I-TASSER results

I-TASSER results for job id Rv1120c

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

Input Sequence in FASTA format

>protein (164 residues)
MLSGGREAVKTVWQTANLVRKEGFGAAVRSSIEDPADWAEVERPDLARVTPDGRVVILFS
DIEESTALDERIGDRTWVKLIGAHDKLVHELVRRWSGHMVTSQGDGFMIAFARAEQAVRC
GIDIQDALRNSAKRKRNQGIRVRIGTTWGARCGTVTICSAATSQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MLSGGREAVKTVWQTANLVRKEGFGAAVRSSIEDPADWAEVERPDLARVTPDGRVVILFSDIEESTALDERIGDRTWVKLIGAHDKLVHELVRRWSGHMVTSQGDGFMIAFARAEQAVRCGIDIQDALRNSAKRKRNQGIRVRIGTTWGARCGTVTICSAATSQ
Prediction	CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCEEEEEEEHCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCEEEEHCCCEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEHCCCCCEEEEEEHCCCCC
Conf.Score	98757999999999999999998777766544556677887666655678875899999857985588876999999999999999999999998998998756589998599999999999999999998666655698746888757876569998757899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MLSGGREAVKTVWQTANLVRKEGFGAAVRSSIEDPADWAEVERPDLARVTPDGRVVILFSDIEESTALDERIGDRTWVKLIGAHDKLVHELVRRWSGHMVTSQGDGFMIAFARAEQAVRCGIDIQDALRNSAKRKRNQGIRVRIGTTWGARCGTVTICSAATSQ
Prediction	74433361144025325313554344334432542343352644745554763300000030142030015243620240043025202500562603213233200000042033003001300510462456467450402000214243120100105278
	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

CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCEEEEEEEHCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCEEEEHCCCEEEEHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEHCCCCCEEEEEEHCCCCC
MLSGGREAVKTVWQTANLVRKEGFGAAVRSSIEDPADWAEVERPDLARVTPDGRVVILFSDIEESTALDERIGDRTWVKLIGAHDKLVHELVRRWSGHMVTSQGDGFMIAFARAEQAVRCGIDIQDALRNSAKRKRNQGIRVRIGTTWGARCGTVTICSAATSQ

4yusA2

0.18

0.14

0.78

1.69

MUSTER

--------------------------------QPSIFKIISQGTNLNIRPKAVEKIVFFSDIVSFSTFAEKLPVEEVVSVVNSYFSVCTAIITRQGGEVTKFIGDCVMAYFDCADQAIQASLDILMELEILRNSAPEGSLYSGIGLA----KGKVIEGNIGSEL

4yusA2

0.18

0.14

0.79

2.06

dPPAS

-------------------------------QPSIFKIISQGTNPLNIRPKAVEKIVFFSDIVSFSTFAEKLPVEEVVSVVNSYFSVCTAIITRQGGEVTKFIGDCVMAYFDGADQAIQASLDILMELEILRNSAPEGSLYSGIGLA----KGKVIEGNIGSEL

4wp3A

0.57

0.41

0.72

3.29

wdPPAS

-------------------------------VRSSIEELADWAEVERPDLARVTVVILFTDIEESTALNERIGDRAWVKLISSHDKLVSDLVRRQSGHVVKSQGDGFMVAFARPEQAVRCGIELQRALRR---------IRVRIGIHMGRSVRDDLFG------

4yusA

0.15

0.98

2.90

wMUSTER

INLDENTDFLIRPIKVLLQTLTESHRILEKYTQPSIFKIISQGTNLNIRPKAVEKIVFFSDIVSFSTFAEKLPVEEVVSVVNSYFSVCTAIITRQGGEVTKFIGDCVMAYFDCADQAIQASLDILMELEILRNSAPEGSLYSGIGLAK----GKVIEGNIGSEL

4wp3A

0.71

0.51

0.71

2.97

wPPAS

---------------------------VRSSIEELADWAEVERPD----LARVTVVILFTDIEESTALNERIGDRAWVKLISSHDKLVSDLVRRQSGHVVKSQGDGFMVAFARPEQAVRCGIELQRALRR---------IRVRIGIHMGR----SVRDDFG---

4yusA2

0.18

0.14

0.78

4.16

dPPAS2

--------------------------------QPSIFKIISQGTNLNIRPKAVEKIVFFSDIVSFSTFAEKLPVEEVVSVVNSYFSVCTAIITRQGGEVTKFIGDCVMAYFDGADQAIQASLDILMELEILRNSAPEGSLYSGIGLA----KGKVIEGNIGSEL

4wp3A

0.71

0.51

0.71

2.49

PPAS

---------------------------VRSSIEELADWAEVERPD----LARVTVVILFTDIEESTALNERIGDRAWVKLISSHDKLVSDLVRRQSGHVVKSQGDGFMVAFARPEQAVRCGIELQRALRR---------IRVRIGIHMG----RSVRDDFG---

