I-TASSER results

I-TASSER results for job id Rv3527

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

Input Sequence in FASTA format

>protein (149 residues)
MPDDQPAVPDVDRLARSMLLLHGDHHDHNDSPEQHRTCGSWSKSRDFADDPQRAAAVREA
SRAERDRYLTSGLQPVDCRFCHVTVTVKRLGPGHTAVQWNTEASRRCAYFTELRARGGDS
ARTRSCPRLTDSIEHAVAEGYLEHHDPNR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPDDQPAVPDVDRLARSMLLLHGDHHDHNDSPEQHRTCGSWSKSRDFADDPQRAAAVREASRAERDRYLTSGLQPVDCRFCHVTVTVKRLGPGHTAVQWNTEASRRCAYFTELRARGGDSARTRSCPRLTDSIEHAVAEGYLEHHDPNR
Prediction	CCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCEEEEEHCCCCCCEEHCCHHHHHHCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	98767888849999999999978888888888888899886568888889999999999999999998757985887567675899997588766555785588877899999997799888888989999999999988988889999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MPDDQPAVPDVDRLARSMLLLHGDHHDHNDSPEQHRTCGSWSKSRDFADDPQRAAAVREASRAERDRYLTSGLQPVDCRFCHVTVTVKRLGPGHTAVQWNTEASRRCAYFTELRARGGDSARTRSCPRLTDSIEHAVAEGYLEHHDPNR
Prediction	75676643340440041003020434456455566654442340352674453254146324444541273404424054031202043334620001036604630440353465445433353154035004400453405364688
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCEEEEEHCCCCCCEEHCCHHHHHHCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCC
MPDDQPAVPDVDRLARSMLLLHGDHHDHNDSPEQHRTCGSWSKSRDFADDPQRAAAVREASRAERDRYLTSGLQPVDCRFCHVTVTVKRLGPGHTAVQWNTEASRRCAYFTELRARGGDSARTRSCPRLTDSIEHAVAEGYLEHHDPNR

4h05A2

0.15

0.97

0.72

MUSTER

RPASARWPREAVALAGLARSLHAL--DWERCPFDRSLAVTVPQAVDLEDDEERKGWSGERLLAELERTRPADEDLAVC-LCPDNVLLDPRTCEVTGL-VGRVGR-RHSDLALVLRELAHEEDPWFGPECSAAFLREYGRGWDGAVSEEK

1q0vA

0.21

0.11

0.51

0.75

dPPAS

MDRDYSTPEDEEELIRKAIELSLSASSEPIVPVVESKNEVKRQEIEEEEDPDLKAAIQESLREAEEAKLRSERQKA-------------------------------------------------------------------------

2js3A

0.20

0.12

0.59

0.68

wdPPAS

--------------------MGSSHHHHHHSSGREN---YFQGMTDTAEDVRKIATALLKTAIE-----EDGGAHNQCKLCGA------------SVPWL--------------QTGDEIKHADDC---PVVIAKQILSSRLHAV----

4h05A2

0.16

0.15

0.95

0.77

wMUSTER

RPASARWPREAVALAGLARSLH----DWERCPFDRSLAVTVPQAVDLEDDEERKGWSGERLLAELERTRPADEDLAVC-LCPDNVLLDPRTCEVTGL-V-GRVG-RHSDLALVLRELAHEEDPWFGPECSAAFLREYGRGWDGAVSEEK

2js3A

0.26

0.15

0.58

0.71

wPPAS

-----------------M----GSHHHHHHSSGREN----FQGMTDTAEDVRKIATALLKTAIEEE---DGG-AHNQCKLCGASV------WLQTGIKHADD----CPVVIAKQILSSR-------PKL-----HAV------------

2k42B

0.22

0.05

0.24

0.92

dPPAS2

----GHMLPDVAQRLMQHLAEHGI-QPARNMAEHIPPAPNW------------------------------------------------------------------------------------------------------------

4h05A2

0.15

0.95

0.83

PPAS

RPASARWPREAVALAGLARSLHADRSLAVTVPQAARAVAEGSVDLEDL-DEERKGWSGERLLAELERTRPADEDLAVC-LCPDNVLLDPRTCEVTGL-VGR----RHSDLALVLRELAHEEDPWFGPECSAAFLREYGRGWDGAVSEEK

3gdhA1

0.18

0.15

0.81

0.86

Env-PPAS

LPPEIAAVPELAKYWAQRYRLFSRFDDG-----IKLDREGW-----FSVTPEKIAEHIAGRVSQSF----KCDVVVDA-FCGVTIQFALTGMRVIAIDIDPVKIALARNNAEVYG-------------IADKIECGDFLLLASFLKADV

