I-TASSER results

I-TASSER results for job id Rv3753c

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

Input Sequence in FASTA format

>protein (166 residues)
MQRPAADTPDGFGVAVVREEGRWRCSPMGPKALTSLRAAETELRELRSAGAVFGLLDVDD
EFFVIVRPAPSGTRLLLSDATAALDYDIAAEVLDNLDAEIDPEDLEDADPFEEGDLGLLS
DIGLPEAVLGVILDETDLYADEQLGRIAREMGFADQLSAVIDRLGR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MQRPAADTPDGFGVAVVREEGRWRCSPMGPKALTSLRAAETELRELRSAGAVFGLLDVDDEFFVIVRPAPSGTRLLLSDATAALDYDIAAEVLDNLDAEIDPEDLEDADPFEEGDLGLLSDIGLPEAVLGVILDETDLYADEQLGRIAREMGFADQLSAVIDRLGR
Prediction	CCCCCCCCCCCEEEEEEEHCCEEEEEHCCCHHHCCHHHHHHHHHHCCCCCCEEEEEHCCCCEEEEEEHCCCCEEEEEHCHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHCC
Conf.Score	9988888888679999997997999985656648999999999985778877999875786799999689986999853445665589999999979999999989988888887677777699999999986788899899999999998986999999998589
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MQRPAADTPDGFGVAVVREEGRWRCSPMGPKALTSLRAAETELRELRSAGAVFGLLDVDDEFFVIVRPAPSGTRLLLSDATAALDYDIAAEVLDNLDAEIDPEDLEDADPFEEGDLGLLSDIGLPEAVLGVILDETDLYADEQLGRIAREMGFADQLSAVIDRLGR
Prediction	8636567524100000015744040450445316415501530371455310100000233000000134741200010131034251033005417273556756566323412120023241436202301546422134003300641412630350166268
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCEEEEEEEHCCEEEEEHCCCHHHCCHHHHHHHHHHCCCCCCEEEEEHCCCCEEEEEEHCCCCEEEEEHCHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHCC
MQRPAADTPDGFGVAVVREEGRWRCSPMGPKALTSLRAAETELRELRSAGAVFGLLDVDDEFFVIVRPAPSGTRLLLSDATAALDYDIAAEVLDNLDAEIDPEDLEDADPFEEGDLGLLSDIGLPEAVLGVILDETDLYADEQLGRIAREMGFADQLSAVIDRLGR

3onqA

0.16

0.14

0.92

1.12

dPPAS2

LTNTDDRQGDFNCFAIGGVPSA------SLAST--SLAIRKAVRDLGGEH---VVIGTYGTFLLALACQGEDEPLYLSPAGASHALRETFSLQAAPALSTPSRPLRADELLPEGDDYAREEL--YRNVYQVLRGENPLKYGSSLENTAKELNVRYRLKRAAETTGW

5czdB

0.21

0.09

0.43

1.02

dPPAS2

----------------------------------------------------------------------------------MWDAQFENLLRRYLPFLSADQPLEQDIN--------LRDIGLDVELLSELENTYDVFQDEALT--KETFETPGVLWKTLSQM--

5dggA

0.12

0.98

0.81

MUSTER

RDQMQDHDMT---LLMPKSQGRIVVAVLNRYDSHSANAIIETLASDNPEVHYIMIPVGPGHWRGVYLSKPTAYDLELFDEGAAVLDDYVLDLLNQCGVPKELVNIRHTGPHPQGDAYSCGDF-YSHKKMKEFGAPEGSYNPILIDTLDNLGNEDNVLRMTTREETR

5dggA

0.09

0.95

0.70

dPPAS

MTLLMPKSQGRIVVMAV-------LNRYDSHSANAIIETLASDVFNPEVHYIMIPVG-PGHWRGVYLSKPTAYDLELFDEGAAVLDDYVLDLLNQCGVPKELRHTGPKHPQGDAYSCGDFTCAYSHKKMKEFGAPEGSYNPILIDTLDNLGNEDNVLRMTTREETR

5hafA2

0.08

0.07

0.87

0.58

wdPPAS

LVQESPLLSVNYPIGLIHP--------TTKENI--STQLLEKIAQSGLSHNEVFLVNTGDHWLLCLFYKAEKIKCLIFNTYYDLNENTKQEIIEAAKI---------AGISESDEVNFIMNL-VPYHTIQLLSNAGQNDPATTLREFAENF-LSVEEQALFNTQTR

5dggA

0.14

0.13

0.92

0.78

wMUSTER

MQMPKSQGRIVVMAVLNRYDSH------SANAI--IETLASDVFN-PEVHYIMIPVG-PGHWRGVYLSKPTAYDLELFDEGAAVLDDYVLDLLNQCGV---PKELVNGPKHPQGDAYSCGDF-YSHKKMKEFGAPEGSYNPILIDTLDNLGNEDNVLRMTTREETR

