I-TASSER results

I-TASSER results for job id Rv0477

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

Input Sequence in FASTA format

>protein (148 residues)
MKALVAVSAVAVVALLGVSSAQADPEADPGAGEANYGGPPSSPRLVDHTEWAQWGSLPSL
RVYPSQVGRTASRRLGMAAADAAWAEVLALSPEADTAGMRAQFICHWQYAEIRQPGKPSW
NLEPWRPVVDDSEMLASGCNPGSPEESF

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MKALVAVSAVAVVALLGVSSAQADPEADPGAGEANYGGPPSSPRLVDHTEWAQWGSLPSLRVYPSQVGRTASRRLGMAAADAAWAEVLALSPEADTAGMRAQFICHWQYAEIRQPGKPSWNLEPWRPVVDDSEMLASGCNPGSPEESF
Prediction	CCCCHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCEEEEEHCHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCC
Conf.Score	9753434566666536888888898888888888899988888865799999968955899986887755567788578999999999977888976699999999988853478998767888899999899999878999998899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MKALVAVSAVAVVALLGVSSAQADPEADPGAGEANYGGPPSSPRLVDHTEWAQWGSLPSLRVYPSQVGRTASRRLGMAAADAAWAEVLALSPEADTAGMRAQFICHWQYAEIRQPGKPSWNLEPWRPVVDDSEMLASGCNPGSPEESF
Prediction	4411331312110101214434353644444444646444434320430413437433202021262024245444462334003300542475426103400300242043344745413032323515355113441247356668
	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

CCCCHCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCEEEEEHCHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCC
MKALVAVSAVAVVALLGVSSAQADPEADPGAGEANYGGPPSSPRLVDHTEWAQWGSLPSLRVYPSQVGRTASRRLGMAAADAAWAEVLALSPEADTAGMRAQFICHWQYAEIRQPGKPSWNLEPWRPVVDDSEMLASGCNPGSPEESF

4a54B

0.16

0.05

0.29

1.15

dPPAS2

SVDVDADASSQLLSLLKSSTAPSDLATPQPSTFPQPPVESHSS---------------------------------------------------------------------------------------------------------

2n73B

0.18

0.09

0.51

1.02

dPPAS2

-----GAMVEARSLAVAMGDTVVEPAPLKPTSEPTSGPPGNNG-------------GSLLSVITEGVG--ELSVIDPEVAQKACQEVLEKVGGVAV----------------------------------------------------

5cwjA

0.11

0.99

0.76

MUSTER

EEQERIRRILKEARKSGTEESLRQAIEDVAQLAKKSQDSEVLEEAIRVIL-KESGSEEALRQAIRAVAEIAKEAQDSEVLEEAIRVILRIAKESGSEALRQAIRAVAEIAKEAQDPRVL-AIRVIRSGSEEARRQAERAEEEIRRRAQ

2muxA

0.10

0.07

0.72

dPPAS

LKDSNGNLELAVAFLTAKNAKTPQQEETTYYQTALPGNDRYISVG---------------SQADTNVIDLTGDDKDDLQRAIALSLAESNRAFRETGITDEEQAISRVLEASIAENKACLKR--------------------------

4xhjB

0.11

0.08

0.77

0.80

wdPPAS

FGAKPLSDVSLIITEPCVSSVYEAWDYAAPPVSNLSEA-TKCPV--EVILWFK-DKQMAYWTNPYVTLKGLTQSVGEEHKSGDIRDALLDALSG------------------VWVDSTPSSTNIPEN----------GCW--GADRLF

4xhjB

0.13

0.10

0.78

0.80

wMUSTER

AKPLSDVSLIITEPCVSSVYEAWDYAAPPVSNLSEALSGTKCPV-PEVILWFK-DKQMAYWTNPYVTLKGLTQSVGEE--------------HKSGD-IRDAL---LDALSGVWVDSTPSSTNI-PEN---------GCW--GADRLF

4xhjB

0.14

0.11

0.77

0.89

wPPAS

FGAKPLSDVSLIITEPCVSSVYEAWAAPPVSNLSEALS-TKCPV-PEVILWFK-DKQMAYWTNP------VTLKGLT-------QSVGEEHKSGD---IRDAL---LDALSGVWVDSTPSSTNI-PEN---------GCW-GA-DRLF

2pq4B

0.23

0.05

0.21

0.97

dPPAS2

RRSFMKANAVAAAAAAAGLSVPGVARAVVGQ---------------------------------------------------------------------------------------------------------------------

4xhjB

0.10

0.08

0.80

0.83

PPAS

FGAKPLSDVSLIITEPCVSSVYEAWDYAAPPVSNLSEALSTKCPVPEVILWFK-DKQMAYWTNPYVTLKGLTQSVGEEHKSGDIRDALLDALSG------------------VWVDSTPSSTNIPEN----------GCVWGA-DRLF

