I-TASSER results

I-TASSER results for job id Rv2417c

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

Input Sequence in FASTA format

>protein (280 residues)
MTVVVVTDTSCRLPADLREQWSIRQVPLHILLDGLDLRDGVDEIPDDIHKRHATTAGATP
VELSAAYQRALADSGGDGVVAVHISSALSGTFRAAELTAAELGPAVRVIDSRSAAMGVGF
AALAAGRAAAAGDELDTVARAAAAAVSRIHAFVAVARLDNLRRSGRISGAKAWLGTALAL
KPLLSVDDGKLVLVQRVRTVSNATAVMIDRVCQLVGDRPAALAVHHVADPAAANDVAAAL
AERLPACEPAMVTAMGPVLALHVGAGAVGVCVDVGASPPA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MTVVVVTDTSCRLPADLREQWSIRQVPLHILLDGLDLRDGVDEIPDDIHKRHATTAGATPVELSAAYQRALADSGGDGVVAVHISSALSGTFRAAELTAAELGPAVRVIDSRSAAMGVGFAALAAGRAAAAGDELDTVARAAAAAVSRIHAFVAVARLDNLRRSGRISGAKAWLGTALALKPLLSVDDGKLVLVQRVRTVSNATAVMIDRVCQLVGDRPAALAVHHVADPAAANDVAAALAERLPACEPAMVTAMGPVLALHVGAGAVGVCVDVGASPPA
Prediction	CCEEEEHCCCCCCCHHHHHHHCCEEEEEEEEHCCEEEHCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCHHHHHHHHHHHHCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCEEEEEHCCHHHHHHHCCCCHHHHHHHHHHCCEEEEEEHCCEEEEEEEHCCHHHHHHHHHHHHHHHHCCCEEEEEEEHCCCHHHHHHHHHHHHHHCCCCCEEEEEHCCCEEEEHCCCCEEEEEEEHCCCCCC
Conf.Score	9799998589999999999889989999999899999589999999999985568999999999999999998699889999757876678999999999859988998588557999999999999999899999999999999985868999489678887599868999999976877899996988999876567889999999999999699757899997799999999999999987999669999688567776499989999995899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 280 \| \| \| \| \| \| \| \| \| \| \| \| \| \| MTVVVVTDTSCRLPADLREQWSIRQVPLHILLDGLDLRDGVDEIPDDIHKRHATTAGATPVELSAAYQRALADSGGDGVVAVHISSALSGTFRAAELTAAELGPAVRVIDSRSAAMGVGFAALAAGRAAAAGDELDTVARAAAAAVSRIHAFVAVARLDNLRRSGRISGAKAWLGTALALKPLLSVDDGKLVLVQRVRTVSNATAVMIDRVCQLVGDRPAALAVHHVADPAAANDVAAALAERLPACEPAMVTAMGPVLALHVGAGAVGVCVDVGASPPA
Prediction	7502000000020246107626021000102044541424351426401631452231224402400352156451220000011231010030022017417440100002000200010011003005542204301510450064010000020052024222043011200320402000104623022223122333004200520273166432310001031462054016203740571440200322123102021200000002365378
	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                 220                 240                 260                 280

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEHCCCCCCCHHHHHHHCCEEEEEEEEHCCEEEHCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCHHHHHHHHHHHHCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCEEEEEHCCHHHHHHHCCCCHHHHHHHHHHCCEEEEEEHCCEEEEEEEHCCHHHHHHHHHHHHHHHHCCCEEEEEEEHCCCHHHHHHHHHHHHHHCCCCCEEEEEHCCCEEEEHCCCCEEEEEEEHCCCCCC
MTVVVVTDTSCRLPADLREQWSIRQVPLHILLDGLDLRDGVDEIPDDIHKRHATTAGATPVELSAAYQRALADSGGDGVVAVHISSALSGTFRAAELTAAELGPAVRVIDSRSAAMGVGFAALAAGRAAAAGDELDTVARAAAAAVSRIHAFVAVARLDNLRRSGRISGAKAWLGTALALKPLLSVDDGKLVLVQRVRTVSNATAVMIDRVCQLVGDRPAALAVHHVADPAAANDVAAALAERLPACEPAMVTAMGPVLALHVGAGAVGVCVDVGASPPA

