I-TASSER results

I-TASSER results for job id Rv2134c

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

Input Sequence in FASTA format

>protein (195 residues)
MARAIHVFRTPDRFVAGTVGQPGNRTFYLQAVHDSRVVSVVLEKQQVAVLAERIGALLFE
VNRRFGTPVPPEPTEIDDLSPLIMPVDAEFRVGTMGLGWDSEAQSVVVELLAVTDAEFDA
SVVLDDTEEGPDAVRVFLTPESARQFATRSYRVISAGRPPCPLCDEPLDPEGHICARTNG
YRRDVLLGSGDDPAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MARAIHVFRTPDRFVAGTVGQPGNRTFYLQAVHDSRVVSVVLEKQQVAVLAERIGALLFEVNRRFGTPVPPEPTEIDDLSPLIMPVDAEFRVGTMGLGWDSEAQSVVVELLAVTDAEFDASVVLDDTEEGPDAVRVFLTPESARQFATRSYRVISAGRPPCPLCDEPLDPEGHICARTNGYRRDVLLGSGDDPAG
Prediction	CCCEEEHCCCCCEEEEHCCCCCCCEEEEEEEHCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHEEEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	996678668987799855789986699999985987898656799999999999999999999789999999888898888889998656346566576589988999987588755666556788888987799998999999999999999998999999999999988886567888766765787788889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MARAIHVFRTPDRFVAGTVGQPGNRTFYLQAVHDSRVVSVVLEKQQVAVLAERIGALLFEVNRRFGTPVPPEPTEIDDLSPLIMPVDAEFRVGTMGLGWDSEAQSVVVELLAVTDAEFDASVVLDDTEEGPDAVRVFLTPESARQFATRSYRVISAGRPPCPLCDEPLDPEGHICARTNGYRRDVLLGSGDDPAG
Prediction	655433514323200000214345120101036533000011134104300530450053037437453346555264563154324541300300022147332000101325456355634366576414201020337203400520450063323412304422437302013432243444347745568
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCEEEHCCCCCEEEEHCCCCCCCEEEEEEEHCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHEEEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MARAIHVFRTPDRFVAGTVGQPGNRTFYLQAVHDSRVVSVVLEKQQVAVLAERIGALLFEVNRRFGTPVPPEPTEIDDLSPLIMPVDAEFRVGTMGLGWDSEAQSVVVELLAVTDAEFDASVVLDDTEEGPDAVRVFLTPESARQFATRSYRVISAGRPPCPLCDEPLDPEGHICARTNGYRRDVLLGSGDDPAG

4g6tA

0.15

0.08

0.53

1.39

dPPAS2

---------------------------------------------PVDMSNLFYKTLLDDFSRSLEMQ----PLVFDDHGTCNMIIDNT---FALTLSCDYARERLLLIGLLEPHKDIPQQCLLADEKSGLYHAYQSIPKREMAGLLEWMRGWREA---------------------------------------

4bhrA

0.11

0.05

0.42

1.36

dPPAS2

-----------------------------------------------TAAQAYVRNVATAVEAERDPTTGALPQLPQACDQFVANPPAS--VTQCNVTANNDGVNFTVTAQ------LTYGSVSFDSSTG--QFSFQL---------------------------------------------------------

4r1dB1

0.16

0.13

0.79

0.71

MUSTER

MDKITHCF----RFLID-L--PPDAINAGYYLWGDRIEYLDDK---PTELAARVDRLEQEWRTQ---RHKSKGNMFLRKIDFGNE-------SVGLLSWSSESKTYLLDTYVTSKPTW------------VYRWKGKVSVDREQHAVEISRALARNSRAP----EIPSEP-G-FC--DHAYIAGDSFQVERFGVG

3gh7A1

0.12

0.09

0.80

0.97

dPPAS

ATSQPSILPKPVSYTVG------SGQFVL--TKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISSNQPTAGSIYLTTVGGNAALGNEGYDLITTSN--QVTLTANKLLPAGIEKNTVVSGVQWVIPHSNISDNDDFKERLIEHTPRLQNKG---IKFFADPIV--------------------------

4r1dB1

0.16

0.12

0.75

0.64

wdPPAS

MDKITHCF----RFLID----PPDAV-AGYYLWGDRIEYLDDKPTELAARVDRLEQEWRTQRHKSKGNMFLRKIDFGNES-------------VGLLSWSSESKTYLLDTYVTSKPTW--------------RWKGKVSVDREQHAVEISRALARNSRAP----EIPSEP-G-FC--DHAY----IAGDSFQVVG

5dfzC

0.15

0.13

0.88

0.67

wMUSTER

PDVLICDVCPETSKVFKSSLSP--LKITFKTTLN-QPYHLMFKVLRQDQLVVQIISLMNELLKNENVDLKLTPYKILATGP---------QEGAIEFIPNDTLASILSKYHGILGYLKLHYPDENATLGVQGWVL----DNFVKSCAGYCVITYILGRHLDNLL---VTPDGHFFHADFGY----ILGQDPKPFP

