I-TASSER results

I-TASSER results for job id Rv0364

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

Input Sequence in FASTA format

>protein (227 residues)
MSTAVTAMPDILDPMYWLGANGVFGSAVLPGILIIVFIETGLLFPLLPGESLLFTGGLLS
ASPAPPVTIGVLAPCVALVAVLGDQTAYFIGRRIGPALFKKEDSRFFKKHYVTESHAFFE
KYGKWTIILARFVPIARTFVPVIAGVSYMRYPVFLGFDIVGGVAWGAGVTLAGYFLGSVP
FVHMNFQLIILAIVFVSLLPALVSAARVYRARRNAPQSDPDPLVLPE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MSTAVTAMPDILDPMYWLGANGVFGSAVLPGILIIVFIETGLLFPLLPGESLLFTGGLLSASPAPPVTIGVLAPCVALVAVLGDQTAYFIGRRIGPALFKKEDSRFFKKHYVTESHAFFEKYGKWTIILARFVPIARTFVPVIAGVSYMRYPVFLGFDIVGGVAWGAGVTLAGYFLGSVPFVHMNFQLIILAIVFVSLLPALVSAARVYRARRNAPQSDPDPLVLPE
Prediction	CCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCCCHHHHHHHHHHHHHHCCEEEEEHHCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	85799999998668999999999999999999999999976544799966899999999975898866999999999999999999999999976888874555579999999999999998874676544568899999898876589867899999999999999999999998678888888899999999999999999999999998776666556778899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MSTAVTAMPDILDPMYWLGANGVFGSAVLPGILIIVFIETGLLFPLLPGESLLFTGGLLSASPAPPVTIGVLAPCVALVAVLGDQTAYFIGRRIGPALFKKEDSRFFKKHYVTESHAFFEKYGKWTIILARFVPIARTFVPVIAGVSYMRYPVFLGFDIVGGVAWGAGVTLAGYFLGSVPFVHMNFQLIILAIVFVSLLPALVSAARVYRARRNAPQSDPDPLVLPE
Prediction	64301420341131221131233323311220020012211211223332321230000002352403112113213200210130012012321330053244330456205203500643212000202331331031022001141433201300111131313320220120022320352032211121222223323221222244454555576555468
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCCCHHHHHHHHHHHHHHCCEEEEEHHCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MSTAVTAMPDILDPMYWLGANGVFGSAVLPGILIIVFIETGLLFPLLPGESLLFTGGLLSASPAPPVTIGVLAPCVALVAVLGDQTAYFIGRRIGPALFKKEDSRFFKKHYVTESHAFFEKYGKWTIILARFVPIARTFVPVIAGVSYMRYPVFLGFDIVGGVAWGAGVTLAGYFLGSVPFVHMNFQLIILAIVFVSLLPALVSAARVYRARRNAPQSDPDPLVLPE

4bwzA2

0.13

0.11

0.85

1.18

dPPAS

------RLKDILAVGKEAFLVAVLGVALPFLGGYLYGLEIGFET-----LPALFLGTALVATGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLG-ALTQGVRSALTVGCGMAP-----------RGEVGLIVAALGLKAGAVN--EEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------

4hzuS

0.17

0.11

0.63

0.93

wPPAS

MT-------------------GSLKENTIAAVLIAMTVALSILV-PIPCEVGIYTSAIL---GRR---------MGLLVGGASGFLIDILT------------------------------YPV-----CLFSLVIHGTQGLVVGWL-KGIRSMLLPLLVGSLVMVIGYCLATTLLGWPAGLASIFGNVVQVGFGAGVTLSIVGPLTRLKPD---------------

4bwzA2

0.13

0.11

0.85

2.21

dPPAS2

------RLKDILAVGKEAFLVAVLGVALPFLGGYLYGLEIGFET-----LPALFLGTALVATGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLG-ALTQGVRSALTVGCGMAP-----------RGEVGLIVAALGLKAGAVN--EEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------

4bwzA2

0.10

0.09

0.88

1.13

PPAS

---RLKDILAVGKEAFLVAVLGVALPFLGGYLYGLEITLPALFL--LVATSVGITARVLQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGK--VLGGFLGALTQVRSALTVGCGMAP-----------RGEVGLIVAALGLKAGAVN--EEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------

4ke2A

0.11

0.10

0.85

1.06

dPPAS

IDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAA------DDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINV--------------------------KAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-

