I-TASSER results

I-TASSER results for job id Rv0964c

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

Input Sequence in FASTA format

>protein (160 residues)
MGLLGFGGAAAEAAQVATHHTTVLLDHHAGACEAVARAAEKAAEEVAAIKMRLQVIRDAA
REHHLTIAYATGTALPPPDLSSYSPADQQAILNTAIRRASNVCWPTPRPPMRIWPRRFDA
PPGPCRASRSMPNSAMRHPQCRRCRRRTATLRRSSGGGIR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGLLGFGGAAAEAAQVATHHTTVLLDHHAGACEAVARAAEKAAEEVAAIKMRLQVIRDAAREHHLTIAYATGTALPPPDLSSYSPADQQAILNTAIRRASNVCWPTPRPPMRIWPRRFDAPPGPCRASRSMPNSAMRHPQCRRCRRRTATLRRSSGGGIR
Prediction	CCCCCCCHHHHHHHHHHHHHCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHEHCCCCCCCC
Conf.Score	9865777468899999876444543455568999999999999999999999999999876546466556688899877777896568999999999866888889999866676667899988766678886555675566666655444446899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MGLLGFGGAAAEAAQVATHHTTVLLDHHAGACEAVARAAEKAAEEVAAIKMRLQVIRDAAREHHLTIAYATGTALPPPDLSSYSPADQQAILNTAIRRASNVCWPTPRPPMRIWPRRFDAPPGPCRASRSMPNSAMRHPQCRRCRRRTATLRRSSGGGIR
Prediction	6322523343242142234312010343352052114125532641320422031035205523020331444313354146244444421142014315511133443324113542734534143445245513534404504543341445654548
	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

CCCCCCCHHHHHHHHHHHHHCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHEHCCCCCCCC
MGLLGFGGAAAEAAQVATHHTTVLLDHHAGACEAVARAAEKAAEEVAAIKMRLQVIRDAAREHHLTIAYATGTALPPPDLSSYSPADQQAILNTAIRRASNVCWPTPRPPMRIWPRRFDAPPGPCRASRSMPNSAMRHPQCRRCRRRTATLRRSSGGGIR

5cwjA

0.14

0.96

0.81

MUSTER

-DSEEEQERIRRILKEARKSGT--EESLRQAIEDVAQLAKKSQDSEVLEEAIRVILRIAKESGSEEALRQAIRAVAEIAKEAQDSEVLEEAIRVILRIAKESGSEALRQAIRAVAEIAKEAQDPIRVIRQIAEESGSEEARRQAERAEEEIRRRAQ----

2p2uB

0.13

0.11

0.84

0.57

dPPAS

--VIVADIRQAEGALAEIATIDRKVGEIEAQNEAIDAAKARASQKSAPLLARRKELEDGVATFEFSLDLGFGTLSTQIVQSKITKDTLERLRQFGISEGIRIKEDVNKEAQ-GWPDEVGLKRRTTDAFYIEINREEV-----------------------

4ykbA

0.18

0.14

0.78

0.53

wdPPAS

------------SGKEAVMEVQLSSTDYTVLRDHLANGEFREAEDETRALLIKLAGPEAVKRNWVYFTEVK--NISVTDFKASS-SVQKEIWVQNQKRWPKFFW---TQNYRKWPMEFDAPRGPLTNGTQLFQAIMEHPAFEK-----------------

5b68A3

0.17

0.16

0.92

0.68

wMUSTER

TSILWFQPGRQEETTVTTHDLPPTAGYLEGEHIALRERLTDPAAELAEDLQWQAEILDVAASANAL--PAREYVGLERDQRGELAELLEGLHTFVAKTPSALTCVCLV--MVGEKRAQNQ-PGT--TRDMYPNDSEGNSENELYHRVAKASKRD------

5b68A3

0.22

0.19

0.84

0.57

wPPAS

TSILWFPGRQEELTTVTTH-PTALEGEHIALRERLGVLNTDPAAELAEDLQWQAEILDVAASAN---------ALPAREYVGLQRGELAELLEGLHTFVAK----TP--ALTCVCRAQN--PGT--TRDMYPNDSEGNSENELYHRVAKASKRD------

5b68A3

0.17

0.16

0.91

0.50

dPPAS2

TSILWFPGRQEELTTVTTHDPTALEGEHIALRERLGVLNTDPAAELAEDLQWQAEILDVAASANAL--PAREYVGLERDQRGELAELLEGLHTFVAKTPSALTCVCLKRAQNQWCIPLCDSEGNSVLIESLREN-------ELYHRVAKASKRD------

