I-TASSER results

I-TASSER results for job id Rv1269c

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

Input Sequence in FASTA format

>protein (124 residues)
MTTMITLRRRFAVAVAGVATAAATTVTLAPAPANAADVYGAIAYSGNGSWGRSWDYPTRA
AAEATAVKSCGYSDCKVLTSFTACGAVAANDRAYQGGVGPTLAAAMKDALTKLGGGYIDT
WACN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTTMITLRRRFAVAVAGVATAAATTVTLAPAPANAADVYGAIAYSGNGSWGRSWDYPTRAAAEATAVKSCGYSDCKVLTSFTACGAVAANDRAYQGGVGPTLAAAMKDALTKLGGGYIDTWACN
Prediction	CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEHCCCCCEEEEHCCCCHHHHHHHHHHHHCCCCCEEEEEHCCEEEEEHCCCCCEEHCCCCHHHHHHHHHHHCCCCEEEEEHCC
Conf.Score	9986545678899999999999988754678888888758999959998789858999999999999995999988999988969999859976554579999999999998699889987759
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTTMITLRRRFAVAVAGVATAAATTVTLAPAPANAADVYGAIAYSGNGSWGRSWDYPTRAAAEATAVKSCGYSDCKVLTSFTACGAVAANDRAYQGGVGPTLAAAMKDALTKLGGGYIDTWACN
Prediction	7542343433200223332322323332333435444200000014434202023154464045301740475502011224301000235742221324335402540275045231341318
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEHCCCCCEEEEHCCCCHHHHHHHHHHHHCCCCCEEEEEHCCEEEEEHCCCCCEEHCCCCHHHHHHHHHHHCCCCEEEEEHCC
MTTMITLRRRFAVAVAGVATAAATTVTLAPAPANAADVYGAIAYSGNGSWGRSWDYPTRAAAEATAVKSCGYSDCKVLTSFTACGAVAANDRAYQGGVGPTLAAAMKDALTKLGGGYIDTWACN

1r5tA

0.09

0.08

0.89

0.78

MUSTER

VGGIEDRQLEALKRAALKACELS--------SPYSHFRVGCSILTNNDVTGANVENASYSNAERSAMIQVLMAGHRSGW---KCMVICGDSEDQ---CVSPCGVCRQFINEFVVKFPIVMLNST

1r5tA

0.08

0.07

0.90

0.66

dPPAS

VGGIEDRQLEALKRAALKACELSY-------SPYSHFRVGCSILTNNDVTGANVENASYSNAERSAMIQVLMAGHRSGW---KCMVICGDSEDQ---CVSPCGVCRQFINEFVVKDFPIVMLNS

1ysdB

0.17

0.15

0.91

0.97

wdPPAS

VTGGMASKWDQKGMDIAYEEALLGYKEGGVP--------GGCLINKDGSLGRGHNMRFQKGGEISTLENCGRKDTTLYTTLSPCGAIIMYGIP-VVGENVNFKSKGEKYLQT--RGHEVVVRCK

3tsyA2

0.15

0.13

0.84

0.77

wMUSTER

MAPSLNIRQEIITAEVPKLGKEAALKALKEWGQPKSKITHLVFCTTSG-----VEMPG---ADYKLANLLGEPSVRVMLYHQGCYAGGTV-----------LRTAKDLAENN-AGARVLVVCSE

1ysdB

0.20

0.17

0.85

0.96

wPPAS

VTGGMQKGMDIAYEEALLGYKE-------GVP-------GGCLINKDGSLGRGHNMRFQKGGEISTLENCGRKDTTLYTTLSPCGAIIMYGIP-VVGENVNFKSKGEKYLQT--RGHEVVV-CK

1y04A

0.21

0.06

0.27

0.99

dPPAS2

MNAPARAAAKTAADALAAAKKTAADAAAAAAAA-------------------------------------------------------------------------------------------

1r5tA

0.09

0.08

0.88

0.89

PPAS

VGGIEDRQLEALKRAALKACELS--------SPYSHFRVGCSILTNNDVTGANVENASYSNAERSAMIQVLMAGHRS---GWKCMVICGDSED----QCVSPCGVCRQFINEFVVKDFPIVMLN

