I-TASSER results

I-TASSER results for job id Rv0264c

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

Input Sequence in FASTA format

>protein (210 residues)
MDAALACTVLDYGDHALMLQCDSTADAMAWTDALRAAALPGVVDIVAASRTVLVKLDAPR
YQGVTRQRLRRLRVTPEAVAAADHRCDLVIDVVYDGPDLAEVARCTGLTTAAVINAHTAT
GWRAGFSGSAPGFAYLIDGDPSLRVPRRPERRTSMPPGSVALADGFSAIYPSQAPSDWQI
IGHTDAVLWDVDRPQPALLTPGMWVQFRAA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDAALACTVLDYGDHALMLQCDSTADAMAWTDALRAAALPGVVDIVAASRTVLVKLDAPRYQGVTRQRLRRLRVTPEAVAAADHRCDLVIDVVYDGPDLAEVARCTGLTTAAVINAHTATGWRAGFSGSAPGFAYLIDGDPSLRVPRRPERRTSMPPGSVALADGFSAIYPSQAPSDWQIIGHTDAVLWDVDRPQPALLTPGMWVQFRAA
Prediction	CCCCCCEEEEHCCCCEEEEHCCCHHHHHHHHHHHHHCCCCCEEEHCCCCEEEEEEHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEHCCCCCHHHHHHHHCCCHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCEEEEHCCCCCCCEEEEEEHCCHCCCCCCCCCCCCCCCEEEEEEHC
Conf.Score	998886799986897999987986899999999999699987986567658999988877879999999998866776666677679999877699899999999899999999999899789999857778866789985447999999877889984777476689876899997579988586446899999877899979999969
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MDAALACTVLDYGDHALMLQCDSTADAMAWTDALRAAALPGVVDIVAASRTVLVKLDAPRYQGVTRQRLRRLRVTPEAVAAADHRCDLVIDVVYDGPDLAEVARCTGLTTAAVINAHTATGWRAGFSGSAPGFAYLIDGDPSLRVPRRPERRTSMPPGSVALADGFSAIYPSQAPSDWQIIGHTDAVLWDVDRPQPALLTPGMWVQFRAA
Prediction	674634120230312000011454230220141057461710110002012344313044134401420351244355563664433020002144210420163270326201510271403000001100001014244414134356235512420001013100000261321000003021301237364011030313031338
	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                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCEEEEHCCCCEEEEHCCCHHHHHHHHHHHHHCCCCCEEEHCCCCEEEEEEHCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEHCCCCCHHHHHHHHCCCHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCEEEEHCCCCCCCEEEEEEHCCHCCCCCCCCCCCCCCCEEEEEEHC
MDAALACTVLDYGDHALMLQCDSTADAMAWTDALRAAALPGVVDIVAASRTVLVKLDAPRYQGVTRQRLRRLRVTPEAVAAADHRCDLVIDVVYDGPDLAEVARCTGLTTAAVINAHTATGWRAGFSGSAPGFAYLIDGDPSLRVPRRPERRTSMPPGSVALADGFSAIYPSQAPSDWQIIGHTDAVLWDVDRPQPALLTPGMWVQFRAA

3mmlB

0.64

0.62

0.97

4.16

MUSTER

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAITHQPPRVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTD-AVFDVNRDKPALLTPG-WVQFRAV

3mmlB

0.64

0.62

0.97

7.83

dPPAS

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAITHQPPGVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTDA-VFDVNRDKPALLTPG-WVQFRAV

3mmlB

0.64

0.62

0.97

6.70

wdPPAS

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAHQPPGDRVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTDA-VFDVNRDKPALLTPGW-VQFRAV

3mmlB

0.64

0.62

0.96

4.73

wMUSTER

LG-----TVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAITHPGDRVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTD-AVFDVNRDKPALLTPGW-VQFRAV

3mmlB

0.64

0.62

0.97

5.76

wPPAS

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAHQPPGDRVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTD-AVFDVNRDKPALLTPGW-VQFRAV

3mmlB

0.64

0.62

0.97

9.68

dPPAS2

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAITHQPPGVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTDA-VFDVNRDKPALLTPG-WVQFRAV

3mmlB

0.64

0.62

0.97

5.19

PPAS

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAHQPPGDRVDVTIDVVYDGADLHEVASLTG-TPAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTD-AVFDVNRDKPALLTPG-WVQFRAV