3wxvA

0.12

0.10

0.83

1.49

dPPAS2

MPSFRACFKSIFRIHETGNIWTHLLGFVLFLFLGILTMLRMYFMA-----------------PLQEKVVFGMFFLGAVLCLSFSWLFHTVY----------CHS--------EKVSRTFSKLD----YSGIALLIMGSFVPWLYYSFYCSPQPRLIYLSIVCVLGISAIIVAQWDRFATPKHRQTRAGVFLGLGLSGVVPTMHFTIAEGFVKATTVMGWFFLMAVMY

4cadC

0.10

0.09

0.87

1.48

dPPAS2

LWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKFLLMPA---VILLSILLSIPFGGSISQFQFSFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLF--KASILFGIFWSLWHFPLIFVNN-------SYQYEIFNQS----IWYGLNFFLSILPMGIIITWMCLKNRKELLAITQDTKIIETGVLFLVAAAIILYDKKMFFEK--------------

4tq3A

0.09

0.07

0.85

1.41

dPPAS2

ISVREAWLYCIAFLALSLATAAAINEKFFLAMLGANIIGYVYSAPPWPVNALAAVLAFYAGLSIGGAEVPIAIYPAAFFLAATFYIPTAVSDYEFDKKAGLKN--------------TPVFFGPRALKSLYPLSAITVILWAYVFLMAERIEIKVISPLIIAYTLIYTFIINSRWDGEKLNVSPNLILTPFGIISALFIAYGFAVISV-------------------

4pgrA

0.12

0.09

0.76

1.41

dPPAS2

------------HESKQSIMQRILTVFVFTLLIATVGLFIGQFVPVSILEVAMIILAFWMRRRKAVGYAFVYTFAFVSGITLFPIVSHYASIA-----------------------------GAYVVLEAFGSTFVIFAVLGTIGAKMKKDLSFLWSFLLVAVLALAVVGIFNIFSPLNSAAMMAYSVIGTIVFSLYILYDLNQIKHR--------------HITED

4bwzA2

0.13

0.11

0.85

0.95

MUSTER

LKDILAV-----------GKEAFLVAVLGVALPFLGGYLYGLEIGF-ETLPALFLGTALVATQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFALTQGVRSALTVGCGMAP-----------RGEVGLIVAALGLKAGAVN--EEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE--------

(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=-2.34

Estimated TM-score = 0.44±0.14

Estimated RMSD = 11.0±4.6Å

Download Model 2

C-score=-4.66

Download Model 3

C-score=-4.66

Download Model 4

C-score=-4.67

Download Model 5

C-score=-4.90

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	0.752	2.45	0.115	0.850
2	4czbA	0.655	3.84	0.078	0.877
3	4n7wA	0.621	4.15	0.102	0.841
4	4cz8A2	0.620	3.17	0.082	0.771
5	3zuxA	0.610	3.77	0.063	0.806
6	1zcdA	0.602	3.56	0.065	0.762
7	1mhzD	0.513	5.26	0.040	0.828
8	3dhiA	0.493	5.46	0.055	0.811
9	1xmgC	0.489	5.13	0.040	0.758
10	2innA	0.483	5.67	0.056	0.811

(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	4wd7B	ZN	Rep, Mult	84,88
2	0.04	2	3qoqD	NUC	Rep, Mult	131,137
3	0.04	2	3zuxA	PTY	Rep, Mult	118,121,125,142,195,199,202,203,206
4	0.04	2	1xvfA	3CL	Rep, Mult	34,41,112,115,116
5	0.02	1	1xvgA	BRJ	Rep, Mult	61,85,88,165,168,169
6	0.02	1	5jqhB	CLR	Rep, Mult	170,193,194
7	0.02	1	2abmA	POQ	Rep, Mult	52,199
8	0.02	1	2v46M	NUC	Rep, Mult	144,145
9	0.02	1	1xvgA	BRJ	Rep, Mult	33,52,56
10	0.02	1	1xveA	3BB	Rep, Mult	34,37,38,42,43
11	0.02	1	3f34A	DIE	Rep, Mult	54,57,58,88,189
12	0.02	1	2jk8B	CL	Rep, Mult	123,130,131
13	0.02	1	4n7wB	MPG	Rep, Mult	36,122,125,126,128,129,137
14	0.02	1	2a5vA	SCN	Rep, Mult	154,174
15	0.02	1	4ac8A	CA	Rep, Mult	158,200
16	0.02	1	4jtcB	PGW	Rep, Mult	15,19
17	0.02	1	2nr9A	PA6	Rep, Mult	90,94
18	0.02	1	1azs1	III	Rep, Mult	113,114,116,120,124
19	0.02	1	1xveD	3BB	Rep, Mult	75,79,82
20	0.02	1	3arcJ	MG	Rep, Mult	161,172,173,176

