I-TASSER results

I-TASSER results for job id Rv0488

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

Input Sequence in FASTA format

>protein (201 residues)
MMTLKVAIGPQNAFVLRQGIRREYVLVIVALCGIADGALIAAGVGGFAALIHAHPNMTLV
ARFGGAAFLIGYALLAARNAWRPSGLVPSESGPAALIGVVQMCLVVTFLNPHVYLDTVVL
IGALANEESDLRWFFGAGAWAASVVWFAVLGFSAGRLQPFFATPAAWRILDALVAVTMIG
VAVVVLVTSPSVPTANVALII

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MMTLKVAIGPQNAFVLRQGIRREYVLVIVALCGIADGALIAAGVGGFAALIHAHPNMTLVARFGGAAFLIGYALLAARNAWRPSGLVPSESGPAALIGVVQMCLVVTFLNPHVYLDTVVLIGALANEESDLRWFFGAGAWAASVVWFAVLGFSAGRLQPFFATPAAWRILDALVAVTMIGVAVVVLVTSPSVPTANVALII
Prediction	CCEEEHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Conf.Score	965775788748999999987575789999999999999999999899999998999999999999999999999999975666655566667788999999999986585568877886654468887579999999999999999999999999999975968999999999999999999999996544444554569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MMTLKVAIGPQNAFVLRQGIRREYVLVIVALCGIADGALIAAGVGGFAALIHAHPNMTLVARFGGAAFLIGYALLAARNAWRPSGLVPSESGPAALIGVVQMCLVVTFLNPHVYLDTVVLIGALANEESDLRWFFGAGAWAASVVWFAVLGFSAGRLQPFFATPAAWRILDALVAVTMIGVAVVVLVTSPSVPTANVALII
Prediction	620010323310020021014443311000011111121332332110101333331332233110210221022001222445434556455442230023000001333313113212101112344323111010022013333322133033024215443023121220122133313311121343333322136
	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

CCEEEHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
MMTLKVAIGPQNAFVLRQGIRREYVLVIVALCGIADGALIAAGVGGFAALIHAHPNMTLVARFGGAAFLIGYALLAARNAWRPSGLVPSESGPAALIGVVQMCLVVTFLNPHVYLDTVVLIGALANEESDLRWFFGAGAWAASVVWFAVLGFSAGRLQPFFATPAAWRILDALVAVTMIGVAVVVLVTSPSVPTANVALII

2n4xA

0.14

0.12

0.86

1.41

wPPAS

LMAFA---G--SVFVL--GSRGRALDAFLIVAGLTISMLILGYTASL--FFGFFRVVAMLFLLIFALILLSDELDEKVSIFASR-MTSGLSWKIQTLPSFFFGMLLAFLLPLPFAGIAISQTLL----SENPLVMLSYGLGMAVTIAAVFKMGEKFV------KANFQLIRKVTGAIVLLYLAYFAL--------TEVLLL

4ke2A

0.18

0.16

0.91

1.56

dPPAS2

-------------------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAI

2n4xA

0.12

0.10

0.84

1.26

PPAS

VVPLIFA-----------GSRGRALDAFLIVAGLTISMLILGYTASL--FFGFFRVVAMLFLLIFALILLSDELDEKVSIFASR-MTSGLSWKIQTLPSFFFGMLLAFLLPLPFAGIAISQTLLSEN----PLVMLSYGLGMAVTIAAVFKMGEKFV------KANFQLIRKVTGAIVLLYLAYFAL--------TEVLLL

4bwzA2

0.15

0.13

0.85

0.99

wPPAS

----------RLKDILAV-------GKEAFLVAVLGVALPFLGGYLYGLEIGFE---TLPALFLGTALVVGITARVLQEL----GVLSRPYSRIILGAAVIDDVLGLIV--LACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGRGEVGLIVAALGLKAGA----VNEEEYAIVL

4bwzA2

0.14

0.12

0.87

1.49

dPPAS2

----------RLKDILAV-------GKEAFLVAVLGVALPFLGGYLYGLEIGFE---TLPALFLGTALVVGITARVLQEL----GVLSRPYSRIILGAAVIDDVLGLIV--LACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGRGEVGLIVAALGLKAGAVNEEEYAIVLFMVV

4ke2A

0.19

0.18

0.95

1.16

PPAS

-----MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKD------TAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAI

