I-TASSER results

I-TASSER results for job id Rv2102

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

Input Sequence in FASTA format

>protein (238 residues)
MLEDIGLGNRLQRGRSYARKGQVISLQVDAGLVTALVQGSRARPYRIRIGIPAFGKSQWA
HVERTLAENAWYAAKLLSGEMPEDIEDVFAGLGLSLFPGTARELSLDCSCPDYAVPCKHL
AATFYLLAESFDEDPFAILAWRGREREDLLANLAAARADGAAPAADHAEQVAQPLTDCLD
RYYARQADINVPSPPATPSTALLDQLPDTGLSARGRPLTELLRPAYHALTHHHNSAGG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MLEDIGLGNRLQRGRSYARKGQVISLQVDAGLVTALVQGSRARPYRIRIGIPAFGKSQWAHVERTLAENAWYAAKLLSGEMPEDIEDVFAGLGLSLFPGTARELSLDCSCPDYAVPCKHLAATFYLLAESFDEDPFAILAWRGREREDLLANLAAARADGAAPAADHAEQVAQPLTDCLDRYYARQADINVPSPPATPSTALLDQLPDTGLSARGRPLTELLRPAYHALTHHHNSAGG
Prediction	CCCCCCCCCHHHHHHHHHHCCCEEEEEEHCCEEEEEEHCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
Conf.Score	9876677665589999987798679999899999999789999879999996699999999999999769999999979999799999999899989998555788899999999758999999999999867968999887999999999999955666655677778788887655777656888998889999986568887588988778887999999999999975555789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MLEDIGLGNRLQRGRSYARKGQVISLQVDAGLVTALVQGSRARPYRIRIGIPAFGKSQWAHVERTLAENAWYAAKLLSGEMPEDIEDVFAGLGLSLFPGTARELSLDCSCPDYAVPCKHLAATFYLLAESFDEDPFAILAWRGREREDLLANLAAARADGAAPAADHAEQVAQPLTDCLDRYYARQADINVPSPPATPSTALLDQLPDTGLSARGRPLTELLRPAYHALTHHHNSAGG
Prediction	4034243740062024104633035040563303030344555215030305504672043015202730310030145512640251057261401143364042401021373102000000010042026201000302425254015304735466446546646644443452254124465516334444363420163045241346453025103500541366456668
	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

CCCCCCCCCHHHHHHHHHHCCCEEEEEEHCCEEEEEEHCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCC
MLEDIGLGNRLQRGRSYARKGQVISLQVDAGLVTALVQGSRARPYRIRIGIPAFGKSQWAHVERTLAENAWYAAKLLSGEMPEDIEDVFAGLGLSLFPGTARELSLDCSCPDYAVPCKHLAATFYLLAESFDEDPFAILAWRGREREDLLANLAAARADGAAPAADHAEQVAQPLTDCLDRYYARQADINVPSPPATPSTALLDQLPDTGLSARGRPLTELLRPAYHALTHHHNSAGG

5ikjB

0.12

0.03

0.28

1.50

dPPAS2

-----------------------------------------------------------------------------------------------------------------------------------------------QSKDKIIAALAKRNVYKSFAGLYDSKGNYARVG--------RHGSFILPVSKSVPTPSLLIE-GSI-VQRKNIKIE-------------------

2miiA

0.09

0.03

0.34

1.48

dPPAS2

-------------------------------------------------------------------------------------------------------------------------------------------------------------GSHMVGQREPAPVEEVKPAPEQPAEPQQPVPTVPSVPTIPQQPGPIEHEDQTAPPAPHIRHYD-WNGAMQPMVSKMLGADG

5cwnA

0.16

0.13

0.84

0.62

MUSTER

-MDPEEILERAKESLERARE--------------ASERGDEEE-----------FRKAAEKALELAKRLVEQAKKEGDPELVLEAAKVALRVAELAAKNGDKEVFKK---------AESALEVAKRLVEVASKDPELVLEAA--KVALRVAELAAK--NGDKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKLAKKQGDEEVYEKARETAREVKEELKRVREEKGG

2muxA

0.14

0.08

0.57

0.83

dPPAS

-------------------------------------------------------------------------------------------------------MTVEQNVLQQSAAQKHQQTFLNQLREITGNDTQILQQALKDSNGNLELAVAFLTAKNAKTPQQEETTYYQTALPGNDRYISVGSQADTNVIDLTGDRAIALSLAESNRAFRETGITDEEQAISRVLEASIAENKA

