I-TASSER results

I-TASSER results for job id Rv0789c

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

Input Sequence in FASTA format

>protein (199 residues)
MSRRAIHSGRAAPRRSGNSHLVLRNRVPSSKDSPRRRPHHEFMTESIGEPLSTNLIERYL
RARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTIRVSPAYFFPATDHTRLAE
IVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDDFATFVDNAVSAATELFGQ
LTAAGLPPTATPPLLRDAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSRRAIHSGRAAPRRSGNSHLVLRNRVPSSKDSPRRRPHHEFMTESIGEPLSTNLIERYLRARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTIRVSPAYFFPATDHTRLAEIVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDDFATFVDNAVSAATELFGQLTAAGLPPTATPPLLRDAG
Prediction	CCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCEEHCCCCCCCCHHHHHHHHHHHHCCEEEEHCCCCEEEEEHCCCCEEEEEEEHCCCCCCEEEEEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEHCCCCCEEEEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Conf.Score	9855454577777667764445346667788888778764444445677655999999999879647874789868998578867999999858988689999975666787787999999999865888857999867999789999987644579999999999999999999999999998689999987445789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MSRRAIHSGRAAPRRSGNSHLVLRNRVPSSKDSPRRRPHHEFMTESIGEPLSTNLIERYLRARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTIRVSPAYFFPATDHTRLAEIVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDDFATFVDNAVSAATELFGQLTAAGLPPTATPPLLRDAG
Prediction	7644324434434444334311335413556536543332311243244412351043104444241135554332111242443010103024644310302133322131742420141043045663403010322744430202143332645043640241043104202510540463363367544135658
	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                 180

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCEEHCCCCCCCCHHHHHHHHHHHHCCEEEEHCCCCEEEEEHCCCCEEEEEEEHCCCCCCEEEEEEEHCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEHCCCCCEEEEEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
MSRRAIHSGRAAPRRSGNSHLVLRNRVPSSKDSPRRRPHHEFMTESIGEPLSTNLIERYLRARGRRYFRGHHDAEFFFVANAHLRLHVHLEISPAYRDVFTIRVSPAYFFPATDHTRLAEIVNAWNLQNHEVTAIVHGSSDPHRIGVAAERSLIRDRIRFDDFATFVDNAVSAATELFGQLTAAGLPPTATPPLLRDAG

2plgA

0.12

0.09

0.72

1.13

wdPPAS

------------------------------LTVSEVQPVSPASLDAPLE--AVEIIETVISSLHQGLVGQTDSGKIWFRYGS---AEVFVQLSGHEEDFLTIWSPV--PLPVADELALYRKLLTLNWLTTFEAHFAIAEE----QVQVVASRTLG-GITAGEISRLITIVATLADDYDDALRAEFK-------------

2plgA

0.12

0.09

0.72

0.96

wPPAS

------------------------------LTVSEVQPVSPASLDAPLE--AVEIIETVISSLHQGLVGQTDSGKIWFRYGS---AEVFVQLSGHEEDFLTIWSPV--PLPVADELALYRKLLTLNWLTTFEAHFAIAEE----QVQVVASRTLG-GITAGEISRLITIVATLADDYDDALRAEFK-------------

4g6tA

0.05

0.03

0.64

1.24

dPPAS2

-------------------------------------------PVDMSNLFYKTLLDDFSRSLEMQPLVFDDHGTCNMIIDNT---FALTLSCDYARERLLLIGLLEPHKDIPQQCLLAGALNPLLNAGP----GLGLDEKSGLYHAYQSIPR--EKLSVPTLKREMAGLLEWMRGWREA-------------------

4h5bA

0.10

0.08

0.74

1.21

dPPAS2

----------------------------------------------ETALLTLDTLAKYLQEKEVQLDIEENGGQRFIRMGWRAAVLVSVNDGPNNTSRLEITCVTQKTY-ADRRAEVAMMLNDRNRERAF---ARSIDQEGNVWLEYVGFYPTLAEMPQETFDTLFGGVLMHFQDDYAALEGY--VPQEGMQIQQPQA

2plgA

0.12

0.09

0.73

1.19

dPPAS2

--------------------------LTVSEVQPVSP-----ASLDAPLENAVEIIETVISSLHQGLVGQTDSGKIWFRYGS---AEVFVQLSGHTEDFLTIWSPVLP-LPVADELALYRKLLTLNWLTTFEAHFAIAEE----QVQVVASRTLG-GITAGEISRLITIVATLADDYDDALRAEFK-------------