5b68A3

0.17

0.16

0.90

0.69

PPAS

TSILWFPGRQEELTTVTTH-PTALEGEHIALRERLGVLNTDPAAELAEDLQWQAEILDVAASANAL--PAREYVGLERDQRGELAELLEGLHTFVAKTPSALTCVCLKRAQNQWCIPLCDSEGNSVLIESLREN-------ELYHRVAKASKRD------

4ykbA

0.20

0.16

0.81

0.76

Env-PPAS

--------SGKEAVMEVQLSSTAGID-YTVLRDHLANGEFREAEDETRALLIKLAGPEAVKRNWVYFTEV--KNISVTDFKASSNSVQKEIWVQNQKRWPKFFW---TQNYRKWPMEFDAPRGPLTNGTQLFQAIMEHPAFEK-----------------

5cwdA

0.14

0.96

0.74

MUSTER

TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAARAAA----SNDEEVAKIAKQAGMPTK--EAARSFCEAAKRDEEVEKIAKKACKEVAKQAGMPW

5b68A3

0.16

0.14

0.91

0.48

dPPAS

EHSPSQPGRQEELTTVTTHDLPPTAGYLEGEHIALRERLTDPAAELAEDLQWQAEILDVAASANAL--PAREYVGLERDQRGELAELLEGLHTFVAKTPSALTCVTTRDMYPNWCIPLCDSEGNSVLIESLREN-------ELYHRVAKASKRD------

(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=-2.49

Estimated TM-score = 0.42±0.14

Estimated RMSD = 10.5±4.6Å

Download Model 2

C-score=-3.58

Download Model 3

C-score=-4.20

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.48

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	5b68A	0.656	3.78	0.144	0.906
2	4s3pA	0.641	3.89	0.127	0.919
3	1cwyA2	0.517	3.85	0.092	0.744
4	2vr5A	0.512	4.55	0.063	0.787
5	4j7rA3	0.511	4.52	0.063	0.787
6	1bf2A	0.502	4.72	0.047	0.787
7	2wskA	0.492	4.44	0.079	0.762
8	1x1nA	0.488	4.18	0.076	0.738
9	5dseB	0.483	4.80	0.073	0.781
10	1tz7A	0.481	4.01	0.043	0.719

(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	0.12	7	2c6rA	FE	Rep, Mult	58,62
2	0.07	4	3hndA	TTP	Rep, Mult	9,10,11,56,57,63
3	0.05	3	3fu1A	ZN	Rep, Mult	54,58
4	0.03	2	1mvyA	GLC	Rep, Mult	23,24,26,87,88,91,92
5	0.03	2	2wghB	DTP	Rep, Mult	53,81,89,90,91
6	0.02	1	3rj1J	SE	Rep, Mult	51,52
7	0.02	1	3u7qB	IMD	Rep, Mult	40,43
8	0.02	1	3ictA	FAD	Rep, Mult	83,85
9	0.02	1	4a8fA	MG	Rep, Mult	79,123
10	0.02	1	3hncB	TTP	Rep, Mult	97,153,157
11	0.02	1	3b2sA	MG	Rep, Mult	100,101
12	0.02	1	1m9nB	AMZ	Rep, Mult	29,30,47,80
13	0.02	1	1ipsA	MN	Rep, Mult	62,63
14	0.02	1	3qsjA	CA	Rep, Mult	7,58,62
15	0.02	1	2hi8X	BR	Rep, Mult	35,52,53
16	0.02	1	1pl0B	BW2	Rep, Mult	10,11,95,97,98
17	0.02	1	4ea2A	MG	Rep, Mult	26,83