2fbqA1

0.16

0.09

0.54

0.72

wdPPAS

-------------------------------------------------------------AQSETVERILDAAEQLFAE----LRLITSKAGVN------------------------LAAVNYHFG----------------SKKALIQAVFSRFLGPLDRRQAKPEAQHATLEDLLHLLVSQAMAVKPRSG---NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLL-A

2vosA

0.20

0.16

0.81

0.60

wMUSTER

KVEVL-LAESVRADASVAREDSVLRRQIAVGGQVLQLQGLGGVYSDIYLPLHG------EHQAHNAVL-ALASVEAFFGQLDDAVRAGFAAV--TS-PGRLERRSA----PDAA----HNPAGASALAQTLAHRFVGVLS-GDKDVDGILAALEP----------------------VFDSVVV----THNGSPRALDVEALALAAGERFGPDRAENLRDAIDVATSLVDDAAADPDV

2zcxA

0.20

0.16

0.76

0.61

wPPAS

ILD------ELGTERGIRE----ITLT-----IAATV-GHKSALLR-------FEEQIFLKITAEGWKEAELCARLREGAAPDAVGQVFAAT-----------LAAR---PLF---CDLLAQAPLNLER--NVSVESVRSFK-IATLDEVGRIGAELRRLLGVDETQAVDVIATATSLAGALWQ-----------ATPGPHIQTLYSDPRLAHAVVEVEPRLNRVLGALLRGIADG--

2k8fB

0.18

0.03

0.16

1.40

dPPAS2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------MEEPQSDPSVEPPLSETFSDLWKLLPENNVLSPLPSQA---------------------------------------

5cwpA

0.09

0.08

0.87

0.66

PPAS

LIERA--KEAAERAQEAAERTGDPRVRELARELKRLAQKRDPSSSDVNEALKLIAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEEVQRN--PSS----------SDVNEALKLIVEAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEEQRNPSSEEVNEALKKIVKAIQEAVES--------------REAEESGDPE----KREKARERVREAVERAEEVQRDPSG

2dqmA3

0.14

0.08

0.60

0.61

Env-PPAS

------QSGIVTVKDDYNPETEQYTLTIS--QRTPATPDAEKQPLHIPFAIELYD-NEGKVI--PLQKGGHPVNSVL--NVTQA-EQTFVFDNVYFQPVPA--LLCEFSAPEYKWS---DQQLTFLMRHA--RNDFSRWDAAQSLATYIKLNVARHQQGQPLS---------------------------------------------------------------------------

(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=-3.98

Estimated TM-score = 0.29±0.09

Estimated RMSD = 15.4±3.4Å

Download Model 2

C-score=-3.97

Download Model 3

C-score=-4.49

Download Model 4

C-score=-4.95

Download Model 5

C-score=-5.00

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	2zcxA	0.529	3.84	0.087	0.710
2	2gfnB	0.502	3.77	0.055	0.660
3	3lsjA	0.501	3.87	0.074	0.672
4	4g12A	0.497	4.16	0.075	0.664
5	5d18A	0.493	3.92	0.108	0.660
6	2uxuA	0.493	3.95	0.114	0.660
7	3on4A	0.492	3.92	0.085	0.639
8	5fglA	0.491	4.14	0.100	0.672
9	5gp9A	0.489	4.10	0.073	0.655
10	3e7qB	0.488	3.96	0.090	0.660

(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	0.08	4	2uxpA	CLM	Rep, Mult	74,90,149,153,172,175
2	0.08	4	3af8X	PLL	Rep, Mult	132,135,138,142
3	0.08	4	2yiuC	SMA	Rep, Mult	117,119
4	0.06	3	3mhhE	ZN	Rep, Mult	108,110,119
5	0.04	2	1gdtA	NUC	Rep, Mult	146,149,150,157
6	0.04	2	1hw7A	ZN	Rep, Mult	108,110
7	0.04	2	2uxiB	G50	Rep, Mult	66,121,142,146,176
8	0.02	1	1smyF	MG	Rep, Mult	66,123,124
9	0.02	1	1mheC	III	Rep, Mult	37,116,119
10	0.02	1	4ismA	ZN	Rep, Mult	132,135
11	0.02	1	3btjB	DEQ	Rep, Mult	78,81,156,157
12	0.02	1	3adcA	MG	Rep, Mult	57,112