3zt9A

0.24

0.22

0.91

0.64

wPPAS

LEAREGEIACGDACLVKRVEGVIFLAVGDIASMEGLVNIFQLCHREGTRGAVAALCRVDQGLWQAAIVGNIHVKILSAKGI--------ITPLATLGYNYPHQLLIAKGSYQEGDL-LISD-GIQEGVPLALLANYRLTAEELVRLIGEKYG-DDDV--VI--VAR

1ezwA2

0.10

0.09

0.86

0.90

dPPAS2

-------------MGAGEIANGVLVNASNPKDFEVAVPKIEEGAKEAGRSLIDVAAYT----CFSIDKDEDKAIEATKIVVAFIVMGSPDVVLERHGID-TEKAEQIAEAIGKGDFGTAIGL-VDEDMIEAFAGD----PDTVVDKIEELLKAGPDKEKAIELVGQ

1ezwA2

0.13

0.11

0.86

0.69

PPAS

-----------MGAQAGEIANGVLVNASNPKDFEVAVPKIEEGAKERSLDEIDVAAYT----CFSIDKDEDKAIEATKIVVAFIVMGSPDVVLERHGID-TEKAEQIAEAIGKGDFGTAIGL-VDEDMIEAFS------PDTVVDKIEELLKIGPDKEKAIELVGQ

5dggA

0.12

0.11

0.97

0.74

Env-PPAS

---RDQMQDHDMTLLMPKSQGRIVVMAVDSHSANAIIETLASDVFNPEVHYIMIPVG-PGHWRGVYLSKPTAYDLELFDEGAAVLDDYVLDLLNQCGVPKELVNIRHTGPHPQGDAYSCGDFTYSHKKMKEFGAPEGSY-NPILIDTLDNLGNDNVLRMTTREETR

(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=-2.11

Estimated TM-score = 0.46±0.15

Estimated RMSD = 9.6±4.6Å

Download Model 2

C-score=-3.90

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.64

Download Model 5

C-score=-4.96

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	5dggA	0.684	3.58	0.068	0.952
2	5hamA	0.618	4.07	0.071	0.910
3	5hafA	0.608	4.18	0.067	0.904
4	2bkqA	0.604	4.37	0.070	0.934
5	2oixA	0.593	4.19	0.079	0.855
6	1euvA	0.590	4.48	0.073	0.898
7	2iy0A	0.586	4.54	0.045	0.916
8	1th0A	0.583	4.41	0.052	0.904
9	3eayA	0.579	4.35	0.081	0.892
10	5klpA	0.577	4.25	0.066	0.861

(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	0.12	6	2no5A	CNR	Rep, Mult	37,40
2	0.08	4	5e9uG	MG	Rep, Mult	37,94
3	0.06	3	2btdA	MG	Rep, Mult	115,121,152
4	0.04	2	3rtdA	III	Rep, Mult	121,126,129,130
5	0.04	2	3cr3A	MG	Rep, Mult	97,115,121
6	0.02	1	3dc7B	MG	Rep, Mult	120,121
7	0.02	1	1y7pC	RIP	Rep, Mult	74,76,106,132
8	0.02	1	3rt9A	COA	Rep, Mult	28,36,89
9	0.02	1	2b0qA	MG	Rep, Mult	115,134
10	0.02	1	5dnmG	RAX	Rep, Mult	42,45
11	0.02	1	1t0lA	NAP	Rep, Mult	87,91,94
12	0.02	1	1yt3A	ZN	Rep, Mult	59,104
13	0.02	1	3g1fC	2OM	Rep, Mult	79,81

