I-TASSER results

I-TASSER results for job id Rv1986

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

Input Sequence in FASTA format

>protein (199 residues)
MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQREHVLPVVALCTVSDIVLIAAGIAGFGA
LIGAHPRALNVVKFGGAAFLIGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCAAFTFL
NPHVYLDTVVLLGALANEHSDQRWLFGLGAVTASAVWFATLGFGAGRLRGLFTNPGSWRI
LDGLIAVMMVALGISLTVT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQREHVLPVVALCTVSDIVLIAAGIAGFGALIGAHPRALNVVKFGGAAFLIGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCAAFTFLNPHVYLDTVVLLGALANEHSDQRWLFGLGAVTASAVWFATLGFGAGRLRGLFTNPGSWRILDGLIAVMMVALGISLTVT
Prediction	CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	8579999999999999587875788888888757578999999999999999999999999999899999999999999999999999985666655666667778999999999998567668999899766546898767999999999999999999999999999997585899999999999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQREHVLPVVALCTVSDIVLIAAGIAGFGALIGAHPRALNVVKFGGAAFLIGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCAAFTFLNPHVYLDTVVLLGALANEHSDQRWLFGLGAVTASAVWFATLGFGAGRLRGLFTNPGSWRILDGLIAVMMVALGISLTVT
Prediction	6423333333313111322332001001101344331100000121121123223220011123333133323331121022101200132245443456645534212002201020324332311331321111244432311101102321333333213303302421444302310122112212333332237
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHC
MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQREHVLPVVALCTVSDIVLIAAGIAGFGALIGAHPRALNVVKFGGAAFLIGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCAAFTFLNPHVYLDTVVLLGALANEHSDQRWLFGLGAVTASAVWFATLGFGAGRLRGLFTNPGSWRILDGLIAVMMVALGISLTVT

4bwzA2

0.12

0.98

1.02

MUSTER

ILAVGKEAFLVAVLGVALP---FLGGYLYGLEIGFETLPALFLGTALVATSVGITARVLQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIA-ILGKVLGGFLGALTQGVRSALTVGCGMAPRGEVGLIVAALGLKAGAVEEEYAIVLFMVVFTTLFAPFALKPLIAWTER

4ke2A

0.12

0.97

0.92

dPPAS

IDPAARAAAAAAASKAAV----TAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAA--AATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAA

2n4xA

0.10

0.08

0.84

0.90

wdPPAS

----QLMAFALGILSVFSP------VL------GSRGRALDAFLIVAGLTISMLILGYTA------LFFGFFRVVAMLFLLIFALILLSDELDESRMTSGLSWKIQTLPSFFFGMLLAFL-PAILPFAGIAISQTLLSEN--PLVMLSYGLGMAVTIAAVFKMGEKFV------KANFQLIRKVTGAIVLLYLAYFALT

4bwzA2

0.12

0.93

1.05

wMUSTER

ILAVGKEAFLVAVLGVALP---GGYLYGLEIGFETLPALFLGTALVASVGITARVLQELGVLPYSRIILGAAVIDDVLGLIVLACVNGVA---ETGQELSALASPVVLVAGTVVTVIAIL-GKVLGGFLGALTQ-----VRSALTVGCGMAPRGEVGLIVAALGLKA-EEEYAIVLFMVVFTTLFAPFALKPLIAWTER

2n4xA

0.11

0.09

0.84

1.41

wPPAS

----QLMAFALGILSVFSP------VL--GSRGRALDAFLIVAGLTISMLILGYTASL---------FFGFFRVVAMLFLLIFALILLSDELDESRMTSGLSWKIQTLPSFFFGMLLAFLLPLPFAGIAISQTLL----SENPLVMLSYGLGMAVTIAAVFKMGEKFV------KANFQLIRKVTGAIVLLYLAYFALT

4ke2A

0.12

0.97

1.47

dPPAS2

IDPAARAAAAAAASKAAV----TAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAA--AATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAA

2n4xA

0.10

0.09

0.89

1.31

PPAS

----QLMAFALGILSVFSP------VL--AGSRGRALDAFLIVAGLTISMLILGYT-ASLFFGFFRVVAMLFLLIFALILLSDELDEKVSIFASR-MTSGLSWKIQTLPSFFFGMLLAFLLPAILPFAGIAISQTLLSEN--PLVMLSYGLGMAVTIAAVFKMGEKFV------KANFQLIRKVTGAIVLLYLAYFALT

1qorA2

0.13

0.11

0.82

Env-PPAS

---SFLKGLTVYYLLRKTPD-EQFLFH------------AAAGGVGLIACQWAKALGAKLITVGTAQKAQSALKAGAWQVINYREEDLVERLK----EITGGKKVRVRDTWERSLDC--LQRRGLMVSFGNSSGAVTG-VNLGILNQKGSLYVTRPS----------LQGYITT---REELTEASNELFSLIASVIKVD

4o6yA

0.12

0.97

0.91

MUSTER

FMVVRVLGFIIAALVLT-----WTVHYRGGLANKDHIFNVHPVMMVIGLILFNGEAMLAYKSKNLKKLVHLTLQLTAFILSLIGVWAALKFHIDKGIENFYSLHSWLGLACLFLFAFQWAAGFVTYWYPGGSRNSRASLMPWHVFLGISIYALALVTATTGILEKVTFLQVNQV-STEAMLVNTMGVLILILGGFVILG

4bwzA2

0.12

0.98

0.83

dPPAS

ILAVGKEAFLVAVLGVALP---FLGGYLYGLEIGFETLPALFLGTALVATSVGITARVLQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIA-ILGKVLGGFLGALTQGVRSALTVGCGMAPRGEVGLIVAALGLKAGAVEEEYAIVLFMVVFTTLFAPFALKPLIAWTER

(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=-2.15

Estimated TM-score = 0.46±0.15

Estimated RMSD = 10.2±4.6Å

Download Model 2

C-score=-3.42

Download Model 3

C-score=-4.03

Download Model 4

C-score=-3.82

Download Model 5

C-score=-4.47

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	4bwzA2	0.787	2.59	0.130	0.940
2	1zcdA	0.719	3.06	0.084	0.899
3	4czbA	0.718	3.35	0.061	0.950
4	4n7wA	0.702	3.59	0.115	0.940
5	4cz8A	0.700	3.44	0.046	0.940
6	3zuxA	0.697	3.40	0.063	0.920
7	1xmgC	0.533	4.60	0.056	0.804
8	1mhzD	0.525	4.91	0.052	0.854
9	1mhyB	0.520	4.65	0.055	0.789
10	2j2fA	0.506	5.60	0.059	0.879

(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	1v54B	HEA	Rep, Mult	19,121,124,125
2	0.09	5	4n7wB	MPG	Rep, Mult	30,119,122,123,125,126,129,138,194
3	0.04	2	5irxA	6EU	Rep, Mult	27,116,119,120
4	0.02	1	2o013	CLA	Rep, Mult	72,73
5	0.02	1	1xveD	3BB	Rep, Mult	77,81,84
6	0.02	1	2wieA	CVM	Rep, Mult	51,55
7	0.02	1	1mhy1	III	Rep, Mult	9,10,13,14,16,17,18,21,22,124,128
8	0.02	1	1xvfA	3CL	Rep, Mult	7,14,129,131,132
9	0.02	1	1ea4J	NUC	Rep, Mult	196,197,199
10	0.02	1	2r9rB	PGW	Rep, Mult	181,196
11	0.02	1	3wguG	CLR	Rep, Mult	112,119
12	0.02	1	1xvgB	BRJ	Rep, Mult	12,13,16,74,78
13	0.02	1	1xvgA	BRJ	Rep, Mult	121,122,125,182,185,186
14	0.02	1	3zuxA	PTY	Rep, Mult	122,125,129,137,145,186,190,193,194
15	0.02	1	2zt9G	III	Rep, Mult	61,69
16	0.02	1	1jtxB	CVI	Rep, Mult	50,158
17	0.02	1	1xvbD	3BR	Rep, Mult	81,84,85,88
18	0.02	1	2bhwA	CLA	Rep, Mult	17,19