2g6vB1

0.15

0.14

0.92

0.81

Env-PPAS

-TLYIQGQDEYYARALKLAQRGR--FTTHPNP-----NVGCVIVKDGEIVGEGYHQRAEPHAEVHALRAGEKKGATAYVTLEPCDALIAAGVARVVASQNPQVAGRGLYRLQQAGIDVSHGL--

2fr6A

0.12

0.10

0.85

0.74

MUSTER

VEP----EHVQRLLLSSREAKKSA-------CPYSRFPVGAALLTGDGRSGCNIENACYPLAERTAIQKAISEGYK----FRAIAISSDLQEEFISPC----GACRQVMREFGTDWAVYMTKPD

2ltrA

0.11

0.10

0.85

0.65

dPPAS

NRTDLEMFLKKTPLMVLEEAAKAVYQKTPTWGTVELPEGFEMTLILNEITVKGQATSKKAARQKAAVEYLRK-------------VVEKGKHEIFFIPGTTKEEALSNIDQISDKAEE------

(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=-2.11

Estimated TM-score = 0.46±0.15

Estimated RMSD = 8.9±4.6Å

Download Model 2

C-score=-2.15

Download Model 3

C-score=-4.97

Download Model 4

C-score=-4.90

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	2nx8A	0.662	3.09	0.079	0.919
2	3dh1A	0.645	3.20	0.087	0.911
3	3zpcA1	0.642	3.19	0.098	0.903
4	2b3jC	0.641	3.15	0.136	0.887
5	1wwrC	0.637	3.19	0.115	0.887
6	2d5nD1	0.635	2.86	0.094	0.855
7	1z3aA	0.635	3.19	0.152	0.887
8	4p9cA	0.626	3.01	0.123	0.855
9	1ysdB	0.623	3.33	0.117	0.895
10	2g6vB	0.622	3.33	0.118	0.887

(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	0.06	4	3f1eC	MG	Rep, Mult	63,66
2	0.06	4	3lpeB	ZN	Rep, Mult	70,75,84,123
3	0.05	3	1z3a0	III	Rep, Mult	57,61,68,71
4	0.05	3	1dftA	CD	Rep, Mult	66,70,75,84
5	0.03	2	3m4oA	C7P	Rep, Mult	17,18,21
6	0.03	2	4gqtA	ZN	Rep, Mult	59,63
7	0.03	2	2hvwA	DDN	Rep, Mult	36,37,39,55,58,61,62,63,100,101
8	0.03	2	2bx2L	ZN	Rep, Mult	70,75
9	0.03	2	1pl0D	BW2	Rep, Mult	39,58,59,60
10	0.02	1	4k4aB	0FQ	Rep, Mult	16,20,39,40
11	0.02	1	4x23P	III	Rep, Mult	13,16
12	0.02	1	2ggpB	CU1	Rep, Mult	75,83,84
13	0.02	1	3n0aA	CA	Rep, Mult	90,113
14	0.02	1	1oz0B	PO4	Rep, Mult	42,43,51,52
15	0.02	1	1smyF	MG	Rep, Mult	8,12,42
16	0.02	1	4h83F	BCT	Rep, Mult	2,118
17	0.02	1	1qiyL	IPH	Rep, Mult	106,109

	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	0.066	3ijfX	0.542	3.17	0.121	0.750	3.5.4.5	67
2	0.066	1r5tA	0.559	3.39	0.048	0.823	3.5.4.5	63
3	0.066	2d30A	0.540	3.72	0.120	0.782	3.5.4.5	63
4	0.066	1vq2A	0.603	3.40	0.104	0.855	3.5.4.12	84,88
5	0.066	1mq0A	0.539	3.65	0.124	0.782	3.5.4.5	63
6	0.060	1qbaA	0.499	3.65	0.061	0.758	3.2.1.52	89
7	0.060	1aldA	0.499	4.68	0.055	0.879	4.1.2.13	NA
8	0.060	1xfbA	0.500	4.65	0.036	0.879	4.1.2.13	NA
9	0.060	3dmoA	0.558	3.61	0.133	0.806	3.5.4.5	63
10	0.060	2obcB	0.617	3.27	0.127	0.879	1.1.1.193,3.5.4.26	27,32,63
11	0.060	3dmoD	0.560	3.63	0.132	0.806	3.5.4.5	38
12	0.060	1cttA	0.513	3.19	0.121	0.734	3.5.4.5	38,82,84
13	0.060	1jtkA	0.548	3.54	0.135	0.782	3.5.4.5	63
14	0.060	2z3iA	0.544	3.31	0.081	0.766	3.5.4.23	NA
15	0.060	1fdjA	0.495	4.68	0.082	0.879	4.1.2.13	NA
16	0.060	1ox7B	0.620	3.37	0.108	0.895	3.5.4.1	80
17	0.060	2qubA	0.511	3.86	0.068	0.831	3.1.1.3	59
18	0.060	1zabA	0.552	3.75	0.143	0.798	3.5.4.5	63
19	0.060	1c7sA	0.475	4.97	0.070	0.887	3.2.1.52	NA
20	0.060	2w4lE	0.615	3.23	0.111	0.863	3.5.4.12	38,89
21	0.060	1xdmB	0.407	4.72	0.072	0.734	4.1.2.13	NA
22	0.060	2wanA	0.496	3.47	0.053	0.734	3.2.1.41	NA
23	0.060	1fbaA	0.496	4.70	0.073	0.879	4.1.2.13	NA
24	0.060	1xdmY	0.405	4.64	0.082	0.726	4.1.2.13	97

