I-TASSER results

I-TASSER results for job id Rv1352

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

Input Sequence in FASTA format

>protein (123 residues)
MARTLALRASAGLVAGMAMAAITLAPGARAETGEQFPGDGVFLVGTDIAPGTYRTEGPSN
PLILVFGRVSELSTCSWSTHSAPEVSNENIVDTNTSMGPMSVVIPPTVAAFQTHNCKLWM
RIS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MARTLALRASAGLVAGMAMAAITLAPGARAETGEQFPGDGVFLVGTDIAPGTYRTEGPSNPLILVFGRVSELSTCSWSTHSAPEVSNENIVDTNTSMGPMSVVIPPTVAAFQTHNCKLWMRIS
Prediction	CCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCEEEHCCCCCCCCEHCCCCCCCCCEEEEEHCCCCCCCCCEEHCCCCCCCEEEEHCCCCEEEEHCCCCCCEHCC
Conf.Score	988766677777666655665568999999988877899789976767996788589998865554677788876899876899998765546888898799986775699968988858859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MARTLALRASAGLVAGMAMAAITLAPGARAETGEQFPGDGVFLVGTDIAPGTYRTEGPSNPLILVFGRVSELSTCSWSTHSAPEVSNENIVDTNTSMGPMSVVIPPTVAAFQTHNCKLWMRIS
Prediction	654543453343333343333333436454445442525130303441331314153445434444444565320203224446454430132334643330404444440416515515648
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCEEEHCCCCCCCCEHCCCCCCCCCEEEEEHCCCCCCCCCEEHCCCCCCCEEEEHCCCCEEEEHCCCCCCEHCC
MARTLALRASAGLVAGMAMAAITLAPGARAETGEQFPGDGVFLVGTDIAPGTYRTEGPSNPLILVFGRVSELSTCSWSTHSAPEVSNENIVDTNTSMGPMSVVIPPTVAAFQTHNCKLWMRIS

3a0fA4

0.12

0.11

0.85

1.27

dPPAS2

SYTKKGNGLPCCWTYTGTPVTSNLRAGE------------LWVSVKG--VGIYHSTDFGNTFTALAGSGSSLNPAVFSIGAPQTPNATETLFLW-----GIPSASQPEGLYMSTNGGLWTRLN

3b7fA2

0.12

0.11

0.88

1.23

dPPAS2

ATRPPAFNKAPGRVVDHVFWLTPGHASEPGT---------WYAGTSP--QGLFRSTDHGASW-EPVAGFNDHPRRAWTGGEPDGPKHSILVD---PRDPKHLYIGSSGGVFESTAGTDWKPLN

2ebsB3

0.14

0.13

0.92

0.83

MUSTER

---TCPPGMNASHYQGSTIAVDASGSQIVWSTKLDEQASGPWYS-HD---GVPAGDLKAQTANVLSDKVQTDGGKSYAAKGAVTGTSLMPAVNPWVAGDVWVPV-PEGGLFHSTD-ASFTRV-

2ebsB3

0.11

0.97

0.78

dPPAS

---TCPPGMNASHYQGSTIAVDASGSQIVWSTKLDEQASGPWYSGKTWSVPAGDLKAQTANVLSDKVQDGTDGGKSYAAKGLVTGTSLMPAVNPWVAGDVWVPVPEGGLFHSTDFGASFTRV-

2ebsB3

0.15

0.14

0.93

0.80

wdPPAS

---TCPPGMNASHYQGSTIAVDASGSQIVWSTKLDEQASGPWYS-HD---GTWSVPAKAQTANVLSDKVQTDGGKSYAAKGAVTGTSLMPAVNPWVAGDVWVPVP-EGGLFHSTDFGAFTRV-

2ebsB3

0.15

0.14

0.91

0.88

wMUSTER

C----PPGMNASHYQGSTIAVDASGSQIVWSTKLDEQASGPWYS-HD---GTWSPAGDLKAANVLSDKVQTDGGKSYAAKGAVTGTSLMPAVNPWVAGDVWVPV-PEGGLFHSTD-ASFTRV-