	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	2bkrA	0.593	4.43	0.064	0.922	3.4.22.-	NA
2	0.060	1avpA	0.563	4.27	0.074	0.849	3.4.22.39	NA
3	0.060	3ktnA	0.482	5.04	0.046	0.807	2.7.1.45	NA
4	0.060	1vi9A	0.486	5.21	0.056	0.849	2.7.1.35	129
5	0.060	1t09B	0.500	4.29	0.054	0.741	1.1.1.42	66,74
6	0.060	3blvC	0.486	4.79	0.044	0.747	1.1.1.41	80
7	0.060	3h74A	0.492	5.08	0.038	0.825	2.7.1.35	NA
8	0.060	1jxiA	0.497	5.13	0.101	0.843	2.7.4.7	117
9	0.060	1zorA	0.494	4.36	0.048	0.741	1.1.1.42	NA
10	0.060	1euvA	0.590	4.48	0.073	0.898	3.4.22.68	NA
11	0.060	2ddmB	0.493	4.97	0.084	0.837	2.7.1.35	NA
12	0.060	2agsA	0.493	4.87	0.048	0.813	3.2.1.18	15,127
13	0.060	2qfwD	0.487	4.01	0.027	0.705	1.1.1.42	NA
14	0.060	1cnzA	0.467	4.76	0.141	0.753	1.1.1.85	NA
15	0.060	2qcvA	0.491	4.99	0.099	0.807	2.7.1.92	NA
16	0.060	1wd8A	0.461	4.87	0.126	0.747	3.5.3.15	NA
17	0.060	1kb0A	0.484	4.97	0.075	0.831	1.1.99.-	NA
18	0.060	2i5bA	0.497	5.06	0.070	0.837	2.7.4.7	NA
19	0.060	2fv7A	0.494	4.89	0.098	0.807	2.7.1.15	NA
20	0.060	2f10A	0.441	5.66	0.034	0.849	3.2.1.18	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	0.12	0.684	3.58	0.07	0.95	5dggA	GO:0016020 GO:0016021
1	0.08	0.593	4.43	0.06	0.92	2bkrA	GO:0006508 GO:0008233 GO:0008234 GO:0016787
2	0.07	0.593	4.19	0.08	0.86	2oixA	GO:0006508 GO:0008234
3	0.07	0.586	4.51	0.04	0.91	2xphA	GO:0004175 GO:0005634 GO:0005654 GO:0005737 GO:0005925 GO:0006508 GO:0006919 GO:0008233 GO:0008234 GO:0010724 GO:0016787 GO:0016925 GO:0016926 GO:0016929 GO:0031965 GO:0032435 GO:0045944 GO:0070139 GO:0097190
4	0.07	0.599	4.44	0.08	0.90	3zo5A	GO:0001934 GO:0004175 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0006508 GO:0006810 GO:0007507 GO:0008233 GO:0008234 GO:0009950 GO:0015031 GO:0016020 GO:0016055 GO:0016604 GO:0016605 GO:0016787 GO:0016925 GO:0016926 GO:0016929 GO:0019904 GO:0030111 GO:0031397 GO:0031398 GO:0031410 GO:0031648 GO:0031965 GO:0032091 GO:0032875 GO:0035562 GO:0043518 GO:0045444 GO:0045944 GO:0051028 GO:0051246 GO:0060707 GO:0060711 GO:0060712 GO:0070139 GO:1901797 GO:2000045
5	0.07	0.590	4.48	0.07	0.90	1euvA	GO:0000086 GO:0004175 GO:0005635 GO:0005643 GO:0005730 GO:0006508 GO:0008233 GO:0008234 GO:0016787 GO:0016926 GO:0016929
6	0.07	0.579	4.35	0.08	0.89	3eayA	GO:0005622 GO:0005634 GO:0006508 GO:0008233 GO:0008234 GO:0016787
7	0.07	0.451	5.40	0.06	0.80	2ac1A	GO:0004553 GO:0004564 GO:0004575 GO:0005576 GO:0005618 GO:0005886 GO:0005975 GO:0008152 GO:0009611 GO:0016787 GO:0016798 GO:0048046 GO:0080167
8	0.06	0.369	5.53	0.04	0.66	1wchA	GO:0004721 GO:0004725 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0006470 GO:0014066 GO:0016311 GO:0016787 GO:0016791 GO:0030027 GO:0035335 GO:0036312 GO:0042995 GO:0043005 GO:0044297 GO:0070062
9	0.06	0.346	5.84	0.04	0.67	3debA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
10	0.06	0.338	5.79	0.09	0.65	3ey5A	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0031248
11	0.06	0.352	5.64	0.06	0.64	1wdwE	GO:0000162 GO:0003824 GO:0004834 GO:0006568 GO:0008152 GO:0008652 GO:0009073 GO:0016829
12	0.06	0.338	5.09	0.03	0.60	5bqnA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
13	0.06	0.289	4.35	0.04	0.45	3jb9e	GO:0000398 GO:0005634 GO:0005681 GO:0005684 GO:0006397 GO:0008380 GO:0045292
14	0.06	0.283	5.46	0.08	0.52	4f0cA	GO:0016740
15	0.06	0.308	5.09	0.03	0.52	1uhnA	GO:0005509 GO:0005773 GO:0005774 GO:0009705 GO:0016020 GO:0019722 GO:0022626 GO:0046872 GO:0055075
16	0.06	0.306	4.12	0.11	0.45	1r1pB	GO:0005634 GO:0005654 GO:0005737 GO:0005768
17	0.06	0.330	4.72	0.05	0.55	3tj1A	GO:0000182 GO:0001042 GO:0001082 GO:0001179 GO:0001180 GO:0001181 GO:0005634 GO:0005730 GO:0006351 GO:0006355 GO:0006356
18	0.06	0.344	5.15	0.09	0.60	3tixD	GO:0000122 GO:0000166 GO:0003677 GO:0003727 GO:0005634 GO:0005737 GO:0005816 GO:0005856 GO:0006348 GO:0007049 GO:0007059 GO:0030466 GO:0030958 GO:0031047 GO:0031048 GO:0031493 GO:0031508 GO:0031618 GO:0031934 GO:0034507 GO:0034613 GO:0035064 GO:0044732 GO:0071459 GO:1990141 GO:1990707

Consensus prediction of GO terms

Molecular Function	GO:0070011
GO-Score	0.51
Biological Processes	GO:0019538
GO-Score	0.51
Cellular Component	GO:0031965	GO:0016021	GO:0031410	GO:0016605	GO:0005925	GO:0005643
GO-Score	0.13	0.12	0.07	0.07	0.07	0.07

(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.