(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	0.10	0.645	3.20	0.09	0.91	3dh1A	GO:0002100 GO:0003824 GO:0005654 GO:0006400 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717 GO:0052718
1	0.10	0.643	3.21	0.12	0.90	2g6vB	GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
2	0.09	0.662	3.09	0.08	0.92	2nx8A	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
3	0.09	0.635	3.02	0.12	0.87	4g3mA	GO:0003824 GO:0005829 GO:0008152 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
4	0.08	0.637	3.19	0.12	0.89	1wwrC	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0019239 GO:0046872 GO:0052717
5	0.08	0.642	3.19	0.10	0.90	3zpcA	GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
6	0.08	0.635	3.19	0.15	0.89	1z3aA	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
7	0.08	0.641	3.15	0.14	0.89	2b3jC	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
8	0.08	0.626	3.45	0.11	0.90	2hxvA	GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0019239 GO:0046872 GO:0055114
9	0.08	0.607	3.42	0.11	0.85	2g84A	GO:0003824 GO:0008270 GO:0016787 GO:0046872
10	0.07	0.620	3.37	0.11	0.90	1ox7B	GO:0003824 GO:0004131 GO:0008270 GO:0008655 GO:0009451 GO:0016787 GO:0019858 GO:0044206 GO:0046087 GO:0046872
11	0.07	0.615	3.23	0.11	0.86	2w4lE	GO:0003824 GO:0004132 GO:0005829 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046134 GO:0046872 GO:0070062
12	0.07	0.613	3.20	0.11	0.85	2w4lC	GO:0003824 GO:0004132 GO:0005829 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046134 GO:0046872 GO:0070062
13	0.07	0.603	3.40	0.10	0.85	1vq2A	GO:0003824 GO:0004132 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046872
14	0.07	0.626	3.01	0.12	0.85	4p9cA	GO:0000166 GO:0003824 GO:0004132 GO:0006220 GO:0008270 GO:0016787 GO:0046872
15	0.07	0.614	2.98	0.15	0.85	2a8nB	GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
16	0.07	0.559	3.39	0.05	0.82	1r5tA	GO:0003824 GO:0004126 GO:0005634 GO:0005737 GO:0005829 GO:0006216 GO:0006217 GO:0008270 GO:0008655 GO:0009972 GO:0016787 GO:0042802 GO:0046872
17	0.07	0.606	3.44	0.10	0.86	2hvwA	GO:0003824 GO:0004132 GO:0006220 GO:0008270 GO:0016787 GO:0046872
18	0.07	0.554	3.35	0.15	0.76	1wkqA	GO:0003824 GO:0006144 GO:0006147 GO:0008270 GO:0008892 GO:0009451 GO:0016787 GO:0019239 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0008251	GO:0008270	GO:0016616	GO:0000166	GO:0050662
GO-Score	0.50	0.38	0.35	0.35	0.35
Biological Processes	GO:0002097	GO:0042727	GO:0006771	GO:0042364
GO-Score	0.50	0.35	0.35	0.35
Cellular Component	GO:0052718	GO:0005654	GO:0005829
GO-Score	0.10	0.10	0.09

(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.