I-TASSER results

I-TASSER results for job id Rv0569

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

Input Sequence in FASTA format

>protein (88 residues)
MKAKVGDWLVIKGATIDQPDHRGLIIEVRSSDGSPPYVVRWLETDHVATVIPGPDAVVVT
AEEQNAADERAQHRFGAVQSAILHARGT

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MKAKVGDWLVIKGATIDQPDHRGLIIEVRSSDGSPPYVVRWLETDHVATVIPGPDAVVVTAEEQNAADERAQHRFGAVQSAILHARGT
Prediction	CCCCCCEEEEEHCCCCCCCCEEEEEEEEHCCCCCCCEEEEHCCCCCEEEEHCCCCCEEHCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Conf.Score	9888996999986778887578999999879999987899857996899866999599858887754556677777788887656889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MKAKVGDWLVIKGATIDQPDHRGLIIEVRSSDGSPPYVVRWLETDHVATVIPGPDAVVVTAEEQNAADERAQHRFGAVQSAILHARGT
Prediction	7615342301043543644534030220327845220302144643402001232031434565647564455434323322344668
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEEEHCCCCCCCCEEEEEEEEHCCCCCCCEEEEHCCCCCEEEEHCCCCCEEHCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
MKAKVGDWLVIKGATIDQPDHRGLIIEVRSSDGSPPYVVRWLETDHVATVIPGPDAVVVTAEEQNAADERAQHRFGAVQSAILHARGT

2a7yA

0.60

0.55

0.91

3.45

MUSTER

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGH--------AAT

2a7yA

0.59

0.53

0.91

4.42

dPPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT--------

2a7yA

0.59

0.53

0.91

4.92

wdPPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT--------

2a7yA

0.59

0.53

0.90

3.73

wMUSTER

-HAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGH--------AAT

2a7yA

0.60

0.55

0.91

4.55

wPPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGH--------AAT

2a7yA

0.59

0.53

0.91

7.67

dPPAS2

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT--------

2a7yA

0.59

0.53

0.91

4.50

PPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT--------

2a7yA

0.59

0.53

0.91

4.22

Env-PPAS

MHAKVGDYLVVKGTTTERHDQHAEIIEVRSADGSPPYVVRWLVNGHETTVYPGSDAVVVTATEHAEAEKRAAARAGHAAT--------

1n27A

0.19

0.18

0.97

0.86

MUSTER

GEYKAGDLVFAKMK--GYPHWPARIDELPEGAVKPPYPIFFFGTHETAFLGPK-DLFPYKEYKDKFGKSNKRKGFNEGLWEIENSGPS

2efiA

0.09

0.08

0.92

dPPAS

PKFQEGERVLCF---HGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVD----TNLQKQRELQKANQEQYAEGKM

(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=0.85

Estimated TM-score = 0.83±0.08

Estimated RMSD = 2.1±1.7Å

Download Model 2

C-score=-2.20

Download Model 3

C-score=-2.54

Download Model 4

C-score=-0.47

Download Model 5

C-score=-0.80

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	2a7yA	0.848	0.98	0.587	0.909
2	5aj3j	0.549	3.82	0.098	0.886
3	4bb7A	0.498	3.61	0.115	0.750
4	3j7aF	0.491	3.67	0.085	0.750
5	3mx1A	0.488	3.85	0.108	0.830
6	5g47A	0.487	4.13	0.058	0.852
7	3l83A	0.487	3.81	0.046	0.807
8	3j38E	0.486	3.87	0.060	0.761
9	1kolA	0.486	4.18	0.074	0.841
10	2xzmW	0.485	3.83	0.086	0.761

(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	0.09	4	1izlD	PHO	Rep, Mult	77,78,81,82
2	0.07	3	2onk2	III	Rep, Mult	10,24,25,26,27,28,38,49,83
3	0.04	2	3phxA	ZN	Rep, Mult	6,7
4	0.04	2	4ireA	OXL	Rep, Mult	66,70,73
5	0.04	2	3zt6A	ACX	Rep, Mult	52,53
6	0.02	1	4nx3D	ARF	Rep, Mult	40,45
7	0.02	1	3quiA	ADP	Rep, Mult	10,57,59
8	0.02	1	2ih9B	5AX	Rep, Mult	84,87
9	0.02	1	1f5fA	ZN	Rep, Mult	46,55
10	0.02	1	3aohD	QNA	Rep, Mult	10,11,21,55
11	0.02	1	1a3uA	CA	Rep, Mult	32,55,56
12	0.02	1	1bl3C	MG	Rep, Mult	7,68
13	0.02	1	2ql2C	NUC	Rep, Mult	70,74
14	0.02	1	4h13D	TDS	Rep, Mult	75,78
15	0.02	1	2g4lA	SO4	Rep, Mult	30,32,33

