I-TASSER results

I-TASSER results for job id Rv0348

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

Input Sequence in FASTA format

>protein (217 residues)
MTISFSSSNLRDDATSGNGDYRLDKLPETTPSTSVFDRADVTYRQFTELHGQARDTRREA
HVVELESKTGERARCAPMHALEQLADYGFAWRDIARVVGVSVPAITKWRKGAGVTGENRL
KIARLLALIDMLSDRFIGEPASWLEMPIQAGVGITRMDLLERGRYDLVLALASTHTGDGT
VEYVLNETDKDWRETVVDNAFESYTAEDGVISIRPKR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTISFSSSNLRDDATSGNGDYRLDKLPETTPSTSVFDRADVTYRQFTELHGQARDTRREAHVVELESKTGERARCAPMHALEQLADYGFAWRDIARVVGVSVPAITKWRKGAGVTGENRLKIARLLALIDMLSDRFIGEPASWLEMPIQAGVGITRMDLLERGRYDLVLALASTHTGDGTVEYVLNETDKDWRETVVDNAFESYTAEDGVISIRPKR
Prediction	CCHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHCCCHHHHHHHCCCCCCCCCEEHCCCCCHHHHHHHHCCCCEEEHCCCCEEEEEHCC
Conf.Score	9655676556666667888654457888899875455545444678899999999999999999999999986555899999999988868899999887589888887677899856999999999999877658764556665456789987557667778855777775466778874344346894666655357875787578667776679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MTISFSSSNLRDDATSGNGDYRLDKLPETTPSTSVFDRADVTYRQFTELHGQARDTRREAHVVELESKTGERARCAPMHALEQLADYGFAWRDIARVVGVSVPAITKWRKGAGVTGENRLKIARLLALIDMLSDRFIGEPASWLEMPIQAGVGITRMDLLERGRYDLVLALASTHTGDGTVEYVLNETDKDWRETVVDNAFESYTAEDGVISIRPKR
Prediction	6424244541455244453514355147443443324424233432441354155245443424045315643643235104301532121430041151324104414525724574343034013004204753274324204231466240322101243434101210334456140531154245513443365314313455234314468
	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

CCHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHCCCHHHHHHHCCCCCCCCCEEHCCCCCHHHHHHHHCCCCEEEHCCCCEEEEEHCC
MTISFSSSNLRDDATSGNGDYRLDKLPETTPSTSVFDRADVTYRQFTELHGQARDTRREAHVVELESKTGERARCAPMHALEQLADYGFAWRDIARVVGVSVPAITKWRKGAGVTGENRLKIARLLALIDMLSDRFIGEPASWLEMPIQAGVGITRMDLLERGRYDLVLALASTHTGDGTVEYVLNETDKDWRETVVDNAFESYTAEDGVISIRPKR

3bk7A

0.13

0.98

0.79

MUSTER

PIVK-DGMVVGIVGPNGTGKTTAGQLIPNLCEDNDSWDNVIRAFRGNELQNYFERLKNEIRPVVKPQYVDLLPKAVVRELLKKVDEVG-KFEEVVKELELE-NVLD--RELHQLSGGELQRVAIAAALLRKAHFYFFDEPSSYLDIRQRLKVARVIRRLANEGKDLAVLDYLSDVIGEPGVYGIFSKPKNEFLQGYLKDENVRFRPYEIRFTKLSER

4ogcA1

0.13

0.12

0.88

0.60

dPPAS

----------------GSAVSRVAPDPLPGQGSFRRAPKCDPEFQRFRIISIVANLRISETKGENRPLTADERRH-VVTFLTEDSQADLTWVDVAEKLGVHRRDLRGTRSAARPPIDATDRIRQKISSLKTWWEEADSEQRGAIRYLYEDPTDSECAEIIAELPEEDQAKLDSLHLPAGRAAYSRESLTALSDHLAT---------TDDLHEARKRL