	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	2pywA	0.459	5.10	0.065	0.702	2.7.1.100	NA
2	0.060	1eveA	0.426	5.77	0.041	0.714	3.1.1.7	NA
3	0.060	2fhbA	0.432	5.06	0.086	0.668	3.2.1.41	NA
4	0.060	1jqoA	0.417	5.57	0.056	0.676	4.1.1.31	144
5	0.060	3ffzA	0.428	5.45	0.061	0.693	3.4.24.69	NA
6	0.060	1n63B	0.418	6.29	0.023	0.744	1.2.99.2	NA
7	0.060	2qnoA	0.427	6.16	0.049	0.731	3.2.1.4	NA
8	0.060	2qllA	0.408	5.84	0.053	0.710	2.4.1.1	NA
9	0.060	1aknA	0.434	5.82	0.057	0.731	3.1.1.13,3.1.1.3	NA
10	0.060	2pm8A	0.422	5.77	0.063	0.706	3.1.1.8	NA
11	0.060	1l2aE	0.427	6.22	0.049	0.735	3.2.1.4	NA
12	0.060	2fhcA	0.431	4.97	0.091	0.660	3.2.1.41	NA
13	0.060	1bf2A	0.424	6.10	0.045	0.735	3.2.1.68	19
14	0.060	2tmdA	0.415	5.28	0.070	0.660	1.5.8.2	139,145
15	0.060	1qo9A	0.421	5.76	0.036	0.706	3.1.1.7	NA
16	0.060	1mx9D	0.430	5.84	0.021	0.731	3.1.1.1	NA
17	0.060	3eqoA	0.421	5.08	0.055	0.664	3.2.1.58	NA
18	0.060	3gpbA	0.444	5.69	0.078	0.731	2.4.1.1	NA
19	0.060	1occA	0.428	5.42	0.023	0.664	1.9.3.1	72

(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	0.13	0.468	4.02	0.11	0.64	3angC	GO:0003677 GO:0006351 GO:0006355
1	0.10	0.489	4.24	0.10	0.66	2uxhA	GO:0003677 GO:0006351 GO:0006355
2	0.07	0.529	3.84	0.09	0.71	2zcxA	GO:0003677 GO:0006351 GO:0006355
3	0.07	0.491	4.07	0.08	0.66	4ichA	GO:0003677 GO:0006351 GO:0006355
4	0.07	0.497	4.03	0.10	0.67	3dpjA	GO:0003677 GO:0006351 GO:0006355
5	0.07	0.501	3.87	0.07	0.67	3lsjA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045922
6	0.07	0.496	4.12	0.05	0.66	3f0cA	GO:0003677 GO:0006351 GO:0006355
7	0.07	0.480	3.92	0.10	0.63	2g7sA	GO:0003677 GO:0006351 GO:0006355
8	0.07	0.469	3.96	0.09	0.64	2nx4A	GO:0003677 GO:0006351 GO:0006355
9	0.07	0.493	3.92	0.11	0.66	5d18A	GO:0003677 GO:0006351 GO:0006355
10	0.07	0.472	3.90	0.09	0.63	5f1jA	GO:0003677 GO:0006351 GO:0006355
11	0.07	0.473	4.18	0.04	0.65	3bjbB	GO:0003677 GO:0006351 GO:0006355
12	0.07	0.471	4.09	0.08	0.64	2hyjA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
13	0.07	0.463	4.15	0.07	0.64	2f07A	GO:0003677 GO:0006351 GO:0006355
14	0.07	0.480	3.97	0.09	0.64	4gclB	GO:0003677 GO:0005737 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
15	0.07	0.474	4.26	0.08	0.66	2g3bA	GO:0003677 GO:0006351 GO:0006355
16	0.07	0.480	4.29	0.07	0.68	2id6A	GO:0003677 GO:0006351 GO:0006355
17	0.07	0.486	3.52	0.09	0.63	3whcA	GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
18	0.07	0.489	4.37	0.09	0.67	4l62A	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.36
Biological Processes	GO:0006355
GO-Score	0.36
Cellular Component
GO-Score

(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.