5d18A2

0.19

0.16

0.84

0.71

MUSTER

PTWDEAHGPVEQRSERQLTELVSLQSQH-----PDFLRLFYLLSMERSQDPAVAAVVRRVRNTAIARFRDS---------------ITHLLPSDIP---PGKADLVVAELTAFAVALSDGPDTTDVERMYRRLRQALEA-LIPVLLEET

2mvoA

0.16

0.14

0.89

0.72

dPPAS

SGMKETAAAKFERQHMDSPDLGTDDDDKTGGGRADPAHRSPVPLPSPTSNKQDISEANLAYLWP----LTVDHGTIECLPSDNAVFVAPDG---TTYALNDRAEKAGHPPITPIRAKGSGGGYISLGALLSTTLNLCGKG---------

(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 = 8.5±4.5Å

Download Model 2

C-score=-4.59

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

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	4h05A2	0.808	2.48	0.122	0.987
2	1nd4A	0.737	2.64	0.117	0.919
3	3r78A2	0.721	2.82	0.154	0.913
4	3atsA2	0.705	3.32	0.082	0.960
5	2b0qA	0.700	3.01	0.080	0.919
6	2pulA2	0.674	3.78	0.062	0.966
7	2ppqA	0.669	3.63	0.021	0.940
8	2pywA2	0.663	3.95	0.054	0.987
9	3c5iD	0.661	3.86	0.054	0.960
10	3i0oA2	0.658	3.49	0.087	0.919

(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	0.17	8	1ee8A	ZN	Rep, Mult	78,81,107,126
2	0.07	3	3mmhA	MG	Rep, Mult	21,136,137,140
3	0.07	3	4j4qA	BOG	Rep, Mult	118,130,133
4	0.04	2	1izlD	PHO	Rep, Mult	132,133,136,137
5	0.04	2	3kgwA	PLP	Rep, Mult	94,95
6	0.02	1	3wubA	ZN	Rep, Mult	131,135
7	0.02	1	3i0oA	SMI	Rep, Mult	109,113,116,117,128
8	0.02	1	4bo7D	J2T	Rep, Mult	11,15,128,132
9	0.02	1	2bkk0	III	Rep, Mult	36,37,40,59,61,65,66,67,69,70,71,74
10	0.02	1	3r78B	NA	Rep, Mult	7,11,91