4wp3A

0.69

0.51

0.74

3.02

Env-PPAS

---------------------------VRSSIEELADWAEVERPD----LARVTVVILFTDIEESTALNERIGDRAWVKLISSHDKLVSDLVRRQSGHVVKSQGDGFMVAFARPEQAVRCGIELQRALRRE--------IRVRIGIHMG----RSVRDDFGRNV

1wc4A

0.18

0.13

0.70

1.62

MUSTER

---------------------------------------------SHMRPEPRLITILFSDIVGFTRMSNALQSQGVAELLNEYLGEMTRAVFENQGTVDKFVGDAIMALYGQVRRAIATARQMLVALEKLNQGWQERGVRFRCGIHQ----GMAVVGLFGSQE

4wp3A

0.59

0.41

0.70

2.02

dPPAS

-------------------------------VRSSIEELADWAEVERPDLARVTVVILFTDIEESTALNERIGDRAWVKLISSHDKLVSDLVRRQSGHVVKSQGDGFMVAFARPEQAVRCGIELQRALRRE--------IRVRIGIHMGRSVR-----------

(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=-1.54

Estimated TM-score = 0.53±0.15

Estimated RMSD = 8.3±4.5Å

Download Model 2

C-score=-1.74

Download Model 3

C-score=-2.35

Download Model 4

C-score=-2.08

Download Model 5

C-score=-3.78

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	4yusA	0.717	2.17	0.139	0.823
2	4clfA	0.641	3.76	0.139	0.854
3	1y11A	0.633	3.94	0.130	0.829
4	3i5cB	0.631	4.04	0.109	0.872
5	3r5gA	0.624	1.60	0.214	0.683
6	2w01A	0.623	1.67	0.239	0.689
7	1culA	0.620	1.81	0.190	0.683
8	2ajqA	0.613	3.68	0.072	0.835
9	3pjwA	0.611	3.72	0.146	0.811
10	1wc4A	0.610	2.13	0.147	0.707

(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	0.74	87	2bw7B	APC	Rep, Mult	61,62,63,64,65,66,104,105,143
2	0.10	11	2gvdA	128	Rep, Mult	62,64,65,74,77,78,81,104,105,143
3	0.05	9	1wc0A	APC	Rep, Mult	59,101,108
4	0.03	5	1wc6A	MG	Rep, Mult	61,103,105,106
5	0.02	2	4wp9B	MG	Rep, Mult	61,103,143
6	0.00	1	3i5cA	C2E	Rep, Mult	93,98,113,116,119,120
7	0.00	1	1ybuB	APC	Rep, Mult	59,108
8	0.00	1	1rb4A	III	Rep, Mult	118,119,125,126,128,129,132,135,136
9	0.00	1	1y10D	CA	Rep, Mult	33,150
10	0.00	1	1fx2A	DTT	Rep, Mult	125,128,137,138,140,141,142