3fysA

0.27

0.26

0.97

2.88

MUSTER

MNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEVKTTSQPPIGELVALYEELGK--SYDAVISIHLSSGISGTFSSAAAADSMVDNDVYPFDSEISCLAQGFYALKAAELIKNGASPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASKLPMRAAVIHANREEEAAKIIEELSAKYPHV-EFYNSYFGAVIGTHLGEGALGICWCFK-----

1pzxB

0.24

0.23

0.99

3.49

dPPAS

MPIEIITDSGADLPQSYIREHRIAFLPLVVHWNGQDYKDGITIEPKQVYDAMRKTAQPSPLAMKELFLPYAKEN--RPCLYIAFSSKLSGTYQTAMAVRSELEFRLTIIDSKCASLGQGLAVMKAVELAKQNTPYNLLCETIESYCRHMEHIFTVDNLDYLARGGRISKTAAAFGGLLNIKPLLHVEDGALIPLEKWRGRKKVLKRMVELMGERGDDQKQTIGISHADDEETALELKQMIEETHGCTR-FFLSDIGSAIGAHAGPGTIALFFLNKYIEI-

1pzxB

0.24

0.99

4.00

wdPPAS

MPIEIITDSGADLPQSYIREHRIAFLPLVVHWNGQDYKDGITIEPKQVYDAMRKTAQPSPLAMKELFLPYAKEN--RPCLYIAFSSKLSGTYQTAMAVRSELEFRLTIIDSKCASLGQGLAVMKAVELAKQNTPYNLLCETIESYCRHMEHIFTVDNLDYLARGGRISKTAAAFGGLLNIKPLLHVEDGALIPLEKWRGRKKVLKRMVELMGERGDDQKQTIGISHADDEETALELKQMIEETHG-CTRFFLSDIGSAIGAHAGPGTIALFFLNKYIEI-

3fysA

0.27

0.26

0.97

3.45

wMUSTER

MNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEVKTTSQPPIGELVALYEELGK--SYDAVISIHLSSGISGTFSSAAAADSMVDNDVYPFDSEISCLAQGFYALKAAELIKNGASPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASGLPMRAAVIHANREEEAAKIIEELSAKYPHV-EFYNSYFGAVIGTHLGEGALGICWCFK-----

3fysA

0.27

0.26

0.97

4.33

wPPAS

MNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEV-TTSQPPIGELVALYEELGK--SYDAVISIHLSSGISGTFSSAAAADSMVDNDVYPFDSEISCLAQGFYALKAAELIKNGASPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASKLPMRAAVIHANREEEAAKIIEELSAKYPH-VEFYNSYFGAVIGTHLGEGALGICWCFK-----

1pzxB

0.24

0.99

5.68

dPPAS2

MPIEIITDSGADLPQSYIREHRIAFLPLVVHWNGQDYKDGITIEPKQVYDAMRKTAQPSPLAMKELFLPYAKEN--RPCLYIAFSSKLSGTYQTAMAVRSELEFRLTIIDSKCASLGQGLAVMKAVELAKQNTPYNLLCETIESYCRHMEHIFTVDNLDYLARGGRISKTAAAFGGLLNIKPLLHVEDGALIPLEKWRGRKKVLKRMVELMGERGDDQKQTIGISHADDEETALELKQMIEETHG-CTRFFLSDIGSAIGAHAGPGTIALFFLNKYIEI-

3fysA

0.27

0.26

0.97

3.97

PPAS

MNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEV-TTSQPPIGELVALYEELGK--SYDAVISIHLSSGISGTFSSAAAADSMVDNDVYPFDSEISCLAQGFYALKAAELIKNGASPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASKLPMRAAVIHANREEEAAKIIEELSAKYPH-VEFYNSYFGAVIGTHLGEGALGICWCFK-----