	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	0.066	1l8tA	0.700	3.03	0.080	0.919	2.7.1.95	NA
2	0.060	1ky8A	0.481	4.61	0.076	0.785	1.2.1.9	NA
3	0.060	1zumI	0.476	4.24	0.044	0.752	1.2.1.3	NA
4	0.060	3f2sA	0.635	3.89	0.069	0.960	2.7.1.32	NA
5	0.060	2ckpA	0.617	3.77	0.066	0.893	2.7.1.32	NA
6	0.060	3en9A	0.496	2.67	0.043	0.624	3.4.24.57	NA
7	0.060	2vwbA	0.486	3.09	0.042	0.638	3.4.24.57	NA
8	0.060	2pulA	0.674	3.78	0.062	0.966	2.7.1.100	131
9	0.060	2ve5H	0.497	4.72	0.065	0.812	1.2.1.8	NA
10	0.060	1j7lA	0.697	3.03	0.088	0.919	2.7.1.95	NA
11	0.060	1uxvA	0.481	4.63	0.076	0.785	1.2.1.9	110
12	0.060	1nd4A	0.737	2.64	0.117	0.919	2.7.1.95	NA
13	0.060	2w8oA	0.520	4.41	0.060	0.826	1.2.1.24	140
14	0.060	3ifh6	0.499	4.36	0.046	0.799	1.2.1.16	14
15	0.060	2w8nA	0.516	4.30	0.060	0.812	1.2.1.24	NA
16	0.060	3enhA	0.485	3.08	0.032	0.638	3.4.24.57	NA
17	0.060	3ju8A	0.490	4.45	0.054	0.792	1.2.1.71	NA
18	0.060	2vroB	0.481	4.47	0.061	0.772	1.2.1.3	NA
19	0.060	3k2wB	0.509	4.37	0.046	0.805	1.2.1.8	NA
20	0.060	3fg0C	0.505	4.36	0.069	0.785	1.2.1.8	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	0.18	0.807	2.51	0.12	0.99	4h05B	GO:0005524 GO:0016740 GO:0016773 GO:0046677
1	0.13	0.718	2.84	0.16	0.92	4gkiA	GO:0000166 GO:0005524 GO:0008910 GO:0016310 GO:0016740 GO:0016773 GO:0046677
2	0.13	0.737	2.64	0.12	0.92	1nd4A	GO:0000166 GO:0005524 GO:0008910 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046677 GO:0046872
3	0.11	0.700	3.01	0.08	0.92	2b0qA	GO:0000166 GO:0005524 GO:0008910 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046677
4	0.07	0.604	3.97	0.04	0.90	3hamA	GO:0000166 GO:0005524 GO:0016740
5	0.07	0.601	3.58	0.07	0.87	4dfbB	GO:0000166
6	0.06	0.364	5.49	0.07	0.70	4b7sA	GO:0004497 GO:0005506 GO:0016491 GO:0016705 GO:0017000 GO:0020037 GO:0033068 GO:0046872 GO:0055114
7	0.06	0.319	5.15	0.04	0.56	3berA	GO:0000166 GO:0003676 GO:0003723 GO:0004004 GO:0004386 GO:0005524 GO:0005634 GO:0005654 GO:0005730 GO:0006364 GO:0006397 GO:0006915 GO:0008380 GO:0008625 GO:0010501 GO:0016020 GO:0016787 GO:0044822
8	0.06	0.606	4.08	0.09	0.95	4pdyA	GO:0016740
9	0.06	0.297	5.67	0.05	0.57	3l84A	GO:0003824 GO:0004802 GO:0008152 GO:0016740 GO:0046872
10	0.06	0.396	4.26	0.05	0.62	5i4nA	GO:0000165 GO:0000166 GO:0000186 GO:0002250 GO:0002376 GO:0004672 GO:0004713 GO:0004715 GO:0005088 GO:0005102 GO:0005131 GO:0005143 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005856 GO:0005901 GO:0006468 GO:0006915 GO:0006919 GO:0006928 GO:0006979 GO:0007165 GO:0007167 GO:0007186 GO:0007204 GO:0007259 GO:0007260 GO:0007262 GO:0007498 GO:0007596 GO:0008022 GO:0008284 GO:0008285 GO:0008631 GO:0009755 GO:0010667 GO:0010811 GO:0012505 GO:0014068 GO:0016020 GO:0016301 GO:0016310 GO:0016363 GO:0016477 GO:0016568 GO:0016740 GO:0018108 GO:0019221 GO:0019901 GO:0020037 GO:0022408 GO:0030041 GO:0030154 GO:0030218 GO:0030335 GO:0031103 GO:0031234 GO:0031702 GO:0031904 GO:0031959 GO:0032024 GO:0032496 GO:0032516 GO:0032731 GO:0032760 GO:0033130 GO:0033160 GO:0033194 GO:0033209 GO:0034612 GO:0035401 GO:0035409 GO:0035556 GO:0035722 GO:0038083 GO:0042127 GO:0042169 GO:0042393 GO:0042503 GO:0042506 GO:0042508 GO:0042517 GO:0042523 GO:0042977 GO:0042981 GO:0043065 GO:0043388 GO:0043392 GO:0043524 GO:0043547 GO:0043548 GO:0043560 GO:0045087 GO:0045121 GO:0045429 GO:0045597 GO:0045822 GO:0046677 GO:0046777 GO:0046872 GO:0048008 GO:0050727 GO:0050729 GO:0050731 GO:0050867 GO:0051091 GO:0051428 GO:0051770 GO:0060333 GO:0060334 GO:0060396 GO:0060397 GO:0060399 GO:0061180 GO:0070671 GO:0097191 GO:0097296
11	0.06	0.238	5.06	0.07	0.44	2kucA	GO:0000103 GO:0005737 GO:0006457 GO:0006662 GO:0015035 GO:0016671 GO:0016853 GO:0034599 GO:0045454 GO:0055114
12	0.06	0.301	5.22	0.03	0.54	4yorA	GO:0004527 GO:0090305
13	0.06	0.314	5.41	0.06	0.58	3alnA	GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004702 GO:0004713 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006468 GO:0006915 GO:0007165 GO:0007254 GO:0009611 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0035897 GO:0038095 GO:0071260 GO:2000672
14	0.06	0.362	5.09	0.07	0.64	3lidA	GO:0000155 GO:0000160 GO:0005622 GO:0023014
15	0.06	0.334	5.47	0.06	0.62	4uw0A	GO:0004672 GO:0005524 GO:0006468
16	0.06	0.262	3.54	0.07	0.38	1awcB	GO:0005634 GO:0006351 GO:0006355 GO:0044212 GO:0045944 GO:0046982
17	0.06	0.332	5.48	0.05	0.61	4ax8A	GO:0000166 GO:0004672 GO:0005524 GO:0005886 GO:0006468 GO:0008168 GO:0009103 GO:0009243 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0032259
18	0.06	0.240	4.63	0.04	0.39	2cs5A	GO:0004721 GO:0004725 GO:0004726 GO:0005737 GO:0005856 GO:0005886 GO:0006470 GO:0008092 GO:0009898 GO:0016020 GO:0016311 GO:0016787 GO:0016791 GO:0035335

Consensus prediction of GO terms

Molecular Function	GO:0005524	GO:0008910
GO-Score	0.49	0.33
Biological Processes	GO:0046677	GO:0016310
GO-Score	0.45	0.33
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.