4uc1A

0.19

0.18

0.96

0.69

Env-PPAS

MNMDWALFLTFLAACGAPATTGALLKPDEWYDNLNKP-WWNPPRWVFPLAWTSLYFLMSLAAMLEGSGQALAFYAAQLAFNTLWTPVFFGMKRMATALAVVMVMWLFVAATMWA----FFQLDTWAPYATATTGLNFEANWNRPEAR-

(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=-3.77

Estimated TM-score = 0.31±0.10

Estimated RMSD = 13.6±4.0Å

Download Model 2

C-score=-3.72

Download Model 3

C-score=-4.15

Download Model 4

C-score=-4.56

Download Model 5

C-score=-3.93

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	4xhjB	0.562	3.21	0.103	0.750
2	3rkoN	0.519	4.55	0.051	0.845
3	4he8M	0.514	4.60	0.057	0.851
4	4he8N	0.509	4.80	0.072	0.858
5	1jqoA	0.504	4.84	0.057	0.831
6	3rkoL	0.500	4.74	0.088	0.865
7	4qjyA	0.500	4.62	0.035	0.851
8	1jqnA	0.495	4.69	0.066	0.811
9	1r88A	0.488	4.54	0.083	0.790
10	2okxA	0.482	4.75	0.053	0.818

(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	3rj1D	SE	Rep, Mult	102,106
2	0.06	3	4xniA	78M	Rep, Mult	88,98,102,103,110
3	0.04	2	3ffzA	NA	Rep, Mult	47,64,65,67,68
4	0.04	2	3rl3A	MN	Rep, Mult	121,125
5	0.02	1	2idsA	CU1	Rep, Mult	106,139
6	0.02	1	4ek1A	MTN	Rep, Mult	139,140
7	0.02	1	2rdzA	CA	Rep, Mult	124,126
8	0.02	1	2z5zA	CA	Rep, Mult	47,49,61,63,65
9	0.02	1	3a6pA	III	Rep, Mult	87,94,103
10	0.02	1	1fuiA	FOC	Rep, Mult	69,120
11	0.02	1	2r9rB	PGW	Rep, Mult	48,103
12	0.02	1	4ireB	OXL	Rep, Mult	97,100
13	0.02	1	3attA	MG	Rep, Mult	121,130
14	0.02	1	3mxgA	XLS	Rep, Mult	120,121
15	0.02	1	3ta8A	FE	Rep, Mult	84,103
16	0.02	1	4h10B	NUC	Rep, Mult	66,69

