I-TASSER results

I-TASSER results for job id Rv3013

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

Input Sequence in FASTA format

>protein (218 residues)
MRSYLLRIELADRPGSLGSLAVALGSVGADILSLDVVERGNGYAIDDLVVELPPGAMPDT
LITAAEALNGVRVDSVRPHTGLLEAHRELELLDHVAAAEGATARLQVLVNEAPRVLRVSW
CTVLRSSGGELHRLAGSPGAPETRANSAPWLPIERAAALDGGADWVPQAWRDMDTTMVAA
PLGDTHTAVVLGRPGPEFRPSEVARLGYLAGIVATMLR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MRSYLLRIELADRPGSLGSLAVALGSVGADILSLDVVERGNGYAIDDLVVELPPGAMPDTLITAAEALNGVRVDSVRPHTGLLEAHRELELLDHVAAAEGATARLQVLVNEAPRVLRVSWCTVLRSSGGELHRLAGSPGAPETRANSAPWLPIERAAALDGGADWVPQAWRDMDTTMVAAPLGDTHTAVVLGRPGPEFRPSEVARLGYLAGIVATMLR
Prediction	CCEEEEEEEHCCCCCHHHHHHHHHHHHCCEEEEEEEEEHCCCEEEEEEEEHCCCCCHHHHHHHHHHHCCCEEEEEEHCCCCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHCCCEEEEEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCHHHHCCCEEEEEHCCCCCEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHC
Conf.Score	98599999978999859999999999799578999999769989999999969987589999999989997999997677655677747886446788875899999999856545655688876699977999757766678888777666766655688878787556555758999977999889999679987559999999999999999979
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MRSYLLRIELADRPGSLGSLAVALGSVGADILSLDVVERGNGYAIDDLVVELPPGAMPDTLITAAEALNGVRVDSVRPHTGLLEAHRELELLDHVAAAEGATARLQVLVNEAPRVLRVSWCTVLRSSGGELHRLAGSPGAPETRANSAPWLPIERAAALDGGADWVPQAWRDMDTTMVAAPLGDTHTAVVLGRPGPEFRPSEVARLGYLAGIVATMLR
Prediction	63000000203543231140031016141302101003346520000000203577214301510661560403402320221434240403541444544431133025302210203001002557542330343512233636414223164044155755212630442402000011445300000013216224201410230020122137
	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

CCEEEEEEEHCCCCCHHHHHHHHHHHHCCEEEEEEEEEHCCCEEEEEEEEHCCCCCHHHHHHHHHHHCCCEEEEEEHCCCCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHCCCEEEEEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCHHHHCCCEEEEEHCCCCCEEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHC
MRSYLLRIELADRPGSLGSLAVALGSVGADILSLDVVERGNGYAIDDLVVELPPGAMPDTLITAAEALNGVRVDSVRPHTGLLEAHRELELLDHVAAAEGATARLQVLVNEAPRVLRVSWCTVLRSSGGELHRLAGSPGAPETRANSAPWLPIERAAALDGGADWVPQAWRDMDTTMVAAPLGDTHTAVVLGRPGPEFRPSEVARLGYLAGIVATMLR

2nyiA

0.16

0.12

0.77

1.03

dPPAS

TQSFVVSVAGSDRVGIVHDFSWALKNISANVESSRACLGG---DFAIVLVSLNAKDGKLIQSALESALPGFQISTRRASSVVSPDTREYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLPAPFAGFTLFRGSRVAFPFPLYQEVVTALSR-------------VEEEFGVDIDLEEVV-----------------------------------

2ko1A

0.15

0.06

0.39

2.49

dPPAS2

MTDFLAGIRIVDKNGMTNQITGVISKFDTNIRTIVLNAK-DGIFTCNLMIFVKNTDKLTTLMDKLRKVQGFTVERLSNLEHHHHHH------------------------------------------------------------------------------------------------------------------------------------

1y7pB1

0.15

0.05

0.34

2.14

dPPAS2

HMLRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGKALIYFEIEGGD---FEKILERVKTFDY--IIEIEEE-------------------------------------------------------------------------------------------------------------------------------------------

3hcyA

0.11

0.06

0.56

2.03

dPPAS2

-------------------------------------------------------------------------------------------------SNAIEEVYEATLDAIQGALNCDRASILLFDEAGTMRFVAARGLSRAVDGHSPWINEPEPIFVENAEFSLKESIVGEGAALGFFPLVTEGGKFMTYYDRPRFADSEIGMALTIARQLGFSIQ

2vzwB

0.14

0.08

0.55

1.90

dPPAS2

--------------------------------------------------------------------------------------------------GKLDATLRAIVHTAAELVDARYGALGVRGYDHRLVEFVYEGIDEETRHLIGSLPEGRPIRLDRHPASVGFPLHHPPMRFLGVPVRIRDLYLTEKADGQPFSDDDEVLVQALAAAAGIAVD

