I-TASSER results

I-TASSER results for job id Rv0455c

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

Input Sequence in FASTA format

>protein (148 residues)
MSRLSSILRAGAAFLVLGIAAATFPQSAAADSTEDFPIPRRMIATTCDAEQYLAAVRDTS
PVYYQRYMIDFNNHANLQQATINKAHWFFSLSPAERRDYSEHFYNGDPLTFAWVNHMKIF
FNNKGVVAKGTEVCNGYPAGDMSVWNWA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSRLSSILRAGAAFLVLGIAAATFPQSAAADSTEDFPIPRRMIATTCDAEQYLAAVRDTSPVYYQRYMIDFNNHANLQQATINKAHWFFSLSPAERRDYSEHFYNGDPLTFAWVNHMKIFFNNKGVVAKGTEVCNGYPAGDMSVWNWA
Prediction	CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEHCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHCCCCEEEEEHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Conf.Score	9755678999999999988775478877778876799876455468999999998757884777788766666768899999999999969968999999876688744444577589998585345678889986999888777789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSRLSSILRAGAAFLVLGIAAATFPQSAAADSTEDFPIPRRMIATTCDAEQYLAAVRDTSPVYYQRYMIDFNNHANLQQATINKAHWFFSLSPAERRDYSEHFYNGDPLTFAWVNHMKIFFNNKGVVAKGTEVCNGYPAGDMSVWNWA
Prediction	7542443033102110311212332444334446624224310424042630241046342320231123274345245313530320142537524512562356432123234302010334211340263047235743431628
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEHCCCCHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHCCCCEEEEEHCCCCHHHHHHHHHHHCCCCCCCCCCCC
MSRLSSILRAGAAFLVLGIAAATFPQSAAADSTEDFPIPRRMIATTCDAEQYLAAVRDTSPVYYQRYMIDFNNHANLQQATINKAHWFFSLSPAERRDYSEHFYNGDPLTFAWVNHMKIFFNNKGVVAKGTEVCNGYPAGDMSVWNWA

2ff2B

0.17

0.97

0.72

MUSTER

TSKVEECVIMGGAVDVRGNVFLPSTGTAEWNIYWDPASAKTVFGCP-GLRRIMFSLDSTNTVPVSPYVQRFGEQTNFLLSILVGTMWAMCTHCELLRD-GDGYYAWDALTAAYVVDQKVANVDPVPIDVVVD--KQPNEG-ATVRTDA

5cwiA2

0.08

0.06

0.77

0.58

dPPAS

-ADIAKLCIKAASEAAEAASKAAELAQRHPDSQAARDAIKLASQAAEAVKLACELAQEHPNADIAKKCIKAASEAAEEASKAAEEAQRHPDSQKARDEIKEASQKAEEVKERCER---------------------------------

5cwpA2

0.17

0.13

0.76

0.58

wdPPAS

SSDVNEALKLIVEAIEAAVRAL-----EAAERTGD-P----------EVRELARELVRLAVEAAEEVQRNPSS--EEVNEALKKIVKAIQEAVESLREAEES---GDPEKRE-----------RERVREAVERAEEVQR-DPSGWE--

1ezrA

0.13

0.11

0.91

0.68

wMUSTER

VDRVKEVVLMGGGY--TGNASPV----AEFNVFIDPEAAHIVFNESWNV--TMVGLDLTHLALATPAVQKRREVGTKPAAFMLQILDFYT--KVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELN--GALTTG-MTVADFR

3hdeA

0.15

0.13

0.85

0.71

wPPAS

MPPLRKAVAAAIGGGAIAIASVLITGPSGNDGLE-YKDIVG-VWTTGKDIML----KTYTKAECKALLN-----KDLATVARQINPYI-DIPETMRGALYSFVYNVGAGNFRTSTLLRKI--NQG---DIKGACDQLRR-----WTYA

2pq4B

0.27

0.06

0.22

0.66

dPPAS2

LSR-RSFMKANAVAAAAAAAGLSVPGVARAVVGQ------------------------------------------------------------------------------------------------------------------

3hdeA

0.15

0.13

0.88

0.74

PPAS

MPPLRKAVAAAIGGGAIAIASVLITGPSGNDGLEGYKDIVG-VWTVCH--HTGKDIMLYTKAECKALLN-----KDLATVARQINPYIKDIPETMRGALYSFVYNVGAGNFRTSTLLRKI--NQG---DIKGACDQLRR-----WTYA