	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	1nx9A	0.453	5.06	0.063	0.804	3.1.1.43	63
2	0.060	5coxA	0.417	5.28	0.061	0.770	1.14.99.1	NA
3	0.060	2ocgA	0.443	4.88	0.043	0.777	3.1.-.-	62
4	0.060	1cvuA	0.451	4.69	0.021	0.757	1.14.99.1	NA
5	0.060	1e1hD	0.244	4.95	0.042	0.419	3.4.24.69	NA
6	0.060	2vf2A	0.454	5.31	0.085	0.851	3.7.1.8	NA
7	0.060	2jbwD	0.466	4.66	0.062	0.770	3.7.1.-	NA
8	0.060	2w2dA	0.362	5.53	0.065	0.716	3.4.24.69	NA
9	0.060	1jqnA	0.495	4.69	0.066	0.811	4.1.1.31	NA
10	0.060	1e1hC	0.253	5.65	0.040	0.493	3.4.24.69	NA
11	0.060	1pjaA	0.451	4.92	0.057	0.784	3.1.2.22	NA
12	0.060	2gwhB	0.447	4.98	0.038	0.790	2.8.2.-	NA
13	0.060	1wcgA	0.445	5.01	0.035	0.763	3.2.1.147	NA
14	0.060	3btaA	0.453	5.25	0.049	0.831	3.4.24.69	NA
15	0.060	1jqoA	0.504	4.84	0.057	0.831	4.1.1.31	NA
16	0.060	1iunB	0.463	4.55	0.054	0.757	3.7.1.9	NA
17	0.060	2imcB	0.396	5.18	0.070	0.716	3.4.24.69	NA
18	0.060	3jvpD	0.457	5.27	0.050	0.851	2.7.1.16	47
19	0.060	2og1A	0.461	4.96	0.042	0.838	3.7.1.8	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	0.07	0.495	4.69	0.07	0.81	1jqnA	GO:0000287 GO:0003824 GO:0005829 GO:0006099 GO:0006107 GO:0008152 GO:0008964 GO:0015977 GO:0016829
1	0.07	0.562	3.21	0.10	0.75	4xhjB	GO:0016020 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0046718 GO:0055036
2	0.07	0.509	4.80	0.07	0.86	4he8I	GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
3	0.07	0.445	5.30	0.04	0.79	4he8F	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
4	0.07	0.477	3.85	0.12	0.71	3m1cB	GO:0016020 GO:0019012 GO:0019031 GO:0019064 GO:0020002 GO:0033644 GO:0039663 GO:0046718 GO:0055036
5	0.06	0.514	4.60	0.06	0.85	4he8G	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
6	0.06	0.450	5.27	0.06	0.84	5f0nA	GO:0000070 GO:0000794 GO:0005634 GO:0005829 GO:0006302 GO:0006974 GO:0007064 GO:0007076 GO:0007126 GO:0007129 GO:0034501 GO:0051455 GO:0071168 GO:0071459 GO:2000817
7	0.06	0.360	4.92	0.05	0.61	2xsnD	GO:0001666 GO:0001963 GO:0001975 GO:0003007 GO:0004497 GO:0004511 GO:0005506 GO:0005634 GO:0005737 GO:0005739 GO:0005790 GO:0005829 GO:0006585 GO:0006631 GO:0006665 GO:0007507 GO:0007601 GO:0007605 GO:0007612 GO:0007613 GO:0007617 GO:0007626 GO:0008016 GO:0008021 GO:0008198 GO:0008199 GO:0009072 GO:0009414 GO:0009416 GO:0009635 GO:0009651 GO:0009653 GO:0009887 GO:0009898 GO:0010038 GO:0010043 GO:0010259 GO:0014070 GO:0014823 GO:0015842 GO:0016137 GO:0016491 GO:0016597 GO:0016714 GO:0017085 GO:0018963 GO:0019825 GO:0019899 GO:0019904 GO:0021987 GO:0030424 GO:0030425 GO:0030659 GO:0031410 GO:0031667 GO:0032355 GO:0032496 GO:0033076 GO:0033162 GO:0034617 GO:0035094 GO:0035176 GO:0035240 GO:0035690 GO:0035900 GO:0035902 GO:0042136 GO:0042214 GO:0042416 GO:0042418 GO:0042421 GO:0042423 GO:0042462 GO:0042493 GO:0042745 GO:0042755 GO:0043005 GO:0043025 GO:0043195 GO:0043204 GO:0043434 GO:0043473 GO:0045471 GO:0045472 GO:0046684 GO:0046872 GO:0048545 GO:0048596 GO:0050890 GO:0051412 GO:0051602 GO:0052314 GO:0055114 GO:0070848 GO:0071287 GO:0071312 GO:0071316 GO:0071333 GO:0071363
8	0.06	0.502	4.89	0.06	0.84	4uolA	GO:0003824 GO:0005737 GO:0006099 GO:0008152 GO:0008964 GO:0015977 GO:0015979 GO:0016829
9	0.06	0.354	4.68	0.07	0.56	3la6B	GO:0000166 GO:0000271 GO:0004713 GO:0005524 GO:0005886 GO:0005887 GO:0009103 GO:0009242 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016887 GO:0018108 GO:0038083 GO:0045226
10	0.06	0.338	4.85	0.04	0.59	5g05N	GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0006511 GO:0007049 GO:0007067 GO:0007399 GO:0016567 GO:0030154 GO:0031145 GO:0031625 GO:0031915 GO:0042787 GO:0043161 GO:0045773 GO:0050775 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0061630 GO:0070979 GO:0090129
11	0.06	0.300	5.82	0.05	0.59	1zxxA	GO:0000166 GO:0003824 GO:0003872 GO:0005524 GO:0005737 GO:0006002 GO:0006096 GO:0008152 GO:0008443 GO:0016301 GO:0016310 GO:0016740 GO:0046835 GO:0046872 GO:0061615
12	0.06	0.317	5.88	0.04	0.65	1nfgA	GO:0005737 GO:0016787 GO:0016810 GO:0046872
13	0.06	0.321	4.89	0.04	0.56	4hz4A	GO:0016740
14	0.06	0.501	4.82	0.04	0.82	4bxcA	GO:0003824 GO:0005737 GO:0006099 GO:0008152 GO:0008964 GO:0009760 GO:0015977 GO:0015979 GO:0016829
15	0.06	0.321	4.77	0.03	0.56	3fkkA	GO:0003824 GO:0005975 GO:0008152 GO:0016829 GO:0019568 GO:0019570 GO:0042803 GO:0047449
16	0.06	0.310	4.57	0.03	0.49	2aa1B	GO:0005344 GO:0005506 GO:0005833 GO:0006810 GO:0015671 GO:0019825 GO:0020037 GO:0046872
17	0.06	0.266	5.60	0.03	0.51	1wxqA	GO:0005525
18	0.06	0.287	5.37	0.03	0.53	2gu1A	GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0048038	GO:0008137	GO:0008964	GO:0000287
GO-Score	0.13	0.13	0.07	0.07
Biological Processes	GO:0019064	GO:0042773	GO:0015977	GO:0006810	GO:0006107	GO:0006099
GO-Score	0.13	0.13	0.07	0.07	0.07	0.07
Cellular Component	GO:0055036	GO:0020002	GO:0005886	GO:0016021	GO:0019031	GO:0005829
GO-Score	0.13	0.13	0.13	0.13	0.13	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.