I-TASSER results

I-TASSER results for job id Rv1980c

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

Input Sequence in FASTA format

>protein (228 residues)
MRIKIFMLVTAVVLLCCSGVATAAPKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYY
PDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNA
GGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNA
GLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRIKIFMLVTAVVLLCCSGVATAAPKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA
Prediction	CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEEEHCCCEEEEEEEEEEHCCCCCCCCEEEEEEEHCCCCEEEEHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEHCCEEEEEHCCCCCCCCCCCCEEEEHCHHHHHHHCC
Conf.Score	975899999999999746666666666544456766775789999578768888757766568999999999999999999756666788668998999999975798899999999876888998758999998899958767885689968999999999999999757776666666788777765798699799997775447766786899985888765569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MRIKIFMLVTAVVLLCCSGVATAAPKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA
Prediction	532210111211211012222434465335625424544324142545524140512342454640452055225402531564555633232324344142334472000000132330000132333200001374444030530146566115302520362047425553522563215454142000365101010432100020433130402164046327
	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

CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEEEHCCCEEEEEEEEEEHCCCCCCCCEEEEEEEHCCCCEEEEHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEHCCEEEEEHCCCCCCCCCCCCEEEEHCHHHHHHHCC
MRIKIFMLVTAVVLLCCSGVATAAPKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

2.81

MUSTER

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

4.13

dPPAS

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

6.53

wdPPAS

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

3.53

wMUSTER

-------------------------KTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

5.76

wPPAS

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

8.08

dPPAS2

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

4.49

PPAS

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

2hhiA

1.00

0.89

5.17

Env-PPAS

------------------------PKTYCEELKGTDTGQACQIQMSDPAYNINISLPSYYPDQKSLENYIAQTRDKFLSAATSSTPREAPYELNITSATYQSAIPPRGTQAVVLKVYQNAGGTHPTTTYKAFDWDQAYRKPITYDTLWQADTDPLPVVFPIVQGELSKQTGQQVSIAPNAGLDPVNYQNFAVTNDGVIFFFNPGELLPEAAGPTQVLVPRSAIDSMLA

3cygA

0.16

0.14

0.84

2.12

MUSTER

---------------------------------LRKVFEIVKSSTENEIVRIHVELPRLKKFNSEVEEKIKKFVNEVKGIAQEDHDKDVQHTPYEAYVSVDVRYEGKDFLSFVVYYYQFTGGAHGITFFETYNIDLKNSKVLKLYDIIK--EEAEDTIKSNILKQIEQNNTDFFPDAPNILKDDIFSREFTISKDGLIIY-PHYDLAPYASGP-EFVIPWNVIEKFLK

3cygA

0.16

0.14

0.84

2.96

dPPAS

---------------------------------LRKVFEIVKSSTENEIVRIHVELPRLKYFNSEVEEKIKKFVNEVKGIAQEDHDKDVQHTPYEAYVSVDVRYEGKDFLSFVVYYYQFTGGAHGITFFETYNIDLKNSKVLKLYDIIK--EEAEDTIKSNILKQIEQNNTDFFPDAPNILKDDIFSREFTISKDGLIIY-PHYDLAPYASGP-EFVIPWNVIEKFLK

(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=-0.19

Estimated TM-score = 0.69±0.12

Estimated RMSD = 6.0±3.7Å

Download Model 2

C-score=-1.34

Download Model 3

C-score=-0.28

Download Model 4

C-score=-1.60

Download Model 5

C-score=-4.58

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	2hhiA	0.855	1.25	1.000	0.895
2	4e72A	0.500	5.01	0.097	0.759
3	3cygA	0.487	5.19	0.139	0.759
4	3s5tA	0.483	5.06	0.120	0.737
5	5jenA	0.472	5.27	0.086	0.728
6	3pjzA	0.454	5.78	0.056	0.776
7	2ebsB	0.449	5.66	0.045	0.737
8	4cvbA	0.432	5.92	0.035	0.737
9	4gbfA	0.432	5.45	0.029	0.706
10	1jp4A	0.431	6.14	0.070	0.772

(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	0.06	3	3kegA	FMN	Rep, Mult	192,197,201
2	0.04	2	3iilA	MG	Rep, Mult	208,209
3	0.04	2	2gufA	MPG	Rep, Mult	13,98,99,100,111,113,131
4	0.04	2	3trzA	NUC	Rep, Mult	201,202
5	0.04	2	3kziL	PL9	Rep, Mult	12,13,15
6	0.04	2	3dwrA	0PA	Rep, Mult	100,102,131,133,196
7	0.02	1	5jvgN	MG	Rep, Mult	60,63
8	0.02	1	3dwrA	0PA	Rep, Mult	96,98,114,115,116,117,128
9	0.02	1	3a0bH	CLA	Rep, Mult	70,78
10	0.02	1	3mxgD	XLS	Rep, Mult	135,148
11	0.02	1	1cgpA	CMP	Rep, Mult	14,18
12	0.02	1	5d51L	KR	Rep, Mult	13,14,112
13	0.02	1	2shkB	MG	Rep, Mult	127,133
14	0.02	1	3dwrB	0PA	Rep, Mult	98,111,112,113,115,129
15	0.02	1	1sqj0	III	Rep, Mult	104,135,219,220,221,222,223
16	0.02	1	1tyeA	UUU	Rep, Mult	112,139,142
17	0.02	1	3fcsC	IMD	Rep, Mult	188,201,202,205,206
18	0.02	1	5a43C	DMU	Rep, Mult	219,221
19	0.02	1	4fe1F	CLA	Rep, Mult	5,9
20	0.02	1	2ppqA	MG	Rep, Mult	115,195

