I-TASSER results

I-TASSER results for job id Rv2309A

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

Input Sequence in FASTA format

>protein (95 residues)
MATSSDDITINRHPPLNCAVNRHDESRRSPLRRGLLANGLRERQAGALFERYESQFDSFG
YIEKVRYRGSGYRVEDVYARADSGPSAGAELPVGP

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MATSSDDITINRHPPLNCAVNRHDESRRSPLRRGLLANGLRERQAGALFERYESQFDSFGYIEKVRYRGSGYRVEDVYARADSGPSAGAELPVGP
Prediction	CCCCCCCEEEHCCCCCCCHCCCCCCHHHCHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEHCCCCCEEEEEEEHCCCCCCCCCCCCCCC
Conf.Score	99888866886799974434445555556788878777655776779999998764555646788885888667777665478988887789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MATSSDDITINRHPPLNCAVNRHDESRRSPLRRGLLANGLRERQAGALFERYESQFDSFGYIEKVRYRGSGYRVEDVYARADSGPSAGAELPVGP
Prediction	74466551415533414132544575444413422234314644143215414641542220441434344241441244166345343624658
	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

CCCCCCCEEEHCCCCCCCHCCCCCCHHHCHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCEEEEEHCCCCCEEEEEEEHCCCCCCCCCCCCCCC
MATSSDDITINRHPPLNCAVNRHDESRRSPLRRGLLANGLRERQAGALFERYESQFDSFGYIEKVRYRGSGYRVEDVYARADSGPSAGAELPVGP

2hhpA1

0.25

0.21

0.84

0.78

MUSTER

VHGPGSDIDTL------VVVPKHVT--REDFFTVFDSL-LRERKELDEIAPVP---DAFVPIIKIKF--SGISIDLICARLD-QPQVPLSLTLSD

4ypiC1

0.18

0.17

0.95

0.71

dPPAS

QVNNLEEICQLIIQAFEAGVDFQESA-----DSFLLMLCLHHAYQGLFLESGAVKYEGHGFRFEVKKRDGVKRLEELLPAVSSGKNIKRTLAAMP

4nx9A2

0.27

0.24

0.91

0.61

wdPPAS

AATASGDIAID-GSAVNVKVDKGNET--AEQAAAKIAAAVNDANVGGAF----TDGAQISYVSKASADGTTSAVSGVAIT-DTG-STGAGTAAGT

2zwvA1

0.32

0.25

0.80

0.77

wMUSTER

AAGAYDLVVLA--LPA---------GRGTAYVQASLVAAARARMGGRLFERYFKEARALGYGVVVRREG-PYRVALLEKEKEAPP-----LPS--

1x6fA

0.43

0.32

0.73

0.53

wPPAS

SSGSSGDFIILGNGPQNC---KHCDSKQSELTSHLNIHN-EEFQKRAK-ER-RKQLLS-----KQKY-ADG-------AFADSGPSSG-------

3efcA4

0.23

0.18

0.77

0.73

dPPAS2

-------PTIAS---ITFSGNK--SVKDDMLKQNLEASGVRVGTIADIEKGLEDFYYSVGKYSSVKAVPRN-RVDLKLVF-QEGVSA--------

1x4wA

0.28

0.18

0.63

0.61

PPAS

--GSSGS---SGSRSKQKSRRRCFQCQT---KLELVQQELGSCRCGYVFEQHDCTFD---------HMGRG-----------SGPSSG-------

3trrA1

0.22

0.18

0.80

0.72

Env-PPAS

M---ADEVLIEQRDRV--LLNR-------PDARNAV-NRAVSQGLAAAADQLDSS-AD---LSVAIITGAG-GNMDLKAFVS-GEAVLSERGLGF

5bv3A

0.21

0.20

0.97

0.78

MUSTER

FSEKDDGFLIL-GMNLDAIVYRTDKTIRDYSDRQWLIN-LNNKIRSIVPGCYNYAVHPDELRILVHYQPSYYHF-NIHIVNIKHPGLGNSIAAGK

3efcA4

0.22

0.17

0.78

0.70

dPPAS

-------PTIAS-----ITFSGNKSVKDDMLKQNLEASGVRVGTIADIEKGLEDFYYSVGKVKAVVTPLPRNRVDLKLVF-QEGVSA--------

(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=-3.54

Estimated TM-score = 0.33±0.11

Estimated RMSD = 11.8±4.5Å

Download Model 2

C-score=-3.58

Download Model 3

C-score=-3.72

Download Model 4

C-score=-4.40

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	3ronA	0.572	3.25	0.065	0.884
2	1cbyA	0.521	3.75	0.078	0.874
3	3iygQ	0.520	4.49	0.088	0.905
4	4km3A	0.515	3.79	0.011	0.853
5	4zohA1	0.515	3.57	0.106	0.800
6	1a6jB	0.511	3.84	0.047	0.874
7	4lgvA2	0.509	4.14	0.081	0.895
8	1a6eB	0.509	4.47	0.065	0.905
9	4qr8A	0.508	3.96	0.102	0.895
10	5cnxA2	0.508	3.62	0.080	0.842

(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	0.35	6	5hc9B	MG	Rep, Mult	7,9,73,75
2	0.06	1	1lamA	CO3	Rep, Mult	29,30,32,33,53
3	0.06	1	3aodA	MIY	Rep, Mult	59,62,64
4	0.06	1	2ddsB	CO	Rep, Mult	11,42

