I-TASSER results

I-TASSER results for job id Rv0566c

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

Input Sequence in FASTA format

>protein (163 residues)
MADSSFDIVSKVDRQEVDNALNQAAKELATRFDFRGTDTKIAWKGDEAVELTSSTEERVK
AAVDVFKEKLIRRDISLKAFEAGEPQASGKTYKVTGALKQGISSENAKKITKLIRDAGPK
NVKTQIQGDEVRVTSKKRDDLQAVIAMLKKADLDVALQFVNYR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MADSSFDIVSKVDRQEVDNALNQAAKELATRFDFRGTDTKIAWKGDEAVELTSSTEERVKAAVDVFKEKLIRRDISLKAFEAGEPQASGKTYKVTGALKQGISSENAKKITKLIRDAGPKNVKTQIQGDEVRVTSKKRDDLQAVIAMLKKADLDVALQFVNYR
Prediction	CCCCCCEEEHCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEHCCCCEEEEEHCCHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHCCCCCEEEHCCCEEEEHCCCHHHHHHHHHHHHHCCCCCCCEEEHCC
Conf.Score	9998745776455889999999999999865445898569998699789999789899999999999999998998555567865458987999999955877799999999999968865433454868998657789999999999986889886576579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MADSSFDIVSKVDRQEVDNALNQAAKELATRFDFRGTDTKIAWKGDEAVELTSSTEERVKAAVDVFKEKLIRRDISLKAFEAGEPQASGKTYKVTGALKQGISSENAKKITKLIRDAGPKNVKTQIQGDEVRVTSKKRDDLQAVIAMLKKADLDVALQFVNYR
Prediction	8653301010324354052015204432543140443704031566430303063432051034104530343704252053753643354130303035215573044004303755256043414454140324434201300310475617231426238
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEHCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEHCCCCEEEEEHCCHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHCCCCCEEEHCCCEEEEHCCCHHHHHHHHHHHHHCCCCCCCEEEHCC
MADSSFDIVSKVDRQEVDNALNQAAKELATRFDFRGTDTKIAWKGDEAVELTSSTEERVKAAVDVFKEKLIRRDISLKAFEAGEPQASGKTYKVTGALKQGISSENAKKITKLIRDAGPKNVKTQIQGDEVRVTSKKRDDLQAVIAMLKKADLDVALQFVNYR

1in0A

0.43

0.42

0.98

4.00

MUSTER

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.98

7.88

dPPAS

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.98

6.53

wdPPAS

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.97

4.58

wMUSTER

----SFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.98

5.20

wPPAS

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.98

17.95

dPPAS2

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.98

4.86

PPAS

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1in0A

0.43

0.42

0.98

7.08

Env-PPAS

---PSFDIVSEITLHEVRNAVENANRVLSTRYDFRGVEAVIELNKNETIKITTESDFQLEQLIEILIGSCIKRGIEHSSLDIPAESHHGKLYSKEIKLKQGIETEMAKKITKLVKDSKIK-VQTQIQGEQVRVTGKSRDDLQAVIQLVKSAELGQPFQFNNFR

1u8sB

0.16

0.15

0.93

0.83

MUSTER

LTQ-HLTAVGT-DRPGICNEVVRLVTQA-------GCNSRIAMFGKETLLMLISSPSNITRVETTLPLLGQQHDLITMMKRTSPHDHQTHAYTVEVYVE-SDDKLLTEKFTQFFAQRQIASLSAQTISKSARVDGCNLMQLQEEFDALCT-ALDVQGSLNFIK

4ky3A

0.12

0.10

0.83

1.09

dPPAS

GKNFDYTYTVTTE-SELQKVLNELDYIKKQG------------AKRVRISITARSSKEAYKFLAILAKVFAELGY--------------NDINRKTVRFRGDDLEALEKALKEIRQARKFAVTYTLDGNEITITGVPRQVLEELAKEAERLEFNITITITVTV

(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=1.91

Estimated TM-score = 0.98±0.04

Estimated RMSD = 1.4±1.3Å

Download Model 2

C-score=-2.28

Download Model 3

C-score=-2.51

Download Model 4

C-score=-2.27

Download Model 5

C-score=-2.97

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	1in0A	0.952	0.84	0.421	0.976
2	4a01A	0.521	4.35	0.049	0.785
3	2ajqA	0.500	3.96	0.103	0.693
4	4av3A	0.496	4.61	0.042	0.779
5	5dktA	0.492	4.26	0.050	0.718
6	2hhtA	0.488	4.37	0.063	0.730
7	3k5nA	0.486	4.77	0.058	0.755
8	2kzzA	0.486	4.56	0.062	0.736
9	4q5vA	0.481	4.82	0.032	0.712
10	4igbA	0.474	4.94	0.057	0.797

(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	0.20	2	1in0B	HG	Rep, Mult	20,66,70
2	0.19	2	1in0A	MMC	Rep, Mult	66,70,80
3	0.11	2	1l3vA	SUC	Rep, Mult	111,114,115,118,140,144
4	0.06	1	1nkeA	SUC	Rep, Mult	107,111,124,125,132
5	0.06	1	1in0A	NA	Rep, Mult	33,37,58
6	0.06	1	1njwA	SUC	Rep, Mult	22,41,42,50,80