2n4xA

0.11

0.09

0.83

1.30

dPPAS2

VVPLIFA---------------GSRGRALDAFLIVAGLTISMLILGYTAFFGFFRVVAMLFLLIFALILLSEKVSIFASRMTSGLSWKIQTLPSFFFGMLLAFLWLPAI--LPFAGIAISQTLLSEN----PLVMLSYGLGMAVTIAAVFKMGEKFV------KANFQLIRKVTGAIVLLYLAYFA--------LTEVLLL

4bwzA2

0.15

0.12

0.86

1.07

PPAS

----------RLKDILAV-------GKEAFLVAVLGVALPFLGGYLYGLEIGFE---TLPALFLGTALVVGITARVLQEL---------GVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGPRGEVGLIVAALGLKAGAVNEEEYAIVL

4or2A2

0.11

0.10

0.96

1.25

dPPAS2

CLGILVT----LFVTLIFVLYRDTPVVKSSSRELCYIILAGIFLGYVCPFTLITTSCYLQRLLVGLSSAMCYSALVTKTNR-IARILARKPRFMSAWAQVIIASILIS---VQLTLVVTLIIMEPPMTSNLGVVAPLGYNGLLIMSCTYYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIITTCFAVSL

5ctgA

0.13

0.10

0.80

1.24

dPPAS2

-----------------DSLYDISCFAAGLAGNIFALALFLSPVTTFKRILKAFDGLPYLFSLLNCLICLWYGL----------------PWVADGRLLVATVNGIGA---VFQLAYICLFIFYADS--RKTRMKIIGLLVLVVCGFALVSHASVFFFD--QPLRQQFVGAVSMASLISMFASPLAVMGVVIRSESVEFMP

(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=-2.65

Estimated TM-score = 0.41±0.14

Estimated RMSD = 11.5±4.5Å

Download Model 2

C-score=-2.93

Download Model 3

C-score=-3.17

Download Model 4

C-score=-4.09

Download Model 5

C-score=-4.38

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	4bwzA	0.597	4.53	0.114	0.861
2	4n7wA	0.582	4.67	0.091	0.866
3	3zuxA	0.581	4.69	0.114	0.866
4	4czbA2	0.568	4.20	0.100	0.811
5	1zcdA2	0.549	3.82	0.061	0.776
6	4cz8A2	0.534	4.24	0.086	0.751
7	2f3oA	0.529	4.69	0.052	0.811
8	1r8wA	0.525	5.21	0.054	0.861
9	5i2aA	0.522	4.80	0.066	0.831
10	1smsA	0.519	5.21	0.058	0.841

(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	4hfdE	MBR	Rep, Mult	65,66,106,109
2	0.07	4	4xk8L	CLA	Rep, Mult	40,72
3	0.06	3	3zuxA	PTY	Rep, Mult	34,37,41,59,66,105,109,115
4	0.04	2	1rsvA	AZI	Rep, Mult	72,175,178
5	0.04	2	1lghA	BCL	Rep, Mult	110,111,116
6	0.04	2	1uryA	XE	Rep, Mult	72,76,167,170,174
7	0.02	1	4ca5A	FUC	Rep, Mult	60,61,121
8	0.02	1	3nhjB	FAD	Rep, Mult	138,171
9	0.02	1	3fk7A	4DM	Rep, Mult	166,170
10	0.02	1	1mx1F	THA	Rep, Mult	15,16,70,120,121,178
11	0.02	1	4o6mB	MPG	Rep, Mult	38,39
12	0.02	1	2wieA	CVM	Rep, Mult	40,44
13	0.02	1	1rsrB	UUU	Rep, Mult	32,69,73,102,105
14	0.02	1	1zoyC	EPH	Rep, Mult	44,47
15	0.02	1	2pnqA	MG	Rep, Mult	36,37

