I-TASSER results

I-TASSER results for job id Rv0049

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

Input Sequence in FASTA format

>protein (137 residues)
MDYTLRRRSLLAEVYSGRTGVSEVCDANPYLLRAAKFHGKPSRVICPICRKEQLTLVSWV
FGEHLGAVSGSARTAEELILLATRFSEFAVHVVEVCRTCSWNHLVKSYVLGAARPARPPR
GSGGTRTARNGARTASE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDYTLRRRSLLAEVYSGRTGVSEVCDANPYLLRAAKFHGKPSRVICPICRKEQLTLVSWVFGEHLGAVSGSARTAEELILLATRFSEFAVHVVEVCRTCSWNHLVKSYVLGAARPARPPRGSGGTRTARNGARTASE
Prediction	CCHHHHHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98999999999999968998777557889999999986967898888888887578999866533444676689999999998689779999997699996467777875688999898888887654445655459
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MDYTLRRRSLLAEVYSGRTGVSEVCDANPYLLRAAKFHGKPSRVICPICRKEQLTLVSWVFGEHLGAVSGSARTAEELILLATRFSEFAVHVVEVCRTCSWNHLVKSYVLGAARPARPPRGSGGTRTARNGARTASE
Prediction	76343523420441454624353014033203300522355474413114564033021020351363344243473045027625503011010046040110032112235664545554745554455554468
	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

CCHHHHHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
MDYTLRRRSLLAEVYSGRTGVSEVCDANPYLLRAAKFHGKPSRVICPICRKEQLTLVSWVFGEHLGAVSGSARTAEELILLATRFSEFAVHVVEVCRTCSWNHLVKSYVLGAARPARPPRGSGGTRTARNGARTASE

1orbA2

0.14

0.12

0.90

0.71

MUSTER

-NRSLTYEQVLENLESKRF---QLVDSRA----QGRYLGTQPEPDAVGLDSGHIRGSVNMPFMNFLTEDGFEKSPEELRAMFEAKKDLTKPLIATCRKGVTHIALAAYLCGKPDVA-FHRAPPETWVSQGKG-----

2lmkA

0.18

0.07

0.42

0.82

dPPAS

-----------------------------------------------------------------GSNPDPQEVQRALARILCALGEL-------------DKLVKDQANAGQQEFKLPKDFTGRSKCRSLGRIK--

2cttA

0.20

0.12

0.61

0.67

wdPPAS

GSSGME---TFNQAAKGTVNIMDTCER----------NGEPGTKVCHYCG-----------G------SGMETIN-------------PFVMRSTCRRCG----------GRGSPCVVCRGAGQAKQKKRSGPSSG-

3k70C

0.19

0.18

0.92

0.68

wMUSTER

DQYLVYRPDWLAQWETGH-LVEGLGEAQKALVEYTHQLGQPRWHRANL-CPPGLPSRVFICG--I-----SALPPVYLQALQALGKHIEIHLLFTCRY--WGDILAKLLTRQRRHSFEDRELPLFRDSENAGQLFNS

2cttA

0.20

0.12

0.61

0.73

wPPAS

GSSGME----FNQAAKGTVNIMDTCER----------NGEPTKQHCHYCG-----------G------SGMETINT-----------P-FVMRSTCRRCG----------GRGSPCVVCRGAGQAKQKKRSGPSSG-

2lmkA

0.18

0.07

0.42

1.09

dPPAS2

-----------------------------------------------------------------GSNPDPQEVQRALARILCALGEL-------------DKLVKDQANAGQQEFKLPKDFTGRSKCRSLGRIK--

3aayB2

0.16

0.13

0.82

0.73

PPAS

-N-----RAFRDEVLA-AINVKNLIDVRS----PDEFSGKILAPAHLPQEQSQR--INVPWSRAANE-DGTFKSDEELAKLYADAGDNSKETIAYRIGH--TWFVLRELLGHQNVK-------GSLVGAPIELGS--

1vw452

0.20

0.13

0.66

0.70

Env-PPAS

FE---QPTRELAMLCR----REGLEKPVSKLVAES---GRLSKS--PV-----FIVHVFSGEETLGEGYGS--SLKEAKARAAT-----------------DALMKWYCYEPLAQQEPVIDPGTVVV----------