	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	3epsA	0.401	5.87	0.058	0.671	2.7.11.5	NA
2	0.060	2ac1A	0.418	6.21	0.056	0.763	3.2.1.26	NA
3	0.060	1e1yA	0.357	6.32	0.039	0.649	2.4.1.1	NA
4	0.060	1kb0A	0.405	5.81	0.067	0.689	1.1.99.-	62
5	0.060	1tlbA	0.416	6.04	0.058	0.719	1.3.3.3	NA
6	0.060	1jroB	0.399	6.21	0.039	0.715	1.1.1.204	NA
7	0.060	3gpbA	0.373	5.64	0.034	0.610	2.4.1.1	NA
8	0.060	2w68C	0.289	5.78	0.048	0.491	3.2.1.18	107,195
9	0.060	1vncA	0.369	5.93	0.051	0.667	1.11.1.10	NA
10	0.060	1y4wA	0.409	5.31	0.060	0.649	3.2.1.80	NA
11	0.060	1inpA	0.423	5.73	0.056	0.715	3.1.3.57	NA
12	0.060	1gw0A	0.398	6.02	0.036	0.697	1.10.3.2	NA
13	0.060	3etdA	0.397	6.11	0.049	0.719	1.4.1.3	73,93
14	0.060	1iduA	0.423	5.40	0.039	0.671	1.11.1.10	NA
15	0.060	2qllA	0.352	5.59	0.040	0.588	2.4.1.1	NA
16	0.060	1i19A	0.424	5.70	0.046	0.715	1.1.3.6	NA
17	0.060	1jrpB	0.351	6.17	0.048	0.640	1.17.1.4	NA
18	0.060	1d9qB	0.397	5.27	0.040	0.649	3.1.3.11	153
19	0.060	1mo7A	0.255	5.54	0.026	0.404	3.6.3.9	71

(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	0.65	0.855	1.25	1.00	0.89	2hhiA	GO:0005576 GO:0005618 GO:0009267
1	0.07	0.495	5.22	0.15	0.77	3cygA	GO:0016020 GO:0016021
2	0.06	0.454	5.78	0.06	0.78	3pjzA	GO:0005267 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006812 GO:0006813 GO:0008324 GO:0016020 GO:0016021 GO:0022820 GO:0030955 GO:0035826 GO:0035827 GO:0042803 GO:0055085 GO:0071805
3	0.06	0.418	5.83	0.06	0.71	5fkqA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246 GO:0030247 GO:0030248
4	0.06	0.422	5.75	0.07	0.70	4lgnA	GO:0004553 GO:0005975 GO:0030246 GO:0030247 GO:0030248
5	0.06	0.398	5.36	0.06	0.64	3b69A	GO:0004308 GO:0009405 GO:0016020 GO:0016021
6	0.06	0.366	6.08	0.05	0.68	3b7fA	GO:0016787
7	0.06	0.449	5.66	0.04	0.74	2ebsB	GO:0000272 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033945
8	0.06	0.408	5.80	0.07	0.69	5jwzA	GO:0004553 GO:0005975 GO:0030246 GO:0030247
9	0.06	0.414	5.75	0.03	0.70	2cn2A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
10	0.06	0.384	5.34	0.04	0.61	4q6kA	GO:0004308 GO:0009405
11	0.06	0.416	5.87	0.09	0.71	2cn3A	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030245 GO:0033946 GO:0043263 GO:2000899
12	0.06	0.272	6.41	0.04	0.52	4dvjB	GO:0008270 GO:0016491 GO:0055114
13	0.06	0.322	6.06	0.06	0.57	4r6hA	GO:0005215 GO:0005886 GO:0006810 GO:0016020
14	0.06	0.331	6.04	0.03	0.60	4amyA	GO:0004252 GO:0005737 GO:0006508 GO:0008233 GO:0008236 GO:0016787 GO:0070008
15	0.06	0.315	6.53	0.04	0.61	4chiA	GO:0003824 GO:0008152 GO:0008483 GO:0016740
16	0.06	0.311	6.39	0.03	0.58	3pduA	GO:0000166 GO:0004616 GO:0016491 GO:0051287 GO:0055114
17	0.06	0.313	5.58	0.05	0.53	3r2wC	GO:0003983 GO:0005536 GO:0005634 GO:0005737 GO:0005829 GO:0005978 GO:0006011 GO:0006065 GO:0008152 GO:0016740 GO:0016779 GO:0019255 GO:0032557 GO:0042802 GO:0046872 GO:0070062 GO:0070569
18	0.06	0.314	6.23	0.05	0.58	1r6tA	GO:0000166 GO:0001525 GO:0004812 GO:0004830 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0006418 GO:0006436 GO:0008285 GO:0016874 GO:0045765 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0030248	GO:0004553	GO:0035827	GO:0030955	GO:0022820	GO:0005267	GO:0042803
GO-Score	0.12	0.12	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0009267
GO-Score	0.65
Cellular Component	GO:0005618	GO:0005576
GO-Score	0.65	0.65

(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.