3kxaA

0.12

0.07

0.57

0.58

wdPPAS

--IPVTHKCLRINGQI----KCVKPISPNT----------------TPAAEHIEHVRKNPRRKAADRAAARIADKIALKAFVSLRKKGFTQSELATAAGLPQPYLSRIENSK--QSLQDKTVQKLANALG-----------------------VSPLEVRAAFERRYEYE-----------------------------------------------

4fwiB

0.13

0.12

0.95

0.88

wMUSTER

IKISLDNSVTAIVGESASGKSKT--LPPNLSGRVLYKGKDLLTMR----EEELRKIRKEIALVPQAAQQSLNPTMKVIEHFKDTVEA--LIEKASEKLRVRLNPEAVLNYPLQLSGGMKQRVLIALALLLDPVVLILDEPTSALDVLTQAHIIQLLKELKKMLADKVAVIYGGNLVEYNSTFQIFKNPLHPYTRGLINSIPSLLNPPSGCR--RCEY

3kxaA

0.15

0.08

0.56

0.61

wPPAS

--IPVTHKCLR------NGQIKCVKISPNT----------------TPAAEHIEHVRKNPRRKAADRAAARIADKIALKAFVSLRKKGFTQSELATAAGLPQPYLSRIENSK-QSL-QDKTVQKLANALG-----------------------VSPLEVRAAFERRYEYE-----------------------------------------------

3kxaA

0.12

0.07

0.59

0.74

dPPAS2

----IPVTHIKCLRING----QIKCVKPISPNTT---------PAAEHIEHVRKNPRRKAADRAAARIADKIALKAGGETFVSLRKKGFTQSELATAAGLPQPYLSRIENSKQSLQ--DKTVQKLANALGVSPLEVRAAFERRYEYE----------------------------------------------------------------------

4ogcA1

0.16

0.13

0.86

0.70

PPAS

---GSAVSRVAPDPLPGQGSFRR------APKCDPEFQ---RFRIISIVANRISETKGENRPLT------ADERRHVVTFLTEDSQADLTWVDVAEKLGVHRRDLRGTRSAARPPIDATDRIRQ-ISSLKTWWEEADSEQRGAIRYLYEDPTDSECAEIIAELPEEDQAKLDSLHLPAGRAAYSRESLTALSDHLATTDDHEA----------R-KR

3kxaA

0.16

0.09

0.59

0.86

Env-PPAS

IPVTHIKC-LRI-----NGQIKCVK--PISPNTT---------PAAEHIEHVRKNPRRKAADRAAARIADKIALKAGGETFVSLRKKGFTQSELATAAGLPQPYLSRIENSK-QSL-QDKTVQKLANALGVSPLEVRAAFERRYEYE----------------------------------------------------------------------

3j16B

0.13

0.12

0.98

0.78

MUSTER

PTPR-PGQVLGLVGTNGIGKSTLAGKQKPNLGRFDDPPEWIKYFRGSELQNYFTKMLEDIKAIIKPQYVDNIPRAIPVQKVGELLKLRMSPEDVKRYIKLQLENVLK-RDIEKLSGGELQRFAIGMSCVQEADVYMFDEPSSYLDVKQRLNAAQIIRSLLAPTSDFVCIIYGVPSVY--GVVTLPASVREGINIFLDPAENLRFRTEALQFRIADAT

3kxaA

0.13

0.08

0.59

0.56

dPPAS

----IPVTHIKCLRINGQIKCVKPISPNTT-------------PAAEHIEHVRKNPRRKAADRAAARIADKIALKAGGETFVSLRKKGFTQSELATAAGLPQPYLSRIENSKQSLQ--DKTVQKLANALGVSPLEVRAAFERRYEYE----------------------------------------------------------------------

(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=-2.93

Estimated TM-score = 0.38±0.13

Estimated RMSD = 12.4±4.3Å

Download Model 2

C-score=-4.03

Download Model 3

C-score=-4.76

Download Model 4

C-score=-4.73

Download Model 5

C-score=-4.86

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	3bk7A	0.674	4.17	0.102	0.940
2	3j16B	0.668	4.44	0.086	0.963
3	3ozxA1	0.666	4.28	0.069	0.931
4	5b57C	0.642	4.10	0.087	0.899
5	3fvqB	0.638	4.24	0.102	0.903
6	2qi9C	0.635	4.15	0.078	0.880
7	4ry2A	0.630	4.35	0.118	0.894
8	5d3mB	0.629	4.43	0.107	0.899
9	2awnB	0.628	4.46	0.106	0.903
10	3qf4A	0.624	4.41	0.082	0.894