3mmlB

0.64

0.62

0.97

5.88

Env-PPAS

---STLGTVHNYGDQALLLEFDSTAEVLAWTETLREAELLGVVDIVPAARTVLVKLAGPRYQAPTRQRLGKLRVRPEAITHQPPRVDVTIDVVYDGADLHEVASLTGT-PAQVIAAHTGTPWRVGFCGFAPGFAYLVDGDARLQVPRRAEPRTSVPAGAVALAGEFSGVYPRQSPGGWQLIGHTD-AVFDVNRDKPALLTPG-WVQFRAV

2phcB

0.26

0.25

0.96

3.81

MUSTER

-------IIKPAGDSAFLISFGDNDRVHSLAKAIEKESPEWLVELVPAYSSLLVIYDPLKASYEEVESYLKRISAREVERIK--GKTIEIPVAYGGPDIEFVAQYNGLSVDDVIEIHSKPLYRVYFLGFLPGFAYLGGMDERIATPRLEKPRLKVPAGSVGIAGKQTGWYAIESPGGWRIIGRIPLRTFNPGKVPPSIVLPGDYVKFVPI

2phcB

0.26

0.25

0.96

7.24

dPPAS

-------IIKPAGDSAFLISFGDNDRVHSLAKAIEKESPEWLVELVPAYSSLLVIYDPLKASYEEVESYLKRISAREVERI--KGKTIEIPVAYGGPDIEFVAQYNGLSVDDVIEIHSKPLYRVYFLGFLPGFAYLGGMDERIATPRLEKPRLKVPAGSVGIAGKQTGWYAIESPGGWRIIGRIPLRTFNPGKVPPSIVLPGDYVKFVPI

(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=1.72

Estimated TM-score = 0.96±0.05

Estimated RMSD = 2.1±1.7Å

Download Model 2

C-score=-3.09

Download Model 3

C-score=-3.29

Download Model 4

C-score=-4.33

Download Model 5

C-score=-3.83

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	3mmlB	0.943	1.07	0.652	0.971
2	3va7A	0.842	2.59	0.168	0.991
3	5dudB	0.746	2.76	0.298	0.909
4	3oepA	0.738	2.87	0.333	0.886
5	2phcB	0.578	1.85	0.206	0.619
6	2zp2B	0.519	1.40	0.348	0.548
7	5eufA	0.450	4.78	0.048	0.667
8	2fgeA	0.446	5.21	0.053	0.700
9	3eoqB	0.444	4.93	0.063	0.671
10	3amiA	0.442	5.04	0.065	0.676

(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	5cyhA	UUU	Rep, Mult	126,133,135,163,164,168,176,178
2	0.09	5	1kejA	CO	Rep, Mult	138,140
3	0.06	3	3r57A	N3M	Rep, Mult	155,157,158,159,183
4	0.04	2	1b4bB	ARG	Rep, Mult	20,48,49,50,51
5	0.04	2	3hx9A	CL	Rep, Mult	17,19,34,54
6	0.02	1	5b3pA	CA	Rep, Mult	44,46
7	0.02	1	3va7A	URE	Rep, Mult	168,170,176,177,178
8	0.02	1	1ppjA	AZI	Rep, Mult	102,106,107,143,144,145,146
9	0.02	1	4f8hA	LMD	Rep, Mult	33,36
10	0.02	1	4x64P	MG	Rep, Mult	181,182
11	0.02	1	3ue8A	09M	Rep, Mult	132,170
12	0.02	1	2wse1	CLA	Rep, Mult	119,128
13	0.02	1	3hdiB	III	Rep, Mult	31,35,44,45
14	0.02	1	3t5tB	MG	Rep, Mult	22,26
15	0.02	1	2g9zA	MG	Rep, Mult	14,22