	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	1d8yA	0.546	3.94	0.087	0.750	2.7.7.7	66,72,124
2	0.060	1fx4A	0.596	2.66	0.287	0.695	4.6.1.1	NA
3	0.060	2g49A	0.515	4.99	0.037	0.860	3.4.24.56	NA
4	0.060	1ybtB	0.558	1.82	0.343	0.610	4.6.1.1	NA
5	0.060	1y11A	0.633	3.94	0.130	0.829	4.6.1.1	NA
6	0.060	1clqA	0.414	5.12	0.071	0.713	2.7.7.7	60
7	0.060	1yuyA	0.521	4.75	0.047	0.817	2.7.7.48	NA
8	0.060	2w01A	0.623	1.67	0.239	0.689	4.6.1.2	NA
9	0.060	2uutA	0.480	5.04	0.065	0.787	3.6.1.15	65
10	0.060	1l3sA	0.551	3.79	0.087	0.750	2.7.7.7	105
11	0.060	2imwP	0.438	3.39	0.062	0.585	2.7.7.7	86
12	0.060	1fnoA	0.456	4.57	0.057	0.671	3.4.11.4	NA
13	0.060	1khvB	0.477	5.01	0.105	0.793	2.7.7.48	NA
14	0.060	1wc4A	0.610	2.13	0.147	0.707	4.6.1.1	NA
15	0.060	3c46B	0.504	4.59	0.045	0.774	2.7.7.6	65,91
16	0.060	3bxvA	0.492	4.39	0.081	0.726	1.13.11.55	NA
17	0.060	3c66A	0.523	4.80	0.050	0.854	2.7.7.19	NA
18	0.060	1azsA	0.614	1.87	0.188	0.683	4.6.1.1	NA
19	0.060	1yk9A	0.527	2.78	0.174	0.665	4.6.1.1	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	0.36	0.614	1.87	0.19	0.68	1azsA	GO:0000166 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0005929 GO:0006171 GO:0007189 GO:0007193 GO:0007204 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0019933 GO:0035556 GO:0042995 GO:0046872 GO:0061178 GO:0072372 GO:1904322
1	0.34	0.610	2.13	0.15	0.71	1wc4A	GO:0000155 GO:0000160 GO:0004016 GO:0005622 GO:0006171 GO:0007165 GO:0009190 GO:0016310 GO:0016772 GO:0016829 GO:0016849 GO:0018298 GO:0023014 GO:0035556 GO:0046872
2	0.22	0.570	2.65	0.56	0.64	4wp3C	GO:0004016 GO:0005622 GO:0006171 GO:0009190 GO:0016829 GO:0016849 GO:0035556
3	0.20	0.629	1.62	0.21	0.69	3r5gB	GO:0004016 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0009405 GO:0016020 GO:0016021 GO:0016849 GO:0035556
4	0.16	0.588	1.85	0.18	0.66	3et6A	GO:0000166 GO:0004016 GO:0004383 GO:0005886 GO:0006182 GO:0007165 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556
5	0.15	0.552	2.66	0.20	0.65	3mr7A	GO:0005622 GO:0009190 GO:0016787 GO:0016849 GO:0035556
6	0.11	0.713	2.40	0.14	0.83	4yutA	GO:0005622 GO:0009190 GO:0009785 GO:0009882 GO:0016849 GO:0035556 GO:0071949
7	0.07	0.623	1.67	0.24	0.69	2w01A	GO:0004016 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0016020 GO:0016021 GO:0016849 GO:0035556
8	0.07	0.589	2.14	0.19	0.68	4ni2B	GO:0000166 GO:0004016 GO:0004383 GO:0004872 GO:0005525 GO:0005737 GO:0005886 GO:0006182 GO:0007263 GO:0008015 GO:0008074 GO:0009190 GO:0016829 GO:0016849 GO:0020037 GO:0035556 GO:0038060 GO:0043231 GO:0046872 GO:0071732
9	0.07	0.638	3.71	0.13	0.87	4oyzA	GO:0000166 GO:0000287 GO:0003351 GO:0004016 GO:0005524 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005856 GO:0005886 GO:0005929 GO:0006171 GO:0007283 GO:0009190 GO:0015630 GO:0016020 GO:0016829 GO:0016849 GO:0030145 GO:0030424 GO:0030425 GO:0030426 GO:0031514 GO:0035556 GO:0042995 GO:0043025 GO:0043065 GO:0045177 GO:0045178 GO:0046872 GO:0048471 GO:0051117 GO:0071241 GO:0071890
10	0.07	0.574	2.63	0.15	0.68	4p2fA	GO:0000166 GO:0000287 GO:0004016 GO:0005524 GO:0005622 GO:0005886 GO:0006171 GO:0007165 GO:0009190 GO:0016020 GO:0016021 GO:0016829 GO:0016849 GO:0030145 GO:0035556 GO:0046872
11	0.06	0.398	3.30	0.06	0.53	2hfoA	GO:0000166 GO:0009785 GO:0009882 GO:0042802 GO:0071949
12	0.06	0.405	3.13	0.08	0.54	4hh0A	GO:0000166 GO:0009785 GO:0009882 GO:0071949
13	0.06	0.397	3.28	0.04	0.53	1x0pA	GO:0000166 GO:0009785 GO:0009882 GO:0071949
14	0.06	0.345	4.39	0.04	0.52	3qdlA	GO:0016491 GO:0046677 GO:0055114
15	0.06	0.359	5.43	0.07	0.64	3dwlA	GO:0000147 GO:0000166 GO:0003779 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005885 GO:0006897 GO:0030041 GO:0030479 GO:0032153 GO:0034314 GO:0044396 GO:0051285 GO:0051666 GO:1903475
16	0.06	0.387	4.41	0.08	0.60	5a6cB	GO:0000132 GO:0000166 GO:0000922 GO:0001965 GO:0005092 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005938 GO:0007052 GO:0007155 GO:0007165 GO:0007186 GO:0007267 GO:0008022 GO:0017016 GO:0030054 GO:0030695 GO:0034332 GO:0042802 GO:0043547 GO:0045177 GO:0050790 GO:0051661 GO:0060487 GO:0090557 GO:0097431 GO:0098609 GO:0098641
17	0.06	0.383	3.49	0.07	0.53	3gfxB	GO:0000166 GO:0009785 GO:0009882 GO:0046872 GO:0071949
18	0.06	0.383	3.48	0.07	0.53	3gfyB	GO:0000166 GO:0009785 GO:0009882 GO:0046872 GO:0071949

Consensus prediction of GO terms

Molecular Function	GO:0004016	GO:0046872	GO:0005524	GO:0000155	GO:0046906
GO-Score	0.78	0.58	0.36	0.34	0.33
Biological Processes	GO:0006171	GO:0051704	GO:0019933	GO:0007193	GO:0007204	GO:0007189	GO:0061178	GO:1904322	GO:0018298	GO:0000160	GO:0023014	GO:0046068
GO-Score	0.74	0.41	0.36	0.36	0.36	0.36	0.36	0.36	0.34	0.34	0.34	0.33
Cellular Component	GO:0005886	GO:0016021	GO:0072372	GO:0044445	GO:0043234
GO-Score	0.58	0.49	0.36	0.33	0.33

(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.