(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	0.10	5	1q12B	ATP	Rep, Mult	27,50,51,52,53
2	0.04	2	5a08B	CA	Rep, Mult	158,161
3	0.04	2	4eneA	DMU	Rep, Mult	122,126
4	0.04	2	1g292	MG	Rep, Mult	20,139
5	0.04	2	4pjol	MG	Rep, Mult	117,118,121
6	0.04	2	2j62A	GSZ	Rep, Mult	159,167
7	0.02	1	2z72A	ZN	Rep, Mult	40,50,86
8	0.02	1	3et2A	1BO	Rep, Mult	69,123
9	0.02	1	1mfuA	UUU	Rep, Mult	68,91
10	0.02	1	1ya8B	SMB	Rep, Mult	73,119
11	0.02	1	4ewlB	GOL	Rep, Mult	142,178,217
12	0.02	1	3opxA	MG	Rep, Mult	40,208
13	0.02	1	1rkuB	MG	Rep, Mult	88,208
14	0.02	1	3cmaC	MG	Rep, Mult	110,111
15	0.02	1	1w1iF	BMA	Rep, Mult	162,163
16	0.02	1	4wxlA	BB2	Rep, Mult	22,120
17	0.02	1	1uvhA	FE	Rep, Mult	55,59

	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	0.067	2qi9D	0.635	4.12	0.078	0.880	3.6.3.33	139,144,168
2	0.060	1g72A	0.452	5.55	0.114	0.779	1.1.99.8	NA
3	0.060	1kv9A	0.471	5.74	0.073	0.816	1.1.99.-	178
4	0.060	3g61A	0.606	4.51	0.103	0.885	3.6.3.44	NA
5	0.060	2eqdA	0.453	5.60	0.053	0.779	3.2.1.151	NA
6	0.060	3ivtB	0.452	5.63	0.069	0.765	2.3.3.14	NA
7	0.060	2e1qA	0.449	5.37	0.041	0.714	1.17.3.2,1.17.1.4	NA
8	0.060	1iwpA	0.449	5.41	0.065	0.751	4.2.1.30	NA
9	0.060	1kb0A	0.468	5.60	0.085	0.811	1.1.99.-	178
10	0.060	1p49A	0.471	5.07	0.085	0.742	3.1.6.2	24
11	0.060	1iq8A	0.447	5.63	0.048	0.747	2.4.2.29	13
12	0.060	3a9iA	0.455	5.73	0.045	0.779	2.3.3.14	NA
13	0.060	3aboA	0.456	4.98	0.044	0.710	4.3.1.7	NA
14	0.060	1r0zC	0.601	4.19	0.074	0.843	3.6.3.49	17,19,26,67
15	0.060	1vjpA	0.449	5.28	0.041	0.710	5.5.1.4	140
16	0.060	3gd7A	0.575	5.01	0.097	0.889	3.6.3.49,3.6.3.19	62,139,171
17	0.060	2awnA	0.478	4.68	0.105	0.728	3.6.3.19	132
18	0.060	1dioA	0.445	5.40	0.049	0.737	4.2.1.28	NA
19	0.060	3bliA	0.470	5.86	0.056	0.825	2.3.3.13	NA
20	0.060	1fsuA	0.476	4.87	0.059	0.733	3.1.6.12	65