	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	1ddzA	0.445	4.89	0.049	0.750	4.2.1.1	NA
2	0.060	2wu8A	0.448	4.88	0.121	0.744	5.3.1.9	NA
3	0.060	1occA	0.446	4.63	0.042	0.713	1.9.3.1	NA
4	0.060	3d6nA	0.446	4.61	0.039	0.688	3.5.2.3	18
5	0.060	2e8yA	0.466	3.88	0.055	0.675	3.2.1.41	NA
6	0.060	1r7aA	0.460	4.67	0.094	0.738	2.4.1.7	NA
7	0.060	1xrtA	0.371	4.85	0.044	0.625	3.5.2.3	NA
8	0.060	1p4rA	0.465	5.33	0.033	0.825	2.1.2.3,3.5.4.10	NA
9	0.060	1edqA	0.430	4.72	0.034	0.688	3.2.1.14	NA
10	0.060	1peuA	0.443	4.89	0.044	0.738	1.17.4.1	NA
11	0.060	1jnrA	0.440	5.35	0.035	0.806	1.8.99.2	NA
12	0.060	1pn0C	0.440	5.12	0.013	0.762	1.14.13.7	NA
13	0.060	2vr5A	0.512	4.55	0.063	0.787	3.2.1.-	NA
14	0.060	2f89F	0.411	5.82	0.039	0.812	2.5.1.1,2.5.1.10	NA
15	0.060	2cvtA	0.445	4.74	0.089	0.731	1.17.4.1	NA
16	0.060	1s46A	0.464	4.65	0.061	0.719	2.4.1.4	NA
17	0.060	1g8mA	0.473	5.24	0.040	0.819	3.5.4.10,2.1.2.3	NA
18	0.060	1ta9B	0.451	5.21	0.013	0.775	1.1.1.6	NA
19	0.060	1kq3A	0.443	5.21	0.035	0.762	1.1.1.6	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	0.09	0.641	3.89	0.13	0.92	4s3pA	GO:0000025 GO:0004134 GO:0005737 GO:0005829 GO:0005975 GO:0005977 GO:0016740 GO:0016757
1	0.07	0.512	4.32	0.06	0.78	4okdA	GO:0003824 GO:0004553 GO:0005975
2	0.07	0.492	4.44	0.08	0.76	2wskA	GO:0003824 GO:0004133 GO:0004135 GO:0004553 GO:0005975 GO:0005977 GO:0005980 GO:0006974 GO:0008152 GO:0016787 GO:0016798
3	0.07	0.502	4.72	0.05	0.79	1bf2A	GO:0003824 GO:0004553 GO:0005576 GO:0005975 GO:0005977 GO:0008152 GO:0016787 GO:0016798 GO:0019156 GO:0046872
4	0.07	0.512	4.55	0.06	0.79	2vr5A	GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
5	0.07	0.466	3.96	0.06	0.68	2wanA
6	0.07	0.502	4.13	0.06	0.74	2vncB	GO:0003824 GO:0004133 GO:0004177 GO:0004553 GO:0005975 GO:0005980 GO:0006508
7	0.07	0.406	4.90	0.07	0.68	3fawA	GO:0003824 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0016020 GO:0016021 GO:0030246
8	0.07	0.488	4.12	0.14	0.73	5csuA	GO:0000025 GO:0004134 GO:0005975 GO:0005977 GO:0005983 GO:0006006 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757
9	0.07	0.467	4.01	0.04	0.69	4aioA	GO:0003824 GO:0004553 GO:0005975 GO:0046872 GO:0051060
10	0.07	0.466	3.88	0.06	0.68	2e8yA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0051060
11	0.07	0.463	3.94	0.06	0.68	2ya1A	GO:0003824 GO:0004553 GO:0005576 GO:0005618 GO:0005975 GO:0016020 GO:0016021 GO:0030246
12	0.07	0.418	3.95	0.05	0.62	1ea9C	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0047798
13	0.07	0.462	4.09	0.09	0.68	3wdhA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0051060
14	0.06	0.465	4.59	0.06	0.72	3ueqA	GO:0003824 GO:0005576 GO:0005975 GO:0016740 GO:0016757 GO:0047669
15	0.06	0.393	4.42	0.04	0.62	4howA	GO:0003824 GO:0005975 GO:0016853 GO:0046872
16	0.06	0.409	4.09	0.06	0.62	3a6oA	GO:0003824 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0031216 GO:0046872
17	0.06	0.392	4.13	0.06	0.57	4aieA	GO:0003824 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0043896 GO:0046872
18	0.06	0.419	4.30	0.03	0.64	3amlA	GO:0003824 GO:0003844 GO:0004553 GO:0005975 GO:0005978 GO:0005982 GO:0009501 GO:0009507 GO:0009536 GO:0016740 GO:0016757 GO:0019252 GO:0043169

Consensus prediction of GO terms

Molecular Function	GO:0016798
GO-Score	0.48
Biological Processes	GO:0044723	GO:0006073	GO:0006112
GO-Score	0.41	0.41	0.41
Cellular Component	GO:0005829	GO:0005576
GO-Score	0.09	0.07

(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.