	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	3hlkB	0.440	4.21	0.038	0.761	3.1.2.2	13
2	0.060	1sevA	0.449	4.31	0.076	0.750	1.1.1.37	NA
3	0.060	1lldB	0.412	4.26	0.050	0.727	1.1.1.27	33
4	0.060	2el7A	0.460	3.74	0.095	0.739	6.1.1.2	NA
5	0.060	1jqiA	0.451	3.94	0.045	0.795	1.3.99.2	63
6	0.060	2vumA	0.463	3.91	0.067	0.807	2.7.7.6	NA
7	0.060	2fekA	0.439	4.24	0.027	0.750	3.1.3.48	NA
8	0.060	3cgvA	0.438	4.91	0.114	0.864	1.3.1.-	NA
9	0.060	1y6jA	0.442	3.50	0.013	0.693	1.1.1.37	NA
10	0.060	2g8sA	0.442	4.00	0.054	0.739	1.1.5.-	NA
11	0.060	3k2iA	0.446	3.79	0.037	0.750	3.1.2.2	23
12	0.060	1dt5C	0.374	4.06	0.000	0.602	3.1.1.3	NA
13	0.060	1khoA	0.421	3.63	0.023	0.670	3.1.4.3	20
14	0.060	1ca1A	0.429	3.21	0.023	0.659	3.1.4.3	20
15	0.060	1zggA	0.442	3.88	0.014	0.727	3.1.3.48	NA
16	0.060	2wyhA	0.439	4.58	0.023	0.784	3.2.1.24	2,34
17	0.060	2z1qB	0.468	4.45	0.034	0.807	1.3.99.3	69
18	0.060	1vqwA	0.456	3.96	0.056	0.807	1.14.13.-	NA
19	0.060	1ynnD	0.471	3.68	0.086	0.784	2.7.7.6	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	0.69	0.848	0.98	0.59	0.91	2a7yA	GO:0005618
1	0.07	0.540	3.57	0.10	0.84	5aj3j	GO:0003735 GO:0005739 GO:0032543
2	0.07	0.490	3.75	0.09	0.75	4btsAW	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
3	0.07	0.467	3.17	0.09	0.66	1w4sA	GO:0003677 GO:0003682 GO:0005634 GO:0006351 GO:0006355 GO:0016568
4	0.07	0.486	3.87	0.06	0.76	4v6wAE	GO:0000022 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0007052 GO:0019843 GO:0022627 GO:0030529 GO:0051297 GO:0051298
5	0.07	0.502	3.27	0.10	0.73	5hh7A	GO:0000166 GO:0000808 GO:0003677 GO:0003682 GO:0005524 GO:0005634 GO:0006260 GO:0006351 GO:0006355 GO:0008270 GO:0009567 GO:0010385 GO:0046872
6	0.07	0.480	3.56	0.07	0.74	4kzxE	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
7	0.07	0.498	3.61	0.12	0.75	4bb7A	GO:0000724 GO:0003682 GO:0005634 GO:0006276 GO:0006303 GO:0006337 GO:0006351 GO:0006355 GO:0006368 GO:0007059 GO:0007062 GO:0015616 GO:0016568 GO:0016586 GO:0030435 GO:0042173 GO:0043044 GO:0070914
8	0.07	0.470	3.74	0.07	0.75	4v8mA1	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0022627 GO:0030529 GO:0032403
9	0.07	0.452	3.71	0.05	0.76	1o1yA	GO:0003824 GO:0005829
10	0.07	0.491	3.67	0.09	0.75	3j7aF	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0015935 GO:0019843 GO:0022627 GO:0030529
11	0.07	0.486	3.85	0.07	0.76	5it9E	GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
12	0.06	0.277	4.99	0.02	0.62	3mx4A	GO:0004519 GO:0006259 GO:0009036 GO:0016787 GO:0090305
13	0.06	0.407	4.30	0.03	0.69	2yk0A	GO:0004872 GO:0009405 GO:0016020 GO:0016021 GO:0046872
14	0.06	0.405	4.33	0.08	0.72	2nv2J	GO:0004359 GO:0005829 GO:0006541 GO:0006543 GO:0008614 GO:0016787 GO:0016829 GO:0036381 GO:0042819 GO:0042823 GO:1903600
15	0.06	0.407	4.11	0.06	0.70	1kplB	GO:0005216 GO:0005247 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006821 GO:0015108 GO:0015297 GO:0016020 GO:0016021 GO:0034220 GO:0055085 GO:1902476 GO:1903959
16	0.06	0.366	3.92	0.05	0.65	3tqiA	GO:0000166 GO:0003921 GO:0003922 GO:0005524 GO:0005829 GO:0006164 GO:0006177 GO:0006541 GO:0016462 GO:0016874
17	0.06	0.384	4.27	0.05	0.68	4arvA	GO:0003993 GO:0016311
18	0.06	0.387	3.74	0.05	0.68	4ft4B	GO:0003677 GO:0003682 GO:0003886 GO:0005634 GO:0006351 GO:0006355 GO:0008168 GO:0016568 GO:0016740 GO:0032259 GO:0090116

Consensus prediction of GO terms

Molecular Function	GO:0005198
GO-Score	0.37
Biological Processes	GO:0000022	GO:0016568	GO:0051298	GO:0032543	GO:0006355
GO-Score	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0005618
GO-Score	0.69

(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.