(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	0.11	0.674	4.17	0.10	0.94	3bk7A	GO:0000166 GO:0005524 GO:0016887 GO:0046872 GO:0051536 GO:0051539
1	0.11	0.668	4.43	0.08	0.96	4crmP	GO:0000054 GO:0000166 GO:0003743 GO:0005506 GO:0005524 GO:0005634 GO:0005737 GO:0005852 GO:0006364 GO:0006412 GO:0006413 GO:0006415 GO:0006810 GO:0016887 GO:0022626 GO:0032790 GO:0042254 GO:0042273 GO:0043024 GO:0045727
2	0.09	0.663	4.35	0.08	0.94	3ozxB	GO:0000054 GO:0000166 GO:0005506 GO:0005524 GO:0005623 GO:0005852 GO:0006413 GO:0006415 GO:0016887 GO:0043024
3	0.09	0.632	4.27	0.08	0.88	4yerA	GO:0000166 GO:0005524 GO:0016887 GO:0043215 GO:1900753
4	0.08	0.643	4.62	0.08	0.95	3jagjj	GO:0000166 GO:0005524 GO:0005737 GO:0005739 GO:0016020 GO:0016887
5	0.08	0.630	4.35	0.12	0.89	4ry2A	GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
6	0.08	0.626	4.41	0.08	0.89	4q4aA	GO:0000166 GO:0005524 GO:0006810 GO:0006869 GO:0016020 GO:0016021 GO:0016887 GO:0034040 GO:0042626 GO:0046872 GO:0055085
7	0.08	0.644	4.15	0.08	0.89	4dblC	GO:0000166 GO:0005524 GO:0005829 GO:0005886 GO:0006810 GO:0015420 GO:0015889 GO:0016020 GO:0016787 GO:0016887 GO:0019898 GO:0031234 GO:0035461 GO:0043190
8	0.08	0.617	4.43	0.10	0.89	5d3mA	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016787 GO:0016887 GO:0043190
9	0.08	0.620	4.36	0.10	0.91	4fwiB	GO:0000166 GO:0005524 GO:0006810 GO:0015833 GO:0016887 GO:0046872 GO:0051536 GO:0051539
10	0.07	0.620	4.26	0.08	0.87	4p33A	GO:0000166 GO:0005524 GO:0005737 GO:0005886 GO:0006810 GO:0015437 GO:0015920 GO:0016020 GO:0016787 GO:0016887 GO:0032403 GO:0043190 GO:0055085
11	0.07	0.624	4.52	0.09	0.90	5jszB	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016787 GO:0016887 GO:0043190
12	0.07	0.606	4.57	0.11	0.88	4mycA	GO:0000166 GO:0005524 GO:0005739 GO:0005743 GO:0006810 GO:0006811 GO:0006879 GO:0016020 GO:0016021 GO:0016887 GO:0022857 GO:0042626 GO:0044281 GO:0055072 GO:0055085
13	0.07	0.608	4.46	0.08	0.89	2yz2A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0016020 GO:0016787 GO:0016887 GO:0032217 GO:0032218
14	0.07	0.628	4.46	0.11	0.90	2awnB	GO:0000166 GO:0005215 GO:0005524 GO:0005886 GO:0006810 GO:0008643 GO:0015423 GO:0015609 GO:0015768 GO:0016020 GO:0016787 GO:0016820 GO:0016887 GO:0031234 GO:0033613 GO:0042956 GO:0043190 GO:0055085 GO:1990060
15	0.07	0.609	4.01	0.08	0.85	2nq2C	GO:0000166 GO:0005524 GO:0006810 GO:0016887
16	0.07	0.638	4.24	0.10	0.90	3fvqB	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0015408 GO:0015682 GO:0016020 GO:0016787 GO:0016887 GO:0043190 GO:0055072
17	0.07	0.609	4.56	0.10	0.89	1ji0A	GO:0000166 GO:0005524 GO:0015658 GO:0015803 GO:0016887
18	0.07	0.620	4.24	0.11	0.87	3d31A	GO:0000166 GO:0005524 GO:0016887

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0016887	GO:0043021	GO:0046914
GO-Score	0.40	0.40	0.38	0.38
Biological Processes	GO:0043624	GO:0006412	GO:0042254	GO:0033753	GO:0071428
GO-Score	0.38	0.38	0.38	0.38	0.38
Cellular Component	GO:0043234	GO:0044444
GO-Score	0.38	0.38

(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.