4r1dB1

0.18

0.14

0.75

0.65

wPPAS

MDKITHCF----RFLID-L--PPDAV-AGYYLWGDRIEYLDDK---PTELAARVDRLEQEWRTQ-----RHKSKGNMFLRKIDFGNE-----SVGLLSWSSESKTYLLDTYVTSKPTW--------------RWKGKVSVDREQHAVEISRALARNSRAP----EIPSEP-G-FC--DHAY----IAGDSFQV-G

3gh7A1

0.13

0.09

0.72

1.21

dPPAS2

LP-------KPVSYTVG------SGQFVL--TKNASIFVAGNNVGETDELFNIGQALAKKLNASTGYTISSNQPTAGSIYLTTVGGNAALGNEGYDLITTSN--QVTLTALQLLPAGIEKNTVVSGVQWVIPHSNISDNDDFKERLIEHTPRLQNKG--------------------------------------

5dnkA2

0.10

0.93

0.64

PPAS

IKKFNIIFNKPLKEVDLNNATENLQFFLNGNKESNLSTTSPYMKAILYTFSENFKQVTSEANTKLNNTKLNEIKNE-----LLNNAMKLVLQGYISITNQKHRSKPVLDKPKTTQMVIYQAKYTPSMW-GVNFFEKFALRY-KKAIIEAILGHVEKGELTLSREGQKINKESLFTPMIEKFCSNALLV-------

3h10A2

0.16

0.12

0.73

0.81

Env-PPAS

RQWALEDFEIGRPLGKGKFG----NVYLAREKQSKFILALKLFKAQLEKAG-VEHQLRREVEIQSH---------------LRHP----NILRLYGYFHDATRVYLILEY--APLGTVYRELQKLS----------KFDEQRTATYITELANALSY----CHSKRKPLGSAGELSVHAPSSRR------------

(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=-3.12

Estimated TM-score = 0.36±0.12

Estimated RMSD = 12.6±4.3Å

Download Model 2

C-score=-3.89

Download Model 3

C-score=-4.10

Download Model 4

C-score=-4.56

Download Model 5

C-score=-4.82

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	4r1dB	0.641	2.41	0.123	0.733
2	2eabA1	0.511	4.14	0.083	0.728
3	3wiqA	0.510	4.37	0.066	0.749
4	1h54B	0.504	4.26	0.080	0.728
5	2cqtA	0.496	4.82	0.032	0.759
6	4ktpA	0.493	4.47	0.110	0.723
7	4neiA	0.492	4.36	0.046	0.708
8	1i8qA	0.491	5.42	0.065	0.805
9	3qdeA	0.490	4.71	0.067	0.739
10	1n7qA3	0.489	5.27	0.030	0.790

(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	0.11	6	2ihxA	ZN	Rep, Mult	161,164,173,175
2	0.10	5	4rku4	G3P	Rep, Mult	53,54,57
3	0.06	3	5klgA	6UC	Rep, Mult	58,61
4	0.04	2	1s5lD	CLA	Rep, Mult	46,49,57
5	0.02	1	3c67A	GLC	Rep, Mult	155,156,157
6	0.02	1	3au6A	ZN	Rep, Mult	109,173
7	0.02	1	4fs8A	CA	Rep, Mult	8,20
8	0.02	1	4tnhH	CLA	Rep, Mult	54,58
9	0.02	1	2xquA	CVM	Rep, Mult	46,50
10	0.02	1	3rkoN	LFA	Rep, Mult	58,59,62,81,95
11	0.02	1	2nyyA	CA	Rep, Mult	43,180
12	0.02	1	3o72C	OXY	Rep, Mult	100,182
13	0.02	1	3rkoC	LFA	Rep, Mult	57,60,64,67,68
14	0.02	1	3anuA	ZN	Rep, Mult	173,175

	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	2f8zF	0.430	5.41	0.059	0.739	2.5.1.10,2.5.1.1	172,174
2	0.060	1gojA	0.431	5.13	0.036	0.703	3.6.4.4	NA
3	0.060	2aeyA	0.414	5.62	0.033	0.708	3.2.1.80	88,114
4	0.060	1gtmA	0.371	5.84	0.034	0.682	1.4.1.3	NA
5	0.060	1i8qA	0.491	5.42	0.065	0.805	4.2.2.1	185
6	0.060	1ojnA	0.494	5.37	0.024	0.800	4.2.2.1	158
7	0.060	1rqiA	0.458	5.34	0.056	0.769	2.5.1.10	146
8	0.060	1v9lA	0.429	5.49	0.056	0.733	1.4.1.2	132
9	0.060	1f1sA	0.486	5.29	0.068	0.785	4.2.2.1	NA
10	0.060	1h54B	0.504	4.26	0.080	0.728	2.4.1.8	NA
11	0.060	1bvuA	0.424	5.29	0.028	0.713	1.4.1.3	NA
12	0.060	2bmaA	0.430	5.36	0.079	0.728	1.4.1.4	132
13	0.060	2a7vA	0.435	5.13	0.064	0.697	2.1.2.1	NA
14	0.060	2h8oA	0.436	5.51	0.069	0.759	2.5.1.10	NA
15	0.060	2e0wB	0.447	6.14	0.057	0.846	2.3.2.2	NA
16	0.060	2zxqA	0.445	4.86	0.067	0.692	3.2.1.97	135,147
17	0.060	2f89F	0.430	5.37	0.059	0.733	2.5.1.1,2.5.1.10	146
18	0.060	3i4zA	0.437	6.00	0.109	0.815	2.5.1.34	176
19	0.060	1rw9A	0.455	5.36	0.047	0.759	4.2.2.5	151