2bsjA

0.15

0.10

0.64

1.15

dPPAS2

-------------------------------------------------TTFTELMQQLFLKLGLNHQV-NENDVYTFEVDGH----IQVLIACYHQQWVQLFSELGADLPTNDNL----------FGEHWP-AHVQGRLDGKSILWSQQSL---VGLDIDEMQAWLERFIDDIEQRKE-PQNTKFQPNSTSPILFI--

3epuA

0.10

0.07

0.67

1.05

dPPAS2

-----------------------------------------------MYSRADRLLRQFSLKLNTDSIVFDENRLCSFIIDNR----YRILLTSTNSEYIMIYGFCGK--PPDNLAFEFLNANLWFAENNGP--HLCYDNNSQSLLLALNFSL--NESSVEKLECEIEVVIRSMENLYHILQDKGITLDTD--------

2plgA

0.15

0.11

0.73

0.74

MUSTER

--------------------------LTVSEVQPVSP-----ASLDAPLENAVEIIETVISSLHQGLVGQTDSGKIWFRYGS---AEVFVQLSGHTEDFLTIWSPV-LPLPVADELALYRKLLTLNWLTTFEAHFAIAEE---QVQVVASRTL--GGITAGEISRLITIVATLADDYDDALRAEFK-------------

4h5bA

0.07

0.06

0.74

0.81

dPPAS

----------------------------------------------ETALLTLDTLAKYLQEKEVQLDIEENGGRMGWRFEMGDAAVLVSVNDGPNNTSRLEITCVTQKTYADRRAEVAMMLNDRNRERAF---ARSIDQEGNVWLEYVGFYPTLAEMPQETFDTLFGGVLMHFQDDYAALEG--YVPQEGMQIQQPQA

4h5bA

0.11

0.08

0.72

0.98

wdPPAS

----------------------------------------------ETALLTLDTLAKYLQEKEVQLDIEENGGQRFIRMGEMGDAAVLVSVNPNNTSRLEITCVTQKTY-ADRRAEVAMMLNDRNRERAFARSI----QEGNVWLEYVGFYPTLAEMPQETFDTLFGGVLMHFQDDYAALE----VPQEGMQIQQPQA

(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=-1.89

Estimated TM-score = 0.49±0.15

Estimated RMSD = 9.5±4.6Å

Download Model 2

C-score=-3.71

Download Model 3

C-score=-4.68

Download Model 4

C-score=-4.44

Download Model 5

C-score=-4.24

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	2plgA	0.635	2.27	0.123	0.724
2	4h5bA	0.603	2.57	0.077	0.719
3	3epuA	0.523	3.30	0.082	0.658
4	3kxyA	0.520	3.33	0.076	0.663
5	2fm8A	0.513	3.03	0.079	0.633
6	1jyoA	0.513	3.02	0.070	0.638
7	1s28A	0.510	2.65	0.066	0.608
8	1ry9A	0.497	3.07	0.095	0.623
9	1xkpC	0.493	2.74	0.095	0.583
10	2rjsB	0.491	4.58	0.042	0.729

(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	5	2xgaA	MTN	Rep, Mult	63,80,88,168,171
2	0.06	3	3kxyK	III	Rep, Mult	59,68,71,75,78,79,80,81,89,103,146,164,168,171,172,175
3	0.06	3	5bq6D	EFB	Rep, Mult	170,174,178
4	0.04	2	1n5b0	III	Rep, Mult	99,101,103,118,120,123,124,126,127,135,136,137,146,148,150
5	0.04	2	4a5aA	MG	Rep, Mult	49,91
6	0.04	2	3inmB	AKG	Rep, Mult	158,197
7	0.04	2	2plg0	III	Rep, Mult	99,101,103,115,116,119,120,122,123,126,127,128,131,132,134,135,136,137,138,146,148,150,151,152,154,155,162,165
8	0.02	1	3jskM	FE2	Rep, Mult	141,142
9	0.02	1	1r9cB	MN	Rep, Mult	40,91
10	0.02	1	1ry90	III	Rep, Mult	112,122,123,124,127,136,137,138
11	0.02	1	3d48R	CO3	Rep, Mult	110,125
12	0.02	1	2jstA	HLT	Rep, Mult	125,170
13	0.02	1	4dl1A	0KY	Rep, Mult	49,50
14	0.02	1	2vhgA	MN	Rep, Mult	73,87,89
15	0.02	1	5d57A	78M	Rep, Mult	159,162,170