1u8sB

0.12

0.04

0.36

1.87

dPPAS2

AYTVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTISKNQFHIAISARVDSGCNLMQLQEEFDALCDGSLNFIKN--------------------------------------------------------------------------------------------------------------------------------------------

4e9jA

0.14

0.12

0.89

0.67

MUSTER

VPA--WTINLKDAD--IREFIDQISEI----ETFVVDPRVKGQVSVVSKAQLSL-SEVYQLFLSVMSTHGFTVVAQGDQARIVPNAAPDRLETRVVQQSPVSELIPLIRPLVPGHLAAV-ALIISDRSANIARIED-RQLDQKGSHDYSVINLRYGEVLNNSRGQAKGA---AGAQVIADA--RTNRLIILGP------PQARAKLVQLAQSLDT---

2ko1A

0.14

0.06

0.39

1.00

dPPAS

DFLAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAK-DGIFTCNLMIFVKNTDKLTTLMDKLRKVQGVFTVERLSNLEHHHHHH-----------------------------------------------------------------------------------------------------------------------------------

2ko1A

0.15

0.06

0.39

1.01

wdPPAS

MTDFLAGIRI-DKNGMTNQITGVISKFDTNIRTIVLNAK-DGIFTCNLMIFVKNTDKLTTLMDKLRKVQGFTVERLSNLEHHHHHH------------------------------------------------------------------------------------------------------------------------------------

2zdsB

0.15

0.13

0.88

0.63

wMUSTER

RNFTLFTGQWADLP--LEEVCRLARDFGYD--GLELACWGDHFEVDKA---LADPSYVDSRHQLLDKY-GLKCWAISNHVGQAVCDAIIDLPARIWGDGDAEGVRQRAAAEIKDTARA--AARL-----GVDTVIGFTGSAIWHLVAFP-----------PAPESIERGYQDFADRWILDVFDAEGVRFAHEHPSEIYDYWTTHRALEAVG-PSHFVW

(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=-3.67

Estimated TM-score = 0.31±0.10

Estimated RMSD = 14.3±3.8Å

Download Model 2

C-score=-3.99

Download Model 3

C-score=-3.89

Download Model 4

C-score=-4.28

Download Model 5

C-score=-4.39

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	3p96A	0.529	4.45	0.112	0.739
2	1u8sB	0.521	4.21	0.099	0.729
3	2nyiA	0.516	4.19	0.159	0.716
4	4k0eA	0.505	4.56	0.052	0.720
5	3k07A	0.497	5.87	0.075	0.867
6	4mt1A	0.496	5.08	0.050	0.766
7	2j8sA2	0.494	5.89	0.049	0.872
8	1tt9A	0.492	5.24	0.073	0.784
9	4r86A	0.490	4.47	0.031	0.697
10	2bmbA	0.472	4.97	0.086	0.693

(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	6	4dh9F	NUC	Rep, Mult	2,4,58,59,63,66,73,75,76,77,78
2	0.10	6	3l76B	THR	Rep, Mult	12,13,14,15,16,17,36,44
3	0.03	2	3l76A	LYS	Rep, Mult	17,19,20,21,35,36
4	0.03	2	1fa0A	MN	Rep, Mult	30,47
5	0.03	2	1t9wA	NFN	Rep, Mult	3,5,79,114,116,119
6	0.02	1	1y7pA	RIP	Rep, Mult	48,49,64
7	0.02	1	1y7pA	RIP	Rep, Mult	9,46,48,72
8	0.02	1	2eulD	ZN	Rep, Mult	202,205
9	0.02	1	1uf3A	CA	Rep, Mult	28,30
10	0.02	1	2raqA	CA	Rep, Mult	7,75
11	0.02	1	2f1f0	III	Rep, Mult	14,17,18,21,25,32,33,34,35,36,37,38,45,117,159,160,162
12	0.02	1	3j5fF	NUC	Rep, Mult	2,4,54,76,77,78
13	0.02	1	1u8s0	III	Rep, Mult	5,7,8,9,17,18,21,22,25,30,31,32,33,34,35,36,38,40,42,47,49,72,73,74,76,78,79,82,105,109
14	0.02	1	2p9gA	SER	Rep, Mult	30,31
15	0.02	1	4ey2B	ZN	Rep, Mult	111,164
16	0.02	1	3wc0A	GTP	Rep, Mult	5,77
17	0.02	1	1g42A	CP2	Rep, Mult	42,47
18	0.02	1	3kssA	CU1	Rep, Mult	91,134,136