(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	0.508	4.64	0.07	0.76	3wirA	GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0033831
1	0.07	0.504	4.26	0.08	0.73	1h54B	GO:0003824 GO:0005975 GO:0030246
2	0.07	0.510	4.06	0.08	0.72	2eabA	GO:0003824 GO:0016020 GO:0016021 GO:0046872
3	0.07	0.467	4.33	0.07	0.68	2rdyA	GO:0003824 GO:0004560
4	0.07	0.342	5.49	0.06	0.57	4ufcB	GO:0003824 GO:0004560
5	0.06	0.396	5.77	0.04	0.70	3b1nB	GO:0000166 GO:0016301 GO:0016310 GO:0016740 GO:0016773
6	0.06	0.352	6.12	0.08	0.67	3h3eA	GO:0016787 GO:0046872
7	0.06	0.334	6.07	0.08	0.63	4pz2B	GO:0004029 GO:0008152 GO:0016491 GO:0016620 GO:0055114
8	0.06	0.346	5.78	0.04	0.63	1dbtA	GO:0003824 GO:0004590 GO:0005829 GO:0006207 GO:0006221 GO:0008152 GO:0016829 GO:0016831 GO:0044205
9	0.06	0.285	5.57	0.06	0.50	2mkkA	GO:0000166 GO:0000900 GO:0000932 GO:0003676 GO:0003723 GO:0003730 GO:0005634 GO:0005654 GO:0005737 GO:0005813 GO:0005886 GO:0006397 GO:0006412 GO:0006417 GO:0008135 GO:0008285 GO:0010976 GO:0014069 GO:0016020 GO:0017148 GO:0030054 GO:0030335 GO:0030425 GO:0030426 GO:0030529 GO:0032869 GO:0035925 GO:0042995 GO:0043005 GO:0043022 GO:0043025 GO:0045202 GO:0045211 GO:0045727 GO:0046872 GO:0048471 GO:0051028 GO:0051770 GO:0071222 GO:0071230 GO:0071456 GO:1990124 GO:2000766
10	0.06	0.490	4.71	0.07	0.74	3qdeA	GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738
11	0.06	0.327	5.82	0.05	0.60	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
12	0.06	0.335	6.28	0.06	0.65	3g5sA	GO:0005737 GO:0008033 GO:0008168 GO:0016491 GO:0016740 GO:0030698 GO:0032259 GO:0047151 GO:0050660 GO:0055114
13	0.06	0.315	5.12	0.03	0.50	5d5hA	GO:0000287 GO:0003677 GO:0003916 GO:0003917 GO:0005618 GO:0005829 GO:0005886 GO:0006265 GO:0016853 GO:0040007 GO:0046872 GO:0060701
14	0.06	0.326	6.42	0.06	0.67	4ic6A	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0009507 GO:0009534 GO:0009536 GO:0009543 GO:0009579 GO:0010206 GO:0016787 GO:0031977
15	0.06	0.327	5.76	0.07	0.58	3sqgC	GO:0015948 GO:0016740 GO:0050524
16	0.06	0.316	5.46	0.07	0.54	4gl4A	GO:0004022 GO:0005737 GO:0006069 GO:0008270 GO:0016491 GO:0046872 GO:0051903 GO:0055114
17	0.06	0.307	5.44	0.08	0.52	13gsA	GO:0000302 GO:0002674 GO:0004364 GO:0005615 GO:0005622 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006469 GO:0006749 GO:0006805 GO:0007417 GO:0008144 GO:0008152 GO:0008432 GO:0009636 GO:0009890 GO:0010804 GO:0014003 GO:0016740 GO:0019207 GO:0031100 GO:0031667 GO:0031982 GO:0032355 GO:0032691 GO:0032720 GO:0032869 GO:0032872 GO:0032873 GO:0032930 GO:0033591 GO:0035726 GO:0035730 GO:0035731 GO:0035732 GO:0043066 GO:0043124 GO:0043200 GO:0043295 GO:0043407 GO:0043409 GO:0043508 GO:0045471 GO:0046689 GO:0048147 GO:0051771 GO:0070026 GO:0070062 GO:0070372 GO:0070373 GO:0070664 GO:0071222 GO:0071364 GO:0071385 GO:0071460 GO:0071638 GO:0097057 GO:1901687 GO:2001237
18	0.06	0.279	5.54	0.05	0.48	1z81A	GO:0000413 GO:0003755 GO:0006457 GO:0016853

Consensus prediction of GO terms

Molecular Function	GO:0030246	GO:0004560	GO:0033831	GO:0046872
GO-Score	0.13	0.13	0.07	0.07
Biological Processes	GO:0005975
GO-Score	0.13
Cellular Component	GO:0016021
GO-Score	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.