3nyiA

0.20

0.96

5.55

Env-PPAS

--YKIVSDSACDLSKEYLEKHDVTIVPLSVSFDGEYYRDGVDITRDECYQRVDKTSLPSVESYADVFRSFVEQG--FPVVCFTITTLFSGSYNSAINAKSLVDANICVIDSKQNTVTQALLIDQFVRLEDG-LSFEQASKL--DALASARIFFTVGSLDYL-KGGRIGKVATAATGKLGVKPVIIKD-GDIGLGGIGRNRNKLKNSVLQVAKKYLDEDNFIVSVGYGYDKEEGFEFKEVESTLDVKLDSETNVAIGIVSAVHTGPYPIGLGVIRKYETL-

1pzxB

0.24

0.99

2.88

MUSTER

MPIEIITDSGADLPQSYIREHRIAFLPLVVHWNGQDYKDGITIEPKQVYDAMRKTAQPSPLAMKELFLPYAKEN--RPCLYIAFSSKLSGTYQTAMAVRSELEFRLTIIDSKCASLGQGLAVMKAVELAKQNTPYNLLCETIESYCRHMEHIFTVDNLDYLARGGRISKTAAAFGGLLNIKPLLHVEDGALIPLEKWRGRKKVLKRMVELMGERGDDQKQTIGISHADDEETALELKQMIEETHG-CTRFFLSDIGSAIGAHAGPGTIALFFLNKYIEI-

2dt8A

0.31

0.30

0.96

3.46

dPPAS

-RITLVTDSTSDLPQDLRGRLGVRVVPLYVNLSGAIYRDWEEITPTEIFQKVRTTSQPSPEDFARVYREALE--EADHVLSLHISGKLSGTVQSAELAAQEFPGRVTVVDTQAASLGV--GVLRAKELLEEGQSLEAVLAELERLRRDHFVRFSVATLEFLKRGGRIGGAQAFLGTLLNLKPVLTLKEGRVEAAGRARGEKKAREEILKAFRAWAEGKRIRAYFLYSGDEDAVAALRQEVLASGLPVEEALVNELGAVIASHTGPGTYGFYAYSL-----

(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 1 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=1.20

Estimated TM-score = 0.88±0.07

Estimated RMSD = 3.6±2.5Å

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	1pzxB	0.917	1.65	0.231	0.975
2	2dt8A	0.895	1.81	0.315	0.964
3	3fysA	0.895	1.98	0.262	0.968
4	3pl5A	0.879	1.82	0.232	0.936
5	3nyiA	0.865	2.31	0.208	0.961
6	3lupA	0.862	2.39	0.221	0.968
7	4x9xA	0.862	1.94	0.248	0.936
8	2g7zA	0.848	2.16	0.240	0.936
9	1vpvA	0.848	2.32	0.219	0.943
10	3jr7A	0.841	2.01	0.218	0.918

(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	0.57	10	3lupA	ELA	Rep, Mult	28,55,56,57,84,88,89,114,166,186,191,225,255,259,262,263,270,271
2	0.04	1	3fysA	BR	Rep, Mult	157,158,181
3	0.04	1	3fysA	BR	Rep, Mult	165,166,168,169
4	0.04	1	2dt8A	ZN	Rep, Mult	61,101
5	0.04	1	2g7zA	ZN	Rep, Mult	189,190
6	0.04	1	2g7zA	ZN	Rep, Mult	229,265
7	0.04	1	3fysA	BR	Rep, Mult	15,18,25,41
8	0.03	1	3fysA	BR	Rep, Mult	99,102,105
9	0.03	1	3fysA	BR	Rep, Mult	71,76,104
10	0.02	1	3pnqD	2HA	Rep, Mult	9,56,58,84,88,91,262
11	0.02	1	1hkbA	CA	Rep, Mult	227,255,260,264