	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	2z4yB	0.358	4.91	0.053	0.559	2.5.1.29	NA
2	0.060	1mc0A	0.311	5.22	0.035	0.480	3.1.4.17	60,169
3	0.060	1aorB	0.438	4.89	0.050	0.648	1.2.7.5	NA
4	0.060	3fg3A	0.360	5.66	0.028	0.599	4.2.1.92,1.13.11.40	NA
5	0.060	1smsA	0.423	5.59	0.066	0.700	1.17.4.1	NA
6	0.060	1rqiA	0.419	5.40	0.057	0.674	2.5.1.10	NA
7	0.060	7reqB	0.409	4.88	0.065	0.617	5.4.99.2	NA
8	0.060	1jq5A	0.409	4.86	0.050	0.612	1.1.1.6	NA
9	0.060	2dh4A	0.409	4.99	0.051	0.652	2.5.1.29	NA
10	0.060	1biqB	0.412	5.78	0.044	0.700	1.17.4.1	NA
11	0.060	1vljB	0.414	4.99	0.055	0.604	1.1.1.-	NA
12	0.060	3dy5A	0.427	5.22	0.054	0.683	1.13.11.40,4.2.1.92	NA
13	0.060	2e52A	0.414	5.07	0.018	0.630	3.1.21.4	26,60
14	0.060	3hf1B	0.423	5.54	0.040	0.696	1.17.4.1	NA
15	0.060	2vuxB	0.407	5.49	0.066	0.678	1.17.4.1	NA
16	0.060	1mhyD	0.510	5.18	0.040	0.819	1.14.13.25	NA
17	0.060	1tazA	0.418	5.24	0.043	0.661	3.1.4.17	NA
18	0.060	1uzrB	0.412	5.73	0.077	0.705	1.17.4.1	NA
19	0.060	1jk0A	0.419	5.64	0.100	0.692	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	0.14	0.752	2.45	0.12	0.85	4bwzA	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0046872 GO:0055085 GO:1902600
1	0.07	0.621	4.15	0.10	0.84	4n7wA	GO:0016020 GO:0016021
2	0.07	0.615	3.66	0.08	0.78	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
3	0.07	0.510	5.18	0.04	0.82	1mhyD	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0016491 GO:0046872 GO:0055114
4	0.07	0.493	5.46	0.06	0.81	3dhiA	GO:0004497 GO:0006725 GO:0016491 GO:0019439 GO:0042203 GO:0046872 GO:0055114
5	0.06	0.659	3.36	0.08	0.82	4cz8A	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
6	0.06	0.610	3.77	0.06	0.81	3zuxA	GO:0016020 GO:0016021
7	0.06	0.507	5.51	0.08	0.85	1fziA	GO:0004497 GO:0006725 GO:0006730 GO:0015049 GO:0015050 GO:0015947 GO:0016491 GO:0046872 GO:0055114
8	0.06	0.669	3.46	0.08	0.85	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
9	0.06	0.355	4.90	0.02	0.54	3dhiB	GO:0004497 GO:0006725 GO:0016491 GO:0016709 GO:0019439 GO:0042203 GO:0055114
10	0.06	0.483	5.61	0.06	0.82	2innA	GO:0006725 GO:0016491 GO:0046872 GO:0055114
11	0.06	0.467	5.41	0.04	0.79	2incA	GO:0004497 GO:0006725 GO:0016491 GO:0046872 GO:0055114
12	0.06	0.276	6.06	0.02	0.48	1pv9B	GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0016805 GO:0046872 GO:0102009
13	0.06	0.302	6.44	0.05	0.57	3ug4C	GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046373 GO:0046556
14	0.06	0.291	5.96	0.06	0.50	4rpfA	GO:0000166 GO:0004413 GO:0005524 GO:0005737 GO:0006566 GO:0008652 GO:0009088 GO:0016301 GO:0016310 GO:0016740
15	0.06	0.246	5.38	0.05	0.39	5agsA	GO:0000166 GO:0002161 GO:0004812 GO:0004823 GO:0005524 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006412 GO:0006418 GO:0006429 GO:0006450 GO:0016874 GO:0040007
16	0.06	0.327	5.73	0.03	0.54	1u0uA	GO:0003824 GO:0005737 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747 GO:0050198
17	0.06	0.272	4.79	0.03	0.41	2fckA	GO:0008080 GO:0016740 GO:0016746
18	0.06	0.275	6.63	0.05	0.53	3eiwA

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.50
Biological Processes	GO:0044763	GO:0044765
GO-Score	0.39	0.39
Cellular Component	GO:0031224
GO-Score	0.41

(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.