	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	2dgaA	0.433	5.13	0.037	0.678	3.2.1.21	NA
2	0.060	1myrA	0.431	5.04	0.030	0.668	3.2.1.147	NA
3	0.060	2p0mA	0.428	5.19	0.044	0.694	1.13.11.33	NA
4	0.060	1up8A	0.355	5.70	0.054	0.618	1.11.1.18	123
5	0.060	1zchA	0.429	4.78	0.097	0.648	1.5.1.29	132
6	0.060	1h16A	0.477	5.41	0.074	0.784	2.3.1.54	NA
7	0.060	1p4kA	0.431	5.19	0.034	0.699	3.5.1.26	147
8	0.060	1mhyB	0.520	4.65	0.055	0.789	1.14.13.25	NA
9	0.060	1jk0A	0.435	5.37	0.068	0.709	1.17.4.1	NA
10	0.060	1biqB	0.476	4.97	0.078	0.764	1.17.4.1	NA
11	0.060	1dwaM	0.432	5.11	0.030	0.673	3.2.1.147	NA
12	0.060	1ayyD	0.273	4.83	0.053	0.422	3.5.1.26	NA
13	0.060	2vuxB	0.448	5.59	0.056	0.764	1.17.4.1	NA
14	0.060	1is2A	0.430	5.44	0.044	0.724	1.3.3.6	58
15	0.060	2de3B	0.432	4.93	0.086	0.699	3.13.1.3	NA
16	0.060	1smsA	0.470	4.78	0.061	0.759	1.17.4.1	NA
17	0.060	2bq1I	0.498	4.52	0.093	0.754	1.17.4.1	NA
18	0.060	1fziA	0.498	5.28	0.075	0.814	1.14.13.25	NA
19	0.060	3hf1B	0.467	5.07	0.061	0.769	1.17.4.1	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	0.21	0.531	4.63	0.06	0.80	1fyzC	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0016709 GO:0055114
1	0.15	0.787	2.59	0.13	0.94	4bwzA	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
2	0.14	0.720	3.23	0.06	0.94	4czbB	GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600
3	0.12	0.702	3.59	0.12	0.94	4n7wA	GO:0016020 GO:0016021
4	0.12	0.697	3.40	0.06	0.92	3zuxA	GO:0016020 GO:0016021
5	0.12	0.710	3.35	0.08	0.94	4cz8A	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
6	0.07	0.498	5.28	0.07	0.81	1fziA	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
7	0.07	0.520	4.65	0.06	0.79	1mhyB	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0016709 GO:0055114
8	0.06	0.477	5.41	0.06	0.82	2innA	GO:0006725 GO:0016491 GO:0046872 GO:0055114
9	0.06	0.504	5.10	0.05	0.81	3dhiA	GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
10	0.06	0.524	4.97	0.07	0.85	1mhyD	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
11	0.06	0.476	5.37	0.07	0.81	2incA	GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
12	0.06	0.463	4.58	0.04	0.72	2inpD	GO:0006725 GO:0016491 GO:0016709 GO:0055114
13	0.06	0.733	2.95	0.06	0.90	4atvA	GO:0005886 GO:0006810 GO:0006811 GO:0006814 GO:0006885 GO:0015081 GO:0015297 GO:0015491 GO:0015992 GO:0016020 GO:0016021 GO:0035725 GO:0055085 GO:0098655
14	0.06	0.447	4.02	0.09	0.61	3dhiB	GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0019439 GO:0042203 GO:0055114
15	0.06	0.355	6.21	0.05	0.67	5aa5C	GO:0016151
16	0.06	0.350	5.51	0.03	0.59	1u0uA	GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
17	0.06	0.310	5.23	0.05	0.49	2y1vA	GO:0005618 GO:0016020 GO:0016021
18	0.06	0.307	4.94	0.05	0.48	2fckA	GO:0008080 GO:0016740 GO:0016746

Consensus prediction of GO terms

Molecular Function	GO:0015078	GO:0015298	GO:0016705	GO:0004497	GO:0043169
GO-Score	0.54	0.54	0.42	0.42	0.31
Biological Processes	GO:0098662	GO:0015992	GO:0043446	GO:0044281
GO-Score	0.54	0.54	0.42	0.42
Cellular Component	GO:0016021	GO:1990204
GO-Score	0.43	0.42

(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.