I-TASSER results

I-TASSER results for job id Rv2420c

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

Input Sequence in FASTA format

>protein (126 residues)
MTANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVE
EKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFYALDRLWGDCPVVPVDLSA
NSAGAQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFYALDRLWGDCPVVPVDLSANSAGAQ
Prediction	CCCCHHHHHHHHHHHHHHHHHCCCCEEEEHCCCCCEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHCCCEEEEHCCHHHHHHHHHHHHHHCCCCEHCCCCCCCCCCC
Conf.Score	998889999999999999998898689997899864655899997899799999999999999998998765568888858999879799997799999999799998759755568888987789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFYALDRLWGDCPVVPVDLSANSAGAQ
Prediction	865575044004200510564405302003047313201000000142530040005202630474525134244565240101223300000135632521513511661551617376778568
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCHHHHHHHHHHHHHHHHHCCCCEEEEHCCCCCEEEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHCCCEEEEHCCHHHHHHHHHHHHHHCCCCEHCCCCCCCCCCC
MTANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFYALDRLWGDCPVVPVDLSANSAGAQ

4wcwA

0.99

0.91

0.92

3.97

MUSTER

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.91

0.92

5.83

dPPAS

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.91

0.92

5.70

wdPPAS

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.90

0.91

4.57

wMUSTER

--ANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.91

0.92

5.01

wPPAS

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.91

0.92

10.72

dPPAS2

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.91

0.92

4.64

PPAS

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

4wcwA

0.99

0.91

0.92

5.49

Env-PPAS

-TANREAIDMARVAAGAAAAKLADDVVVIDVSGQLVITDCFVIASGSNERQVNAIVDEVEEKMRQAGYRPARREGAREGRWTLLDYRDIVVHIQHQDDRNFAALDRLWGDCPVVPVD---------

2id1A

0.27

0.25

0.93

3.52

MUSTER

-----EIQEISKLAIEALEDIKGKDIIELDTSKLTSLFQ-RIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEWVLVDAGDVVVHVL-PAVRDYYDIEALWGGQKP-SFAVGAAKPWS-

2id1A

0.27

0.25

0.93

5.17

dPPAS

-----EIQEISKLAIEALEDIKGKDIIELDTSKLTSLFQ-RIVATGDSNRQVKALANSVQVKLKEAGVDIVGSEGHESGEWVLVDAGDVVVHVL-PAVRDYYDIEALWGGQKPSFAVGAAKPWS--

(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=1.41

Estimated TM-score = 0.91±0.06

Estimated RMSD = 1.8±1.5Å

Download Model 2

C-score=-1.15

Download Model 3

C-score=-3.51

Download Model 4

C-score=1.36

Download Model 5

C-score=-3.11

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	4wcwA	0.871	1.16	0.991	0.921
2	2id1A	0.764	2.06	0.287	0.857
3	2o5aA	0.748	1.90	0.355	0.849
4	3upsA	0.653	1.90	0.240	0.738
5	1jmsA	0.620	3.34	0.107	0.857
6	4at7B1	0.618	3.51	0.056	0.929
7	5decA	0.605	3.21	0.057	0.818
8	4txyA	0.597	3.37	0.025	0.841
9	3hx0A	0.592	3.60	0.092	0.841
10	4xj6A	0.591	3.12	0.017	0.825

(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	0.25	2	2o5aA	MN	Rep, Mult	4,39,88
2	0.12	2	1xsnA	D3T	Rep, Mult	31,38,39,41,106,109
3	0.06	1	1rztE	QNA	Rep, Mult	21,22,55,57,58
4	0.06	1	1kdhA	NA	Rep, Mult	19,23,26
5	0.06	1	2gwsI	QNA	Rep, Mult	50,51,54,55
6	0.06	1	3c5gB	UUU	Rep, Mult	82,83,85,90,91,92

