176 GO:0005178 GO:0005200 GO:0005604 GO:0005634 GO:0005654 GO:0005737 GO:0005886 GO:0006605 GO:0007049 GO:0007155 GO:0007165 GO:0007173 GO:0007229 GO:0009925 GO:0016020 GO:0016049 GO:0016323 GO:0030054 GO:0030056 GO:0031965 GO:0032088 GO:0032495 GO:0032496 GO:0038128 GO:0045104 GO:0045175 GO:0045197 GO:0070433 GO:0071356 GO:0071638
15	0.06	0.371	5.82	0.04	0.69	5huxA	GO:0005975 GO:0016301 GO:0016310 GO:0016773
16	0.06	0.286	6.31	0.04	0.57	3wxiA	GO:0000166 GO:0004370 GO:0005975 GO:0006072 GO:0016301 GO:0016310 GO:0016740 GO:0016773
17	0.06	0.404	5.72	0.06	0.74	3l0qB	GO:0005975 GO:0016301 GO:0016310 GO:0016740 GO:0016773
18	0.06	0.340	5.35	0.05	0.59	4ynnA	GO:0004252 GO:0006508 GO:0008233 GO:0016787

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0016772
GO-Score	0.36	0.36	0.36
Biological Processes	GO:0006796	GO:0044238
GO-Score	0.36	0.31
Cellular Component	GO:0032580	GO:0005797
GO-Score	0.07	0.07

(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.