	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	1yuyA	0.466	4.74	0.130	0.697	2.7.7.48	75
2	0.060	1n1eA	0.446	5.09	0.082	0.697	1.1.1.8	NA
3	0.060	2boaA	0.425	5.27	0.079	0.670	3.4.17.-	NA
4	0.060	1tehA	0.427	5.55	0.053	0.716	1.1.1.284,1.1.1.1	NA
5	0.060	1ea9C	0.433	5.67	0.058	0.729	3.2.1.54	184
6	0.060	2f1fA	0.442	4.09	0.107	0.583	2.2.1.6	36,72,117,118
7	0.060	2pc6A	0.431	3.87	0.125	0.564	4.1.3.18	34,36,118
8	0.060	1p0cA	0.429	5.55	0.073	0.720	1.1.1.2	16,19
9	0.060	1diiA	0.425	5.66	0.038	0.711	1.17.99.1	NA
10	0.060	1w6sC	0.423	5.99	0.066	0.771	1.1.99.8	NA
11	0.060	1qleA	0.435	5.69	0.071	0.729	1.9.3.1	193
12	0.060	1fftA	0.430	5.58	0.078	0.725	1.10.3.-	NA
13	0.060	1g72A	0.431	5.93	0.037	0.757	1.1.99.8	NA
14	0.060	1p0fA	0.430	5.56	0.083	0.725	1.1.1.2	NA
15	0.060	3k96A	0.436	5.17	0.076	0.683	1.1.1.94	18
16	0.060	1occA	0.441	5.75	0.062	0.743	1.9.3.1	NA
17	0.060	1qd1B	0.545	4.67	0.104	0.784	2.1.2.5,4.3.1.4	NA
18	0.060	1z82A	0.425	5.15	0.043	0.665	1.1.1.8	NA
19	0.060	2d0vA	0.439	5.93	0.051	0.784	1.1.99.8	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	0.25	0.527	4.17	0.16	0.73	2nyiA	GO:0008152 GO:0016597
1	0.14	0.521	4.21	0.10	0.73	1u8sB	GO:0006355
2	0.07	0.530	4.52	0.12	0.74	5it0A	GO:0000287 GO:0004647 GO:0006564 GO:0008152 GO:0008652 GO:0016311 GO:0016597 GO:0016787 GO:0016791 GO:0046872
3	0.06	0.309	5.94	0.06	0.56	3n28A	GO:0000287 GO:0004647 GO:0005737 GO:0006545 GO:0006564 GO:0008152 GO:0008652 GO:0016311 GO:0016787 GO:0016791 GO:0046872
4	0.06	0.313	6.09	0.02	0.55	1nrwA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
5	0.06	0.314	5.73	0.04	0.54	4lcjA	GO:0000122 GO:0003682 GO:0003713 GO:0003714 GO:0005634 GO:0006351 GO:0006355 GO:0008152 GO:0008285 GO:0016032 GO:0016491 GO:0016616 GO:0017053 GO:0019079 GO:0030054 GO:0030154 GO:0035563 GO:0042803 GO:0042974 GO:0045202 GO:0045892 GO:0045944 GO:0048386 GO:0050872 GO:0051287 GO:0055114 GO:0097470
6	0.06	0.292	6.56	0.07	0.57	4ezeA	GO:0004647 GO:0006564 GO:0008152 GO:0016311 GO:0016787 GO:0016791
7	0.06	0.319	2.51	0.11	0.37	1zpvC	GO:0008152 GO:0016597
8	0.06	0.287	6.02	0.05	0.52	3ga0A	GO:0000122 GO:0003714 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0008152 GO:0016491 GO:0016616 GO:0016746 GO:0017053 GO:0030154 GO:0042803 GO:0045892 GO:0050872 GO:0051287 GO:0055114 GO:0061025
9	0.06	0.284	5.66	0.06	0.48	3dnpA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283
10	0.06	0.283	6.45	0.05	0.55	4zevA	GO:0005737 GO:0010323 GO:0016311 GO:0016787 GO:0044283 GO:0046872 GO:0050308
11	0.06	0.296	6.14	0.05	0.54	3fzqA	GO:0016787
12	0.06	0.279	6.24	0.07	0.53	2rarA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
13	0.06	0.275	6.82	0.03	0.56	1rkqA	GO:0000287 GO:0005829 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872 GO:0050308
14	0.06	0.277	6.76	0.05	0.56	3l7yA	GO:0016787 GO:0046872
15	0.06	0.265	6.36	0.08	0.49	3pgvA	GO:0016787 GO:0046872
16	0.06	0.244	6.19	0.04	0.46	1nf2A	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
17	0.06	0.261	6.59	0.06	0.51	2qyhB	GO:0016787
18	0.06	0.251	5.40	0.04	0.42	3e81A	GO:0005829 GO:0008781 GO:0016311 GO:0016740 GO:0016779 GO:0016787 GO:0019143 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0031406	GO:0043169	GO:0042578
GO-Score	0.59	0.36	0.36
Biological Processes	GO:0006796
GO-Score	0.36
Cellular Component	GO:0005737
GO-Score	0.12

(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.