3hdeA

0.11

0.10

0.95

0.79

Env-PPAS

MPPLRKAVAAAIGGGAIAIASVLITGPSGNDGLEGVTGKDIMLGKTYTKAECKALLNKDLATVARQINPYIKVDPETMRGALYSFVYNVGAGNFRTSTLLRKINQGDGACDQLRRW--TYAGGKGLMTRREIEREIC------LWGQQ

1ezrA

0.12

0.11

0.92

0.69

MUSTER

VDRVKEVVLMGGGY-HTGNAS----PVAEFNVFIDPEAAHIVF--NESWNVTMVGLDLTHLALATPAVQKRREVGTKPAAFMLQILDFYT--KVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELN--GALTTG-MTVADFR

5ewpA1

0.10

0.09

0.90

0.58

dPPAS

LSFTSNDILRFDKAYDENDVQEFVNLCSSTCEIEKLRMHPWAADPKLSATQLAILASKENEPHYKDAIREANHELDRVHAAVVALSFLSVDNVKNCICMFESGALPYLISGMKS-------NIDGMKAACAQTCRNIFVL--------

(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=-3.61

Estimated TM-score = 0.32±0.11

Estimated RMSD = 13.1±4.1Å

Download Model 2

C-score=-4.20

Download Model 3

C-score=-3.85

Download Model 4

C-score=-4.85

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	1ezrA	0.629	3.99	0.094	0.919
2	3b9xA	0.626	3.77	0.066	0.905
3	3g5iA	0.624	3.67	0.159	0.878
4	2ff2B	0.619	4.14	0.144	0.926
5	4wr2A	0.617	3.69	0.112	0.878
6	4kpoA	0.606	4.07	0.145	0.919
7	3t8jA	0.606	3.92	0.095	0.905
8	4kpnA	0.605	4.21	0.109	0.926
9	3t8iA	0.597	4.19	0.050	0.926
10	4i70A	0.586	4.12	0.147	0.858

(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	0.07	3	4wzxA	CO	Rep, Mult	86,90
2	0.07	3	1hp0A	AD3	Rep, Mult	10,103,106,107
3	0.04	2	4dcaA	MG	Rep, Mult	115,141
4	0.04	2	2axtH	CLA	Rep, Mult	87,88,91
5	0.02	1	1m1bA	MG	Rep, Mult	31,66
6	0.02	1	2e1dA	SO3	Rep, Mult	66,94,96
7	0.02	1	3madA	PO4	Rep, Mult	115,116
8	0.02	1	2q97T	ATP	Rep, Mult	76,79
9	0.02	1	1rqfA	III	Rep, Mult	99,101
10	0.02	1	3leeF	MG	Rep, Mult	31,34,35
11	0.02	1	3zxsA	MG	Rep, Mult	31,101
12	0.02	1	1cb2A	MAN	Rep, Mult	106,110
13	0.02	1	5d56D	78M	Rep, Mult	78,79,82
14	0.02	1	2hr0B	THC	Rep, Mult	47,51,112,145
15	0.02	1	1kprA	III	Rep, Mult	17,101
16	0.02	1	4n3eN	2AN	Rep, Mult	84,87
17	0.02	1	2yhgA	MG	Rep, Mult	44,48,52