	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	2gw2A	0.412	3.63	0.073	0.548	5.2.1.8	NA
2	0.060	1ordA	0.409	5.01	0.082	0.633	4.1.1.17	NA
3	0.060	1cynA	0.409	3.71	0.117	0.548	5.2.1.8	NA
4	0.060	1sqbB	0.418	4.89	0.022	0.638	1.10.2.2	NA
5	0.060	3k2cC	0.412	3.63	0.088	0.548	5.2.1.8	133
6	0.060	1ak4A	0.416	3.54	0.079	0.548	5.2.1.8	133
7	0.060	1istA	0.415	3.56	0.122	0.548	5.2.1.8	NA
8	0.060	2he9A	0.412	3.70	0.121	0.548	5.2.1.8	NA
9	0.060	3cxhL	0.443	4.70	0.048	0.652	1.10.2.2	NA
10	0.060	1h0pA	0.411	3.75	0.115	0.552	5.2.1.8	NA
11	0.060	1vncA	0.416	5.87	0.043	0.714	1.11.1.10	169
12	0.060	2bitX	0.413	3.58	0.112	0.548	5.2.1.8	NA
13	0.060	1iduA	0.414	5.56	0.039	0.691	1.11.1.10	NA
14	0.060	1z81A	0.412	3.81	0.078	0.557	5.2.1.8	NA
15	0.060	1ezvB	0.433	4.76	0.068	0.652	1.10.2.2	NA
16	0.060	1q2lA	0.411	4.98	0.054	0.638	3.4.24.55	NA
17	0.060	2wvhA	0.415	5.99	0.058	0.748	4.1.1.1	NA
18	0.060	3eoqB	0.444	4.93	0.063	0.671	3.4.24.56	NA
19	0.060	2g49A	0.409	5.12	0.048	0.648	3.4.24.56	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	0.60	0.956	1.08	0.65	0.99	3mmlB	GO:0016787
1	0.32	0.519	1.40	0.35	0.55	2zp2B	GO:0000166 GO:0004860 GO:0005524 GO:0006469 GO:0030435
2	0.25	0.578	1.85	0.21	0.62	2phcB
3	0.18	0.842	2.59	0.17	0.99	3va7A	GO:0000166 GO:0003824 GO:0004039 GO:0004075 GO:0004847 GO:0005524 GO:0005737 GO:0016874 GO:0043419 GO:0046872
4	0.13	0.734	3.14	0.32	0.91	3opfB
5	0.06	0.431	2.88	0.10	0.51	3mmlE	GO:0004039 GO:0016787 GO:0016829
6	0.06	0.351	5.94	0.06	0.62	1bxrA	GO:0000050 GO:0000166 GO:0003824 GO:0004087 GO:0004088 GO:0005524 GO:0005829 GO:0005951 GO:0006221 GO:0006526 GO:0006807 GO:0008652 GO:0016597 GO:0016874 GO:0019856 GO:0044205 GO:0046872
7	0.06	0.294	5.65	0.03	0.51	3floA	GO:0003677 GO:0003887 GO:0005634 GO:0005635 GO:0005658 GO:0006260 GO:0006270 GO:0006273 GO:0016233 GO:0046982 GO:0071897
8	0.06	0.311	6.04	0.04	0.58	3bg5B	GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
9	0.06	0.304	6.14	0.06	0.56	3tw6B	GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
10	0.06	0.335	5.53	0.05	0.56	3n6rG	GO:0003824 GO:0004075 GO:0004658 GO:0005524 GO:0016874 GO:0019541 GO:0046872
11	0.06	0.295	6.31	0.07	0.57	4hnvB	GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
12	0.06	0.321	5.57	0.09	0.55	3u9sI	GO:0003824 GO:0004075 GO:0004485 GO:0005524 GO:0008300 GO:0046872 GO:1905202
13	0.06	0.306	6.00	0.05	0.55	1dv2A	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005829 GO:0006629 GO:0006631 GO:0006633 GO:0016874 GO:0045717 GO:0046872 GO:2001295
14	0.06	0.305	5.49	0.03	0.50	3jrwA	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005634 GO:0005739 GO:0005741 GO:0005829 GO:0006084 GO:0006629 GO:0006631 GO:0006633 GO:0006768 GO:0006853 GO:0008152 GO:0010629 GO:0010884 GO:0010906 GO:0012505 GO:0016020 GO:0016874 GO:0031325 GO:0031667 GO:0031999 GO:0043086 GO:0046322 GO:0046872 GO:0050995 GO:0051289 GO:0060421 GO:0097009 GO:2001295
15	0.06	0.295	5.54	0.06	0.49	4rzqA	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0006629 GO:0006631 GO:0006633 GO:0016874 GO:0046872 GO:2001295
16	0.06	0.334	5.47	0.04	0.55	4qslD	GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
17	0.06	0.330	5.64	0.04	0.57	4qslA	GO:0000166 GO:0003677 GO:0003824 GO:0004075 GO:0004736 GO:0005524 GO:0006090 GO:0006094 GO:0009374 GO:0016874 GO:0046872
18	0.06	0.303	5.49	0.06	0.50	4rcnB	GO:0003824 GO:0004075 GO:0005524 GO:0016874 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0016811	GO:0043169	GO:0016879	GO:0004860
GO-Score	0.44	0.36	0.36	0.36	0.32
Biological Processes	GO:1901565	GO:0044282	GO:0043605	GO:0019627	GO:0030435	GO:0006469
GO-Score	0.36	0.36	0.36	0.36	0.32	0.32
Cellular Component	GO:0044424
GO-Score	0.36

(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.