2ebsB3

0.16

0.15

0.92

0.84

wPPAS

---TCPPGMNASHYQGSTIAVDASGSQIVWSTKLDEQASGPWYS-HD---GTWSPAGDLKAQTVLSDKVQTDGGKSYAAKGAVTGTSLMPAVNPWVAGDVWVPV-PEGGLFHSTD-ASFTRV-

5fzpA1

0.11

0.10

0.92

1.21

dPPAS2

TSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDTPNLLATHND----ELQ---RSTDAGCTWTKVATLGSGSTWLTA--ATGGRAFAWEKNGGYLARVDG-RTVTKLS

5fzpA1

0.11

0.10

0.92

0.90

PPAS

TSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDTPNLLATHND----ELQ---RSTDAGCTWTKVATLGSGSTWLTA---ATGGRAFAWEKNGGYLARVDGRTVTKLS

2bb5A2

0.11

0.09

0.83

0.76

Env-PPAS

-------TIPQTQEIISVTLQVLSLLPPYRQSISVLAGSTVEDVAHELGGFTYETQASLGPYLTSVMGKAAGEREFWQLLRDPNTPLLQGIADYRPKDG--ETI---ELRLVS-----W----

(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=-1.75

Estimated TM-score = 0.50±0.15

Estimated RMSD = 8.1±4.4Å

Download Model 2

C-score=-2.46

Download Model 3

C-score=-4.22

Download Model 4

C-score=-4.60

Download Model 5

C-score=-4.46

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	2ebsB3	0.605	3.63	0.087	0.935
2	2f27B	0.602	3.88	0.083	0.943
3	4lgnA	0.601	3.49	0.060	0.902
4	1xksA	0.600	3.61	0.062	0.919
5	3vi3A	0.598	3.68	0.058	0.919
6	3a71A	0.591	3.96	0.066	0.959
7	2p9wA	0.590	3.98	0.049	0.959
8	2z3wA	0.590	3.82	0.083	0.943
9	3k71G2	0.588	3.87	0.074	0.927
10	4ci8A2	0.587	3.72	0.067	0.911

(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	6	1pm1X	IMD	Rep, Mult	102,104,109,111
2	0.04	2	2o011	CLA	Rep, Mult	70,77
3	0.04	2	2zypA	AYE	Rep, Mult	115,119
4	0.04	2	3zweB	GLA	Rep, Mult	79,82
5	0.04	2	2vdnA	III	Rep, Mult	32,61,62,77
6	0.04	2	4g55A	VH2	Rep, Mult	64,66,78,100,113,115,117,119
7	0.04	2	3fbyA	CA	Rep, Mult	35,37,39,41,42,47
8	0.04	2	3ugfB	UUU	Rep, Mult	54,56,62,63
9	0.02	1	3k6sA	MG	Rep, Mult	92,94,96,113
10	0.02	1	3lo1A	PG0	Rep, Mult	75,111
11	0.02	1	1rtgA	CA	Rep, Mult	20,21,64,91
12	0.02	1	4gnaB	XYL	Rep, Mult	80,81,83,118,119

	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	1y9mA	0.583	3.63	0.017	0.886	3.2.1.80	NA
2	0.060	1gjqA	0.556	4.13	0.060	0.911	1.7.99.1,1.7.2.1	NA
3	0.060	1w18B	0.564	4.13	0.034	0.943	2.4.1.10	NA
4	0.060	2jkbA	0.565	4.08	0.082	0.919	3.2.1.18,4.2.2.15	NA
5	0.060	1madH	0.548	3.64	0.053	0.854	1.4.99.3	21
6	0.060	1eusA	0.585	3.97	0.074	0.935	3.2.1.18	NA
7	0.060	3c75J	0.566	3.65	0.061	0.878	1.4.99.3	44
8	0.060	2agsA	0.565	4.14	0.100	0.911	3.2.1.18	21
9	0.060	1fwxA	0.557	3.82	0.068	0.894	1.7.99.6	102
10	0.060	2xcyA	0.560	4.32	0.075	0.935	3.2.1.18	78
11	0.060	1cvmA	0.567	4.01	0.059	0.894	3.1.3.8	NA
12	0.060	3dr2A	0.566	3.50	0.078	0.846	3.1.1.17	NA
13	0.060	2d5lA	0.588	3.83	0.083	0.943	3.4.14.-	NA
14	0.060	1pjxA	0.556	4.11	0.076	0.902	3.1.8.2	71
15	0.060	1v04A	0.565	3.98	0.061	0.911	3.1.1.2,3.1.8.1	114
16	0.060	3gvjA	0.563	3.89	0.050	0.902	3.2.1.129	70
17	0.060	1sliA	0.565	4.21	0.041	0.935	4.2.2.15,3.2.1.18	NA
18	0.060	2gc7A	0.566	3.64	0.070	0.878	1.4.99.3	44,67
19	0.060	1euuA	0.570	4.28	0.065	0.951	3.2.1.18	22