	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	1t3qB	0.495	3.99	0.091	0.832	1.3.99.17	NA
2	0.060	1s9rA	0.478	3.96	0.084	0.779	3.5.3.6	31
3	0.060	1jrpB	0.479	3.89	0.055	0.821	1.17.1.4	31,39,44
4	0.060	1jawA	0.497	4.32	0.045	0.853	3.4.11.9	NA
5	0.060	2rfbA	0.481	4.06	0.032	0.789	1.14.14.1	NA
6	0.060	2a9gD	0.483	4.12	0.054	0.789	3.5.3.6	4
7	0.060	1spiA	0.409	4.30	0.066	0.821	3.1.3.11	NA
8	0.060	1wn1A	0.476	4.12	0.045	0.821	3.4.-.-	NA
9	0.060	1pv9B	0.450	4.27	0.046	0.800	3.4.13.9	NA
10	0.060	1wy2A	0.474	4.28	0.045	0.842	3.4.13.9	NA
11	0.060	2b3lA	0.495	4.16	0.046	0.874	3.4.11.18	17
12	0.060	3ctzA	0.490	3.97	0.065	0.884	3.4.11.9	NA
13	0.060	3ejbH	0.493	4.12	0.033	0.800	1.14.-.-	NA
14	0.060	11asA	0.479	4.01	0.133	0.842	6.3.1.1	66
15	0.060	12asA	0.476	4.02	0.133	0.842	6.3.1.1	80
16	0.060	1kp0A	0.483	4.35	0.067	0.853	3.5.3.3	NA
17	0.060	1chmA	0.486	4.37	0.080	0.853	3.5.3.3	NA
18	0.060	2oknA	0.495	4.30	0.045	0.863	3.4.13.9	82,88,90
19	0.060	1o0xA	0.500	4.19	0.034	0.884	3.4.11.18	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	0.07	0.569	3.24	0.05	0.88	3ronB	GO:0005576 GO:0009405 GO:0030435
1	0.07	0.504	3.68	0.08	0.85	1pp0B	GO:0005576 GO:0009405
2	0.07	0.521	3.75	0.08	0.87	1cbyA	GO:0005576 GO:0009405 GO:0030435
3	0.07	0.423	4.58	0.01	0.79	4b2td	GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0005929 GO:0006457 GO:0042470 GO:0042995 GO:0051082
4	0.07	0.409	4.43	0.12	0.78	5da8L	GO:0000166 GO:0005524 GO:0005737 GO:0006457 GO:0042026 GO:0051082
5	0.07	0.527	3.60	0.04	0.89	2rciA	GO:0005576 GO:0009405 GO:0030435
6	0.07	0.422	4.69	0.04	0.80	4b2tG	GO:0000166 GO:0002199 GO:0005524 GO:0005737 GO:0005832 GO:0005874 GO:0005886 GO:0006457 GO:0007339 GO:0043209 GO:0044297 GO:0044822 GO:0046931 GO:0051082 GO:0070062 GO:1901998
7	0.07	0.445	3.93	0.05	0.74	4xciB	GO:0000166 GO:0005524 GO:0006457 GO:0051082
8	0.07	0.444	4.43	0.02	0.81	3iygD	GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0005929 GO:0006457 GO:0042470 GO:0042995 GO:0051082
9	0.07	0.407	4.73	0.09	0.79	4a0oM	GO:0000166 GO:0002199 GO:0005524 GO:0005737 GO:0005832 GO:0005874 GO:0006457 GO:0007339 GO:0031625 GO:0043209 GO:0044297 GO:0051082 GO:0051131 GO:0070062 GO:1901998
10	0.07	0.448	4.53	0.05	0.82	3aq1B	GO:0000166 GO:0005524 GO:0006457 GO:0051082
11	0.07	0.508	4.29	0.12	0.88	1a6dB	GO:0000166 GO:0005524 GO:0006457 GO:0051082
12	0.07	0.431	4.52	0.07	0.78	1iokA	GO:0000166 GO:0005524 GO:0005737 GO:0006457 GO:0042026 GO:0051082
13	0.06	0.507	4.34	0.08	0.87	4b2tq	GO:0000166 GO:0005524 GO:0005737 GO:0005815 GO:0005832 GO:0005856 GO:0005929 GO:0006457 GO:0042995 GO:0051082
14	0.06	0.488	4.33	0.05	0.87	3losA	GO:0000166 GO:0005524 GO:0006457 GO:0051082
15	0.06	0.502	4.63	0.06	0.93	4v94E	GO:0000166 GO:0005524 GO:0005737 GO:0005832 GO:0006457 GO:0051082
16	0.06	0.430	4.66	0.03	0.80	4v81C	GO:0000166 GO:0005524 GO:0005737 GO:0005832 GO:0006457 GO:0051082
17	0.06	0.408	3.48	0.06	0.66	3c5iD	GO:0046872
18	0.06	0.414	4.64	0.10	0.77	5da8M	GO:0000166 GO:0005524 GO:0005737 GO:0006457 GO:0042026 GO:0051082

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0051082
GO-Score	0.13	0.13
Biological Processes	GO:0051704
GO-Score	0.37
Cellular Component	GO:0005576	GO:0005832	GO:0005929	GO:0042470	GO:0005815
GO-Score	0.18	0.07	0.07	0.07	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.