	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	3ikmD	0.427	4.85	0.047	0.730	2.7.7.7	NA
2	0.060	2ixaA	0.429	5.43	0.044	0.790	3.2.1.49	12,30
3	0.060	3b9xA	0.626	3.77	0.066	0.905	3.2.2.8	NA
4	0.060	1wz2A	0.436	5.31	0.049	0.790	6.1.1.4	NA
5	0.060	1r64A	0.433	4.73	0.053	0.737	3.4.21.61	NA
6	0.060	3a04A	0.432	4.63	0.063	0.730	6.1.1.2	NA
7	0.060	2c7gA	0.428	5.55	0.060	0.804	1.18.1.2	NA
8	0.060	1h2bB	0.425	4.63	0.049	0.710	1.1.1.1	86
9	0.060	1yoeA	0.620	3.72	0.159	0.878	3.2.2.8	NA
10	0.060	3iayA	0.433	5.16	0.035	0.770	2.7.7.7	NA
11	0.060	3mogA	0.425	4.41	0.040	0.655	1.1.1.157	64
12	0.060	3b9xC	0.545	3.95	0.066	0.797	3.2.2.8	NA
13	0.060	2oodA	0.450	4.97	0.031	0.811	3.5.4.3	NA
14	0.060	1p8jA	0.438	4.91	0.075	0.763	3.4.21.75	NA
15	0.060	2gafD	0.441	5.50	0.029	0.824	2.7.7.19	58
16	0.060	2ff2B	0.619	4.14	0.144	0.926	3.2.2.1	NA
17	0.060	1z8lA	0.445	4.94	0.053	0.784	3.4.17.21	NA
18	0.060	3e5rA	0.430	4.57	0.047	0.689	1.2.1.12	NA
19	0.060	2dsjA	0.431	4.81	0.043	0.750	2.4.2.2	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	0.10	0.629	3.99	0.09	0.92	1ezrA	GO:0005509 GO:0008152 GO:0008477 GO:0009117 GO:0016787 GO:0016798 GO:0016799 GO:0043101 GO:0045437 GO:0046872 GO:0047724
1	0.09	0.646	3.52	0.15	0.90	4wr2A	GO:0005737 GO:0006206 GO:0008152 GO:0015949 GO:0016787 GO:0016798 GO:0045437 GO:0046872
2	0.09	0.638	3.85	0.09	0.92	2masA	GO:0008152 GO:0009117 GO:0016787 GO:0016798 GO:0016799 GO:0046872
3	0.08	0.624	3.77	0.07	0.91	3mkmA	GO:0005509 GO:0006206 GO:0008152 GO:0016787 GO:0016798 GO:0016799 GO:0046133 GO:0046872 GO:0050263
4	0.08	0.624	3.67	0.16	0.88	3g5iA	GO:0005509 GO:0005737 GO:0005829 GO:0006152 GO:0006206 GO:0008152 GO:0008477 GO:0015949 GO:0016787 GO:0016798 GO:0016799 GO:0045437 GO:0046133 GO:0047405
5	0.08	0.605	4.21	0.11	0.93	4kpnA	GO:0005829 GO:0006152 GO:0008152 GO:0008477 GO:0016787 GO:0016798
6	0.07	0.615	3.91	0.13	0.91	4i72A	GO:0005829 GO:0006152 GO:0006166 GO:0008152 GO:0008477 GO:0016787 GO:0016798 GO:0016810 GO:0020015 GO:0046872
7	0.07	0.597	4.19	0.05	0.93	3t8iA	GO:0005829 GO:0006152 GO:0008152 GO:0008477 GO:0016787 GO:0016798 GO:0016799 GO:0046872
8	0.07	0.606	4.07	0.14	0.92	4kpoA	GO:0008152 GO:0016787 GO:0016798 GO:0046872
9	0.07	0.606	3.92	0.10	0.91	3t8jA	GO:0005829 GO:0006152 GO:0008152 GO:0008477 GO:0016787 GO:0016798
10	0.07	0.619	4.14	0.14	0.93	2ff2B	GO:0016787 GO:0046872
11	0.07	0.578	4.16	0.11	0.88	3fz0B	GO:0005829 GO:0006152 GO:0006179 GO:0006190 GO:0008152 GO:0008477 GO:0016787 GO:0016798 GO:0046872 GO:0047724
12	0.07	0.571	4.23	0.11	0.88	2c40A	GO:0016787 GO:0046872
13	0.07	0.545	3.95	0.07	0.80	3b9xC	GO:0005509 GO:0005829 GO:0006152 GO:0006206 GO:0008152 GO:0008477 GO:0016787 GO:0016798 GO:0016799 GO:0042802 GO:0045437 GO:0046133 GO:0046872 GO:0050263
14	0.06	0.365	5.05	0.08	0.65	4ysnC	GO:0003824 GO:0008483 GO:0016853 GO:0030170
15	0.06	0.322	5.59	0.05	0.64	3nziA	GO:0001558 GO:0001890 GO:0004252 GO:0005520 GO:0005576 GO:0005615 GO:0005737 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008236 GO:0016020 GO:0016787 GO:0019838 GO:0022617 GO:0030512 GO:0030514 GO:0031012 GO:0050679 GO:0050687 GO:0060718 GO:0070062 GO:0097187
16	0.06	0.329	4.43	0.05	0.54	2dx7A	GO:0006520 GO:0006807 GO:0008152 GO:0016853 GO:0016855 GO:0036361 GO:0047689
17	0.06	0.328	5.30	0.03	0.59	3ianA	GO:0004553 GO:0004568 GO:0005576 GO:0005975 GO:0006032 GO:0008152 GO:0016787 GO:0016798 GO:0030246
18	0.06	0.304	4.73	0.07	0.51	3vcoA	GO:0004146 GO:0006545 GO:0009165 GO:0016491 GO:0050661 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0050263	GO:0046872
GO-Score	0.48	0.31
Biological Processes	GO:0009112	GO:0006753	GO:0046135	GO:0042454	GO:0046131
GO-Score	0.46	0.35	0.30	0.30	0.30
Cellular Component	GO:0044424
GO-Score	0.32

(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.