3ippB3

0.13

0.12

0.90

0.71

MUSTER

LD----MEQARGLLHRQDA---SLVSIRS----WPEFIGTTSGYS-YIKPKGEIAGARWGHGSDFHNPDGTMRSADDITAMWKAWNKPEQQVSFYCGTGWRETFMYARAMGWKNVS--SSDPKNPVATGERGPDSSK

2kk9A

0.16

0.07

0.40

0.69

dPPAS

----------------------------------------------------------------KGLRRDLDASREAKKQLEAEQ----------------QKLEEQNKISEASRKGLRRDLDASREAKKQVEKA--

(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=-2.98

Estimated TM-score = 0.38±0.13

Estimated RMSD = 11.3±4.5Å

Download Model 2

C-score=-4.02

Download Model 3

C-score=-4.72

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.83

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	3aayB	0.685	3.16	0.151	0.920
2	1orbA	0.675	3.27	0.093	0.912
3	3utnX	0.665	3.26	0.101	0.942
4	3ippB	0.663	3.51	0.115	0.949
5	1uarA	0.657	3.35	0.144	0.912
6	3olhA2	0.655	3.34	0.115	0.883
7	3hzuA	0.644	3.40	0.157	0.920
8	1urhA1	0.641	3.08	0.092	0.869
9	1h4kX	0.631	3.28	0.127	0.861
10	1okgA1	0.596	3.51	0.086	0.839

(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	0.17	9	2dipA	ZN	Rep, Mult	46,49,96,99
2	0.07	4	3l9rC	NAG	Rep, Mult	7,8,11
3	0.06	3	1qxnA	PS5	Rep, Mult	28,96,99,100
4	0.04	2	1vf5N	CLA	Rep, Mult	11,14,15,95
5	0.04	2	4a0sA	CO8	Rep, Mult	7,14,95
6	0.02	1	4qugA	AZI	Rep, Mult	74,76,77
7	0.02	1	1e08A	SF4	Rep, Mult	23,93,94,104,106,107
8	0.02	1	1iyxB	MG	Rep, Mult	24,93,94,118
9	0.02	1	4bq5A	GAL	Rep, Mult	26,57
10	0.02	1	1hfeL	SF4	Rep, Mult	14,17,22,23,24,25,55
11	0.02	1	4buoA	GLY	Rep, Mult	2,3
12	0.02	1	3cvjD	MG	Rep, Mult	64,66,81