	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	3b8aX	0.448	5.30	0.061	0.671	2.7.1.1	NA
2	0.060	1ig8A	0.430	5.58	0.067	0.661	2.7.1.1	NA
3	0.060	1e1yA	0.400	5.69	0.040	0.639	2.4.1.1	157
4	0.060	2vwbA	0.456	5.68	0.049	0.696	3.4.24.57	NA
5	0.060	1un9A	0.672	3.52	0.144	0.825	2.7.1.29	261
6	0.060	2iu4B	0.680	3.71	0.109	0.839	2.7.1.2	NA
7	0.060	3e1hA	0.441	6.13	0.079	0.739	2.3.1.74	NA
8	0.060	3jvpD	0.446	5.47	0.074	0.682	2.7.1.16	111,125
9	0.060	3gbtA	0.443	5.53	0.052	0.675	2.7.1.12	58,90,109,166
10	0.060	1v4tA	0.401	5.64	0.036	0.625	2.7.1.2,2.7.1.1	39
11	0.060	1fa9A	0.404	6.13	0.087	0.668	2.4.1.1	157
12	0.060	3hm8A	0.460	5.43	0.061	0.693	2.7.1.1	NA
13	0.060	2pkqT	0.444	6.14	0.062	0.743	1.2.1.13	NA
14	0.060	1vsvA	0.443	6.24	0.057	0.754	1.2.1.12	225
15	0.060	1hkgA	0.443	5.81	0.067	0.689	2.7.1.1	126
16	0.060	3lrfA	0.453	5.75	0.092	0.718	2.3.1.41	60,83,90
17	0.060	2pkrB	0.441	6.07	0.063	0.736	1.2.1.13	NA
18	0.060	3e1hB	0.448	5.69	0.063	0.707	2.3.1.74	96
19	0.060	2nztA	0.454	5.41	0.061	0.682	2.7.1.1	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	0.52	0.904	1.86	0.32	0.97	2dt8A	GO:0008289
1	0.51	0.917	1.65	0.23	0.97	1pzxB	GO:0008289
2	0.47	0.862	1.94	0.25	0.94	4x9xA	GO:0008289
3	0.44	0.861	2.29	0.22	0.96	1vpvA	GO:0008289
4	0.43	0.879	1.82	0.23	0.94	3pl5A	GO:0008289
5	0.43	0.866	2.13	0.24	0.95	2g7zA	GO:0008289
6	0.42	0.890	2.32	0.20	0.99	3nyiB	GO:0008289
7	0.42	0.822	2.12	0.34	0.90	3eglB	GO:0008289
8	0.41	0.872	2.36	0.22	0.98	3lupA	GO:0008289
9	0.40	0.895	1.98	0.26	0.97	3fysA	GO:0008289
10	0.37	0.860	2.01	0.22	0.94	3jr7A	GO:0008289
11	0.36	0.837	2.37	0.20	0.94	3fdjA	GO:0008289
12	0.06	0.396	5.61	0.06	0.61	3jruA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
13	0.06	0.346	6.54	0.09	0.62	4wxbA	GO:0003824 GO:0004372 GO:0005737 GO:0006544 GO:0006545 GO:0006563 GO:0006730 GO:0008652 GO:0016740 GO:0019264 GO:0030170 GO:0035999
14	0.06	0.290	6.73	0.05	0.53	3ahmA	GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872
15	0.06	0.329	5.97	0.06	0.54	4hpnA	GO:0003824 GO:0008152 GO:0009063 GO:0016853 GO:0046872
16	0.06	0.344	6.21	0.06	0.58	1bgxT	GO:0001882 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0071897
17	0.06	0.316	5.75	0.04	0.51	3dwcB	GO:0004180 GO:0004181 GO:0006508 GO:0016787
18	0.06	0.288	6.65	0.04	0.52	3jvuA	GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0043107 GO:0043108 GO:0044096

Consensus prediction of GO terms

Molecular Function	GO:0008289
GO-Score	0.96
Biological Processes
GO-Score
Cellular Component
GO-Score

(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.