	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	2hvgA	0.422	5.17	0.043	0.730	4.3.2.2	NA
2	0.060	1eulA	0.375	5.32	0.045	0.693	3.6.3.8	NA
3	0.060	1bgxT	0.474	4.47	0.049	0.718	2.7.7.7	120
4	0.060	2ckjA	0.445	5.49	0.053	0.834	1.17.1.4,1.17.3.2	NA
5	0.060	2cjbB	0.454	3.84	0.080	0.614	6.1.1.11	NA
6	0.060	2ajqA	0.500	3.96	0.103	0.693	2.7.7.7	100,130
7	0.060	1n1hA	0.449	4.97	0.057	0.755	2.7.7.48	NA
8	0.060	2gv9B	0.450	5.04	0.057	0.749	2.7.7.7	4,115
9	0.060	2j3lB	0.455	3.91	0.027	0.632	6.1.1.15	NA
10	0.060	1d8yA	0.492	4.56	0.062	0.742	2.7.7.7	NA
11	0.060	3cmqA	0.456	4.02	0.094	0.650	6.1.1.20	NA
12	0.060	3b9jI	0.307	4.58	0.022	0.478	1.17.1.4,1.17.3.2	NA
13	0.060	2e1qA	0.450	5.32	0.040	0.841	1.17.3.2,1.17.1.4	NA
14	0.060	1q8iA	0.492	4.79	0.058	0.761	2.7.7.7	30,68
15	0.060	2i09B	0.453	5.41	0.041	0.785	5.4.2.7	49,89
16	0.060	3kvnX	0.466	5.29	0.032	0.810	3.1.1.1	NA
17	0.060	2i4nB	0.450	3.79	0.036	0.626	6.1.1.15	NA
18	0.060	1qssA	0.456	4.81	0.029	0.724	2.7.7.7	44
19	0.060	3ikmD	0.468	4.89	0.071	0.755	2.7.7.7	126,132

(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	0.502	3.93	0.10	0.69	1sl0A	GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0006261 GO:0008408 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
1	0.07	0.502	3.93	0.10	0.69	1sksA	GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0006261 GO:0008408 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
2	0.07	0.500	3.96	0.10	0.69	2ajqA	GO:0003676 GO:0003677 GO:0003887 GO:0004518 GO:0004527 GO:0006260 GO:0006261 GO:0008408 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0039693 GO:0071897 GO:0090305
3	0.07	0.474	4.47	0.05	0.72	1bgxT	GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897
4	0.07	0.490	4.50	0.06	0.74	1kfdA	GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006139 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006974 GO:0008408 GO:0008409 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
5	0.07	0.492	4.56	0.06	0.74	1d8yA	GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006139 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006974 GO:0008408 GO:0008409 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
6	0.07	0.465	4.70	0.06	0.72	4dqqD	GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0006139 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0046872 GO:0071897 GO:0090305
7	0.07	0.464	4.44	0.07	0.68	4ds4D	GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0006139 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0046872 GO:0071897 GO:0090305
8	0.07	0.456	4.62	0.03	0.70	4n56A	GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897
9	0.07	0.441	4.83	0.04	0.71	4dleA	GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897
10	0.07	0.447	4.86	0.09	0.72	4x0pA	GO:0000166 GO:0000724 GO:0003676 GO:0003677 GO:0003682 GO:0003684 GO:0003887 GO:0005524 GO:0005634 GO:0005654 GO:0005694 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006302 GO:0006974 GO:0016446 GO:0016740 GO:0016779 GO:0043142 GO:0051260 GO:0051575 GO:0071897 GO:0097681 GO:2000042
11	0.07	0.401	5.21	0.03	0.71	4av3B	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
12	0.06	0.425	4.68	0.07	0.66	3l0mA	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
13	0.06	0.521	4.35	0.05	0.79	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
14	0.06	0.389	5.24	0.06	0.66	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
15	0.06	0.369	5.69	0.06	0.72	5bv7A	GO:0004607 GO:0004623 GO:0005576 GO:0005615 GO:0006629 GO:0006644 GO:0006656 GO:0008202 GO:0008203 GO:0008374 GO:0016740 GO:0016746 GO:0030301 GO:0034186 GO:0034364 GO:0034372 GO:0034375 GO:0034435 GO:0042157 GO:0042158 GO:0042632 GO:0043691 GO:0046470 GO:0046688 GO:0051384 GO:0070062 GO:0090107
16	0.06	0.349	5.11	0.05	0.61	3o65E	GO:0004843 GO:0005634 GO:0006351 GO:0006355 GO:0006508 GO:0008233 GO:0008234 GO:0008242 GO:0016579 GO:0016787 GO:0036459
17	0.06	0.466	4.40	0.05	0.68	4xviA	GO:0000724 GO:0003676 GO:0003677 GO:0003887 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0008409 GO:0016740 GO:0016779 GO:0019985 GO:0030332 GO:0036297 GO:0090305
18	0.06	0.327	5.48	0.07	0.61	3ovwA	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0008810 GO:0016787 GO:0016798 GO:0030245

Consensus prediction of GO terms

Molecular Function	GO:0034061	GO:0003676	GO:0004527
GO-Score	0.58	0.58	0.48
Biological Processes	GO:0006260	GO:0034654	GO:0044034	GO:0019079
GO-Score	0.58	0.58	0.37	0.37
Cellular Component	GO:0005829
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.