	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	0.067	2vswB	0.555	3.37	0.090	0.788	3.1.3.16,3.1.3.48	NA
2	0.066	3d1pA	0.533	3.54	0.086	0.766	2.8.1.1	NA
3	0.066	2gwfC	0.558	3.30	0.093	0.788	3.1.2.15	56,58
4	0.060	1c25A	0.520	3.80	0.083	0.759	3.1.3.48	NA
5	0.060	3lx4A	0.506	4.57	0.140	0.854	1.18.99.1	29
6	0.060	1ex9A	0.503	3.85	0.064	0.737	3.1.1.3	NA
7	0.060	1okgA	0.596	3.49	0.086	0.839	2.8.1.2	NA
8	0.060	1c4aA	0.495	4.53	0.115	0.861	1.12.7.2	NA
9	0.060	1qgeE	0.221	5.57	0.057	0.394	3.1.1.3	78,104
10	0.060	2lipA	0.505	3.92	0.061	0.759	3.1.1.3	55
11	0.060	1gn0A	0.501	3.34	0.072	0.693	2.8.1.1	37,100
12	0.060	1vcnA	0.465	5.11	0.109	0.861	6.3.4.2	NA
13	0.060	3hzuA	0.644	3.40	0.157	0.920	2.8.1.1	NA
14	0.060	1urhA	0.641	3.08	0.092	0.869	2.8.1.2	29
15	0.060	3bfjA	0.497	4.04	0.085	0.774	1.1.1.202	NA
16	0.060	1qgeD	0.467	3.83	0.085	0.708	3.1.1.3	57
17	0.060	3bfjT	0.499	4.09	0.092	0.781	1.1.1.202	130
18	0.060	3f4aB	0.518	3.57	0.162	0.759	3.1.3.16	NA
19	0.060	1hfeL	0.527	4.46	0.115	0.869	1.12.7.2	NA
20	0.060	2oucB	0.547	3.15	0.094	0.752	3.1.3.16,3.1.3.48	NA
21	0.060	3mmrA	0.492	4.43	0.039	0.818	3.5.3.1	NA
22	0.060	1hqdA	0.501	4.04	0.044	0.759	3.1.1.3	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	0.11	0.675	3.27	0.09	0.91	1orbA	GO:0003723 GO:0004792 GO:0005615 GO:0005739 GO:0005743 GO:0005759 GO:0008097 GO:0016740 GO:0030855 GO:0035928 GO:0051029 GO:0070062
1	0.10	0.678	3.22	0.15	0.92	3aaxB	GO:0004792 GO:0005618 GO:0005829 GO:0005886 GO:0016740
2	0.09	0.655	3.48	0.09	0.90	4jgtA	GO:0001822 GO:0001889 GO:0004792 GO:0005737 GO:0005739 GO:0005829 GO:0009440 GO:0009636 GO:0016740 GO:0016784 GO:0019346 GO:0021510 GO:0030054 GO:0042802 GO:0043005 GO:0045202 GO:0070062 GO:0070814
3	0.09	0.657	3.35	0.14	0.91	1uarA	GO:0004792 GO:0016740
4	0.08	0.665	3.26	0.10	0.94	3utnX	GO:0002098 GO:0002143 GO:0004792 GO:0005737 GO:0005739 GO:0016740
5	0.08	0.631	3.28	0.13	0.86	1h4kX	GO:0004792 GO:0005737 GO:0016740
6	0.08	0.663	3.51	0.12	0.95	3ippB	GO:0004792 GO:0016740 GO:0016783 GO:0042597
7	0.08	0.641	3.08	0.09	0.87	1urhA	GO:0004792 GO:0005737 GO:0005829 GO:0016740 GO:0016784 GO:0046677
8	0.07	0.614	3.35	0.09	0.85	1okgA	GO:0005829 GO:0016740 GO:0016784 GO:0019343 GO:0019499
9	0.07	0.639	3.34	0.14	0.90	3p3aA	GO:0004792 GO:0016740
10	0.07	0.644	3.40	0.16	0.92	3hzuA	GO:0004792 GO:0005618 GO:0005829 GO:0005886 GO:0016740
11	0.07	0.561	3.26	0.12	0.77	2eg4A	GO:0004792 GO:0016740 GO:0046872
12	0.07	0.536	3.39	0.12	0.75	1yt8A	GO:0004792 GO:0016740
13	0.07	0.537	3.47	0.09	0.77	3d1pA	GO:0004792 GO:0005739 GO:0016740
14	0.07	0.429	4.26	0.06	0.71	1tq1A	GO:0004792 GO:0009507 GO:0009536 GO:0016740
15	0.06	0.388	4.79	0.07	0.69	1s5pA	GO:0005737 GO:0006476 GO:0006935 GO:0008270 GO:0016787 GO:0034979 GO:0034983 GO:0036047 GO:0036048 GO:0036049 GO:0036054 GO:0036055 GO:0046872 GO:0070403
16	0.06	0.387	4.37	0.04	0.64	1o8oB	GO:0000166 GO:0003824 GO:0005524 GO:0005829 GO:0006777 GO:0008152 GO:0009734 GO:0016740 GO:0018315 GO:0030151 GO:0032324 GO:0046872 GO:0061598 GO:0061599
17	0.06	0.397	4.58	0.07	0.66	3iehA	GO:0008152 GO:0016787 GO:0016788 GO:0046872
18	0.06	0.326	5.49	0.03	0.63	5i1mV	GO:0000220 GO:0000324 GO:0000329 GO:0005773 GO:0005774 GO:0006461 GO:0006797 GO:0006810 GO:0006811 GO:0007035 GO:0015078 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016049 GO:0033179 GO:0046961 GO:0051117 GO:0070072

Consensus prediction of GO terms

Molecular Function	GO:0004792
GO-Score	0.40
Biological Processes	GO:0035928	GO:0030855	GO:0009440	GO:0001822	GO:0019346	GO:0021510	GO:0001889	GO:0009636	GO:0070814	GO:0002143
GO-Score	0.11	0.11	0.10	0.10	0.10	0.10	0.10	0.10	0.10	0.08
Cellular Component	GO:0044444	GO:0043231	GO:0031988	GO:1903561
GO-Score	0.51	0.51	0.38	0.38

(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.