	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	1q78A	0.561	3.78	0.049	0.849	2.7.7.19	NA
2	0.060	2nomB	0.360	4.68	0.064	0.611	2.7.7.52	NA
3	0.060	3hx0A	0.592	3.60	0.092	0.841	2.7.7.7,	NA
4	0.060	3c66A	0.580	3.60	0.073	0.857	2.7.7.19	NA
5	0.060	1vpeA	0.504	4.40	0.043	0.809	2.7.2.3	NA
6	0.060	1u2zC	0.505	4.29	0.044	0.778	2.1.1.43	14,26,57
7	0.060	1skyE	0.480	4.44	0.102	0.778	3.6.3.14,3.6.1.34	NA
8	0.060	1adjA	0.371	5.09	0.083	0.706	6.1.1.21	69
9	0.060	2f43B	0.496	4.59	0.073	0.802	3.6.3.14	NA
10	0.060	3f2bA	0.542	4.10	0.054	0.857	2.7.7.7	11
11	0.060	1jmsA	0.620	3.34	0.107	0.857	2.7.7.31	NA
12	0.060	2qe7A	0.500	4.23	0.064	0.778	3.6.1.34	NA
13	0.060	1px5B	0.545	4.09	0.058	0.849	2.7.7.-	NA
14	0.060	1bpxA	0.568	3.48	0.101	0.849	2.7.7.7	NA
15	0.060	2z8gB	0.508	3.70	0.026	0.754	3.2.1.57	43
16	0.060	1knyA	0.511	3.74	0.073	0.754	2.7.7.46	59
17	0.060	1m5sD	0.533	4.60	0.089	0.857	2.3.1.101	NA
18	0.060	1jajA	0.524	4.03	0.061	0.825	2.7.7.7	NA
19	0.060	2q0eA	0.562	4.03	0.066	0.881	2.7.7.52	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	0.68	0.871	1.28	0.99	0.93	4wcwC	GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0043023 GO:0090071
1	0.46	0.756	1.89	0.35	0.86	2o5aA	GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0090071
2	0.41	0.781	2.18	0.28	0.88	2id1A	GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0090071
3	0.37	0.676	1.88	0.23	0.76	3upsA	GO:0005737 GO:0006417 GO:0017148 GO:0042256 GO:0090071
4	0.07	0.517	2.64	0.11	0.67	1ylqA	GO:0016779
5	0.07	0.627	3.56	0.08	0.87	4i27A	GO:0003677 GO:0003887 GO:0003912 GO:0005634 GO:0005654 GO:0005737 GO:0006259 GO:0006304 GO:0016740 GO:0016779 GO:0034061 GO:0046872 GO:0071897
6	0.07	0.599	3.45	0.11	0.83	4k4iA	GO:0003677 GO:0003887 GO:0005634 GO:0005654 GO:0006260 GO:0006281 GO:0006289 GO:0006303 GO:0006974 GO:0016446 GO:0016740 GO:0016779 GO:0016829 GO:0034061 GO:0046872 GO:0071897
7	0.07	0.558	3.54	0.05	0.80	3au2A	GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006281 GO:0046872 GO:0071897
8	0.07	0.596	3.31	0.09	0.82	4i2iA	GO:0003677 GO:0003887 GO:0003912 GO:0005634 GO:0005654 GO:0005737 GO:0006259 GO:0006304 GO:0016740 GO:0016779 GO:0034061 GO:0046872 GO:0071897
9	0.07	0.549	3.55	0.06	0.81	4p4oA	GO:0003677 GO:0003887 GO:0005634 GO:0006281 GO:0034061 GO:0071897
10	0.07	0.422	5.04	0.07	0.77	3cjtA	GO:0005737 GO:0006479 GO:0008168 GO:0008276 GO:0016740 GO:0032259
11	0.07	0.341	4.08	0.05	0.54	4jjfA	GO:0006730 GO:0015948 GO:0016491 GO:0018537 GO:0019386 GO:0047068 GO:0055114
12	0.06	0.366	4.70	0.12	0.61	3uk6L	GO:0000166 GO:0000812 GO:0000979 GO:0000980 GO:0001094 GO:0003678 GO:0004003 GO:0004386 GO:0005524 GO:0005622 GO:0005634 GO:0005654 GO:0005719 GO:0005737 GO:0006281 GO:0006310 GO:0006338 GO:0006351 GO:0006355 GO:0006457 GO:0006974 GO:0016020 GO:0016363 GO:0016568 GO:0016787 GO:0016887 GO:0030529 GO:0031011 GO:0031490 GO:0032508 GO:0034644 GO:0035066 GO:0035267 GO:0040008 GO:0042802 GO:0042803 GO:0043141 GO:0043531 GO:0043967 GO:0043968 GO:0045944 GO:0051082 GO:0051117 GO:0070062 GO:0071169 GO:0071339 GO:0071392 GO:0071733 GO:0071899 GO:0097255 GO:1904874
13	0.06	0.366	4.10	0.10	0.59	2nsmA	GO:0004180 GO:0004181 GO:0004185 GO:0005576 GO:0005615 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0010815 GO:0016485 GO:0016787 GO:0046872 GO:0051384
14	0.06	0.377	5.69	0.10	0.76	3ip3B	GO:0008152 GO:0016491 GO:0055114
15	0.06	0.342	4.71	0.07	0.56	3dwlF	GO:0000147 GO:0003779 GO:0005634 GO:0005737 GO:0005829 GO:0005856 GO:0005885 GO:0006897 GO:0015629 GO:0030041 GO:0030479 GO:0034314
16	0.06	0.338	4.63	0.07	0.55	4xeiF	GO:0003779 GO:0005200 GO:0005737 GO:0005829 GO:0005856 GO:0005885 GO:0015629 GO:0019899 GO:0030041 GO:0030674 GO:0034314 GO:0042995 GO:0051015 GO:0070062
17	0.06	0.583	3.29	0.06	0.82	4rq2A	GO:0003677 GO:0003684 GO:0003887 GO:0003906 GO:0005634 GO:0005654 GO:0005737 GO:0005874 GO:0005876 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006286 GO:0006287 GO:0006288 GO:0006290 GO:0006297 GO:0006915 GO:0006954 GO:0006974 GO:0007435 GO:0007568 GO:0008017 GO:0008630 GO:0010332 GO:0016445 GO:0016446 GO:0016740 GO:0016779 GO:0016829 GO:0019899 GO:0034061 GO:0043234 GO:0045471 GO:0046872 GO:0048535 GO:0048536 GO:0048872 GO:0051402 GO:0055093 GO:0071707 GO:0071897
18	0.06	0.336	4.07	0.06	0.51	4pobA	GO:0005623 GO:0006662 GO:0015035 GO:0045454 GO:0055114
19	0.06	0.603	3.48	0.07	0.85	4lzdA	GO:0003677 GO:0003887 GO:0005634 GO:0005654 GO:0006281 GO:0006303 GO:0006310 GO:0006974 GO:0016446 GO:0016740 GO:0016779 GO:0030183 GO:0034061 GO:0046872 GO:0071897

Consensus prediction of GO terms

Molecular Function	GO:0043023
GO-Score	0.68
Biological Processes	GO:0090071	GO:0042256	GO:0017148
GO-Score	0.94	0.94	0.94
Cellular Component	GO:0005737
GO-Score	0.94

(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.