	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	1i1qA	0.430	5.53	0.057	0.784	2.4.2.18,4.1.3.27	NA
2	0.060	1i7qA	0.440	5.45	0.061	0.759	4.1.3.27	NA
3	0.060	2boaA	0.446	5.08	0.041	0.704	3.4.17.-	NA
4	0.060	2hvgA	0.448	5.21	0.066	0.749	4.3.2.2	NA
5	0.060	1tlbA	0.440	4.67	0.047	0.688	1.3.3.3	171,185
6	0.060	1gytA	0.447	5.19	0.055	0.759	3.4.11.1	NA
7	0.060	1y2mB	0.479	4.96	0.042	0.754	4.3.1.24	NA
8	0.060	2nyfA	0.489	4.79	0.067	0.754	4.3.1.5	NA
9	0.060	2fenD	0.452	4.91	0.060	0.719	5.5.1.2	NA
10	0.060	1b8fA	0.460	5.36	0.083	0.764	4.3.1.3	NA
11	0.060	1up8A	0.443	5.93	0.088	0.789	1.11.1.18	NA
12	0.060	2ohyB	0.491	4.57	0.048	0.729	5.4.3.6	NA
13	0.060	3gzhA	0.470	4.91	0.041	0.739	4.3.2.2	NA
14	0.060	1q5nA	0.441	5.20	0.062	0.714	5.5.1.2	174
15	0.060	1dofA	0.443	5.29	0.075	0.739	4.3.2.2	71
16	0.060	1h8lA	0.473	4.92	0.025	0.734	3.4.17.22	NA
17	0.060	2hb6A	0.428	5.28	0.041	0.734	3.4.11.1	NA
18	0.060	1f1oA	0.421	5.25	0.065	0.709	4.3.2.2	NA
19	0.060	1uwkA	0.451	4.85	0.068	0.699	4.2.1.49	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	0.14	0.603	2.57	0.08	0.72	4h5bA	GO:0016049
1	0.12	0.478	2.89	0.05	0.58	1xkpB	GO:0005737 GO:0005886 GO:0009306 GO:0016020
2	0.10	0.523	3.30	0.08	0.66	3epuA	GO:0005737 GO:0050708
3	0.09	0.522	2.73	0.06	0.63	1s28A	GO:0005737 GO:0050708
4	0.09	0.520	3.33	0.08	0.66	3kxyA	GO:0005737 GO:0005886 GO:0016020 GO:0016021 GO:0030254 GO:0045893 GO:0050708
5	0.08	0.513	3.02	0.07	0.64	1jyoA	GO:0005737 GO:0009405 GO:0050708
6	0.08	0.497	3.07	0.10	0.62	1ry9A	GO:0009405
7	0.08	0.481	3.30	0.07	0.61	4g6tA	GO:0005737 GO:0050708
8	0.07	0.493	2.74	0.10	0.58	1xkpC	GO:0005737 GO:0005886 GO:0016020 GO:0050708
9	0.07	0.513	3.03	0.08	0.63	2fm8A	GO:0009405
10	0.07	0.491	4.55	0.05	0.73	3kdyA	GO:0003824 GO:0009403 GO:0016829 GO:0016841 GO:0016853 GO:0017000 GO:0050368 GO:0052883
11	0.07	0.478	4.89	0.07	0.75	2o6yA	GO:0003824 GO:0006572 GO:0009698 GO:0009699 GO:0016829 GO:0016841 GO:0042802 GO:0051289 GO:0052883
12	0.07	0.489	4.79	0.07	0.75	2nyfA	GO:0003824 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
13	0.07	0.487	4.92	0.04	0.75	3unvA	GO:0003824
14	0.07	0.476	5.17	0.07	0.77	1gk2A	GO:0003824 GO:0004397 GO:0005737 GO:0006547 GO:0006548 GO:0016829 GO:0016841 GO:0019556 GO:0019557
15	0.06	0.496	4.80	0.07	0.77	3nz4B	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
16	0.06	0.492	4.94	0.07	0.77	3czoB	GO:0003824 GO:0004397 GO:0005737 GO:0009072 GO:0009698 GO:0009699 GO:0009800 GO:0016829 GO:0016841 GO:0045548 GO:0051289
17	0.06	0.416	3.06	0.09	0.51	1k3eB	GO:0005737 GO:0009405 GO:0050708
18	0.06	0.482	4.86	0.04	0.74	4c6gB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289
19	0.06	0.484	4.90	0.04	0.74	4v2rB	GO:0003824 GO:0005737 GO:0006558 GO:0006559 GO:0009698 GO:0009800 GO:0009820 GO:0009821 GO:0016829 GO:0016841 GO:0016853 GO:0016869 GO:0042617 GO:0045548 GO:0051289

Consensus prediction of GO terms

Molecular Function
GO-Score
Biological Processes	GO:0009306	GO:0051223	GO:1903530
GO-Score	0.52	0.52	0.52
Cellular Component	GO:0071944	GO:0005737
GO-Score	0.40	0.35

(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.