	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	1h16A	0.357	6.40	0.037	0.731	2.3.1.54	NA
2	0.060	2vuxB	0.480	5.23	0.089	0.801	1.17.4.1	NA
3	0.060	1z1lA	0.394	5.70	0.020	0.652	3.1.4.17	46,56
4	0.060	1mhyB	0.487	5.41	0.113	0.831	1.14.13.25	NA
5	0.060	2j2fA	0.491	4.77	0.045	0.751	1.14.19.2,1.14.99.6	NA
6	0.060	3b8eC	0.461	5.19	0.061	0.746	3.6.3.9	39,67
7	0.060	3b8cA	0.466	5.50	0.072	0.786	3.6.3.6	NA
8	0.060	1fo4A	0.445	5.36	0.038	0.731	1.17.1.4	NA
9	0.060	1h0nA	0.490	5.28	0.075	0.826	1.17.4.1	NA
10	0.060	1sojL	0.445	5.47	0.081	0.741	3.1.4.17	155
11	0.060	3b9jI	0.272	4.72	0.057	0.428	1.17.1.4,1.17.3.2	62
12	0.060	1fziA	0.478	5.42	0.040	0.821	1.14.13.25	NA
13	0.060	3b9jJ	0.376	5.19	0.060	0.597	1.17.1.4,1.17.3.2	173
14	0.060	3b8eA	0.464	5.27	0.050	0.756	3.6.3.9	NA
15	0.060	3b9jC	0.440	5.60	0.075	0.756	1.17.3.2,1.17.1.4	NA
16	0.060	2e1qA	0.449	5.49	0.051	0.746	1.17.3.2,1.17.1.4	NA
17	0.060	1qi9B	0.484	4.93	0.062	0.756	1.11.1.10	NA
18	0.060	2bq1I	0.510	5.22	0.058	0.821	1.17.4.1	NA
19	0.060	1smsA	0.519	5.21	0.058	0.841	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	0.07	0.582	4.67	0.09	0.87	4n7wA	GO:0016020 GO:0016021
1	0.07	0.603	4.40	0.07	0.89	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
2	0.07	0.581	4.69	0.11	0.87	3zuxA	GO:0016020 GO:0016021
3	0.07	0.525	5.10	0.04	0.86	4mtjA	GO:0003824 GO:0008152
4	0.06	0.387	5.85	0.06	0.68	3owaC	GO:0000166 GO:0003995 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114
5	0.06	0.599	4.66	0.08	0.89	4cz8A	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
6	0.06	0.387	5.77	0.04	0.68	5i2gA	GO:0003824 GO:0008152
7	0.06	0.597	4.53	0.11	0.86	4bwzA	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
8	0.06	0.302	5.87	0.03	0.55	3zq5A	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0005524 GO:0005622 GO:0006355 GO:0007165 GO:0009584 GO:0009585 GO:0009639 GO:0009881 GO:0009883 GO:0016301 GO:0016310 GO:0016740 GO:0018106 GO:0018298 GO:0023014 GO:0042802 GO:0046777 GO:0050896
9	0.06	0.401	4.04	0.12	0.57	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
10	0.06	0.354	6.05	0.04	0.70	1cm5A	GO:0003824 GO:0005737 GO:0005829 GO:0005975 GO:0006006 GO:0006567 GO:0008152 GO:0008861 GO:0016020 GO:0016740 GO:0016746
11	0.06	0.529	4.69	0.05	0.81	2f3oA	GO:0003824 GO:0008152 GO:0016829
12	0.06	0.351	5.31	0.04	0.58	3ug4C	GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
13	0.06	0.518	5.01	0.06	0.84	2yajC	GO:0003824 GO:0008152 GO:0016829 GO:0043722
14	0.06	0.351	5.26	0.05	0.57	1u0uA	GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
15	0.06	0.388	5.95	0.05	0.69	5i2aB	GO:0003824 GO:0008152
16	0.06	0.283	5.70	0.05	0.50	2gauA	GO:0003677 GO:0006351 GO:0006355
17	0.06	0.319	4.79	0.06	0.51	2k60A	GO:0002020 GO:0002115 GO:0005246 GO:0005509 GO:0005513 GO:0005737 GO:0005783 GO:0005789 GO:0005856 GO:0005874 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006816 GO:0006874 GO:0016020 GO:0016021 GO:0016529 GO:0030176 GO:0032237 GO:0032541 GO:0033017 GO:0042802 GO:0046872 GO:0051010 GO:0051924 GO:0070166 GO:1903779
18	0.06	0.311	5.83	0.03	0.54	1pv9B	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009

Consensus prediction of GO terms

Molecular Function	GO:0015491	GO:0015081	GO:0003995	GO:0050660
GO-Score	0.07	0.07	0.07	0.07
Biological Processes	GO:0015992	GO:0035725	GO:0006885	GO:0055114
GO-Score	0.07	0.07	0.07	0.07
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.19	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.