(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	0.08	0.586	3.72	0.10	0.93	2ebsB	GO:0000272 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033945
1	0.08	0.600	3.61	0.06	0.92	1xksA	GO:0000775 GO:0000776 GO:0000777 GO:0000940 GO:0000972 GO:0005487 GO:0005634 GO:0005635 GO:0005643 GO:0005694 GO:0005829 GO:0006325 GO:0006355 GO:0006406 GO:0006409 GO:0006606 GO:0006810 GO:0006999 GO:0007062 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0021915 GO:0022008 GO:0031047 GO:0031080 GO:0031081 GO:0031965 GO:0048339 GO:0051028 GO:0061053 GO:0075733 GO:1900034
2	0.07	0.601	3.49	0.06	0.90	4lgnA	GO:0004553 GO:0005975 GO:0030246 GO:0030247 GO:0030248
3	0.07	0.564	3.85	0.11	0.88	2cn2A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
4	0.07	0.565	3.80	0.12	0.89	5jwzA	GO:0004553 GO:0005975 GO:0030246 GO:0030247
5	0.07	0.585	3.91	0.14	0.89	5fkqA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0030248
6	0.07	0.565	3.85	0.11	0.88	2cn3A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
7	0.07	0.586	3.65	0.06	0.90	4q6kA	GO:0004308 GO:0009405
8	0.07	0.584	3.81	0.08	0.90	4bbwA	GO:0004308 GO:0005737 GO:0006689 GO:0009313 GO:0009405 GO:0016020 GO:0043231
9	0.07	0.563	4.12	0.08	0.90	2bf6A	GO:0004308 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872 GO:0052794 GO:0052795 GO:0052796
10	0.07	0.537	4.09	0.09	0.88	3b7fA	GO:0016787
11	0.07	0.593	3.91	0.07	0.94	2berA	GO:0004308 GO:0005576 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
12	0.07	0.513	4.16	0.05	0.84	3h71B	GO:0004308 GO:0005576 GO:0005618 GO:0005737 GO:0005975 GO:0006689 GO:0008152 GO:0009313 GO:0016020 GO:0016787 GO:0016798 GO:0043231 GO:0052794 GO:0052795 GO:0052796
13	0.07	0.580	3.83	0.06	0.90	4fj6D	GO:0004308 GO:0009405 GO:0016787
14	0.07	0.524	4.17	0.08	0.89	4m4nA	GO:0004308 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
15	0.07	0.554	4.12	0.07	0.88	2f25A	GO:0004308 GO:0005737 GO:0005829 GO:0005975 GO:0006629 GO:0006687 GO:0006689 GO:0008152 GO:0009313 GO:0010831 GO:0016020 GO:0016042 GO:0016787 GO:0016798 GO:0043231 GO:0045471 GO:0045663 GO:0052794 GO:0052795 GO:0052796
16	0.07	0.569	3.90	0.08	0.89	3b69A	GO:0004308 GO:0009405 GO:0016020 GO:0016021
17	0.06	0.555	4.24	0.06	0.93	5f9tA	GO:0004308 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0052794 GO:0052795 GO:0052796
18	0.06	0.360	4.74	0.06	0.63	2zatA	GO:0000253 GO:0001758 GO:0004090 GO:0005739 GO:0005777 GO:0016491 GO:0042574 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016798
GO-Score	0.37
Biological Processes	GO:0044238	GO:0071704
GO-Score	0.44	0.41
Cellular Component	GO:0000940	GO:0031080	GO:0005829	GO:0031965	GO:0043263
GO-Score	0.08	0.08	0.08	0.08	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.