I-TASSER results

Input Sequence in FASTA format

>protein (120 residues)
MPNPVTMLYGRKADLVILPHVLAEERPHPYSTPGRKRGAQIALTTGIDALASFAPQIVNP
RHGLSRVVQCLGGCENKRHAYFRSISKTPHIRARGVPSVCAVRTVGVDGAKRPPKPIPVQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPNPVTMLYGRKADLVILPHVLAEERPHPYSTPGRKRGAQIALTTGIDALASFAPQIVNPRHGLSRVVQCLGGCENKRHAYFRSISKTPHIRARGVPSVCAVRTVGVDGAKRPPKPIPVQ
Prediction	CCCCEEEEHCCCCCEEEEHHHHHCCCCCCCCCCCCCCCEEEEEEHCHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCC
Conf.Score	998645665566766774466654689889998866565688643467888766554687666799999886655566556667788975776588866788886578888999999999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MPNPVTMLYGRKADLVILPHVLAEERPHPYSTPGRKRGAQIALTTGIDALASFAPQIVNPRHGLSRVVQCLGGCENKRHAYFRSISKTPHIRARGVPSVCAVRTVGVDGAKRPPKPIPVQ
Prediction	854322302445130100121136645443635446442412132314201511441243442142014012204345423144246344144542442121322326336435553548
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCEEEEHCCCCCEEEEHHHHHCCCCCCCCCCCCCCCEEEEEEHCHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCC
MPNPVTMLYGRKADLVILPHVLAEERPHPYSTPGRKRGAQIALTTGIDALASFAPQIVNPRHGLSRVVQCLGGCENKRHAYFRSISKTPHIRARGVPSVCAVRTVGVDGAKRPPKPIPVQ

2jqnA

0.13

0.12

0.88

0.62

MUSTER

MT----LIY-SRAE----WDAAKAQGRFEGSAVDLADG--IHLSA-GEQAQETAAKWFRGQANL--VLLAVEAEPLGEDLKWEASRGGAHLYRPEVTREADLD-LDADGVPQLGDHLALE

4q0cA4

0.16

0.12

0.78

0.67

dPPAS

-----------RNGMVIV----TRQDPDAPVDADHLDGRTVALVRNIPLLQRRYPQAVVTADNPSEAMLMVANGQA-DAVVQTQISASYYVNRYFAGKLRIASALDLPPA----------

2e5vA2

0.27

0.21

0.76

0.60

wdPPAS

--HP-TVTSGEV--------FLLTE---------RGEGAQIINENGERFLFNYDKR-LAPRDILSRAIYIE--MLKGHKV-FIDLSKIEDFERK-FPVVAKYARHGHN----YKVKIPIF

4dqyC2

0.21

0.20

0.93

0.72

wMUSTER

LHN-RRLLW-RTTNFAILSQGL-RIAPPEAPVTGYMFGKGIYFADMVSKSANYCH--TSQGDPLGEV--ALGNMELKHASHISKLPKGKH-SVKGLGKTTPDPSANIDGVDVPLTGISSG

1knrA3

0.35

0.23

0.67

0.53

wPPAS

---P-TALYHPQA-----RNFLLTER-------G---GAYLKRPDGFDERGELAPRIV--R-AIDHEMKRLGA----DCMF-------SHIRQH--PMIL--LGLGIDLTQ---EPVPIV

3mpkA2

0.21

0.14

0.68

0.58

dPPAS2

--NG----------MVIVTR---QDPDAP-VDADHLDGRTVALVRNIPLLQRRYPQAKNPSEAMLMVANG------------QAISASYYVNRYFAGKLRIASALDLPPA----------

1ptoE

0.28

0.23

0.83

0.54

PPAS

VPY---VLV--KTNMVVTSVAM-----KPYETPTRMLVCGIAAKLG--AAAS-SPDAHVPRPGSSPMEVMLRAVFMQQR-PLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP------

4b09A2

0.29

0.20

0.70

0.79

Env-PPAS

---------S---PLIIDE-----GR---FQA--SWRGKMLDLTAEFRLLKTLSPGKVFSRQLLNHLYDDVV-----TD---RTI--DSHIRRKAEQSF--IRAVGV-GYREADACRIV-

3mpkA2

0.20

0.15

0.73

0.57

MUSTER

--NG----------MVIVTR---QDPDAP-VDADHLDGRTVALVRNIPLLQRRYPQAVNPSEAMLMVAN-----QA-DAVVQTQISASYYVNRYFAGKLRIASALDLPPA----------

1qm9A1

0.17

0.15

0.89

0.58

dPPAS

MGNSVLLVSNLNPE-RVTPQSLFIL----FGVYGDVQRVKILFNKKENALVQMADG-----NQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPRFKKPG---

(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=-3.94

Estimated TM-score = 0.29±0.09

Estimated RMSD = 13.4±4.0Å

Download Model 2

C-score=-4.09

Download Model 3

C-score=-4.13

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.36

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	2fncA	0.486	3.84	0.045	0.783
2	4wepA	0.485	4.10	0.112	0.792
3	4hs7A	0.485	3.76	0.045	0.767
4	4mfiA	0.484	4.43	0.060	0.825
5	3vxbA	0.484	4.56	0.051	0.842
6	4r2fA	0.483	4.03	0.053	0.792
7	3osqA3	0.482	3.86	0.061	0.775
8	3waiA	0.481	4.26	0.071	0.808
9	4aq4A2	0.479	4.46	0.097	0.817
10	5k2xA	0.478	4.35	0.052	0.817

(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	2xx8C	1NE	Rep, Mult	13,14,15,16,102,103,104
2	0.04	2	2d2cA	CLA	Rep, Mult	51,68
3	0.04	2	4fd8A	MA4	Rep, Mult	15,67
4	0.04	2	3e78A	CA	Rep, Mult	48,52,53,107
5	0.04	2	2qmuC	ZN	Rep, Mult	70,74,93,100
6	0.04	2	4ofgA	N2P	Rep, Mult	65,69
7	0.04	2	1gzmA	C8E	Rep, Mult	68,71
8	0.04	2	2ae8A	MG	Rep, Mult	62,66
9	0.02	1	1dd6A	ZN	Rep, Mult	20,28,90
10	0.02	1	4aqyH	MG	Rep, Mult	11,90,91
11	0.02	1	4kaeA	TGG	Rep, Mult	39,66
12	0.02	1	4zb0B	MN	Rep, Mult	25,70
13	0.02	1	2vwhA	ZN	Rep, Mult	48,62
14	0.02	1	5cfuA	MN	Rep, Mult	61,62
15	0.02	1	3v20A	CA	Rep, Mult	14,43
16	0.02	1	1c9uB	CA	Rep, Mult	25,30

	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	3flcX	0.425	4.88	0.043	0.792	2.7.1.30	NA
2	0.060	3d1rA	0.433	4.93	0.043	0.817	3.1.3.11	8,41
3	0.060	1cjmA	0.374	5.16	0.021	0.717	2.8.2.1	NA
4	0.060	2vd3A	0.418	3.99	0.081	0.675	2.4.2.17	86,104
5	0.060	2x0sA	0.412	4.97	0.046	0.758	2.7.9.1	NA
6	0.060	2plaA	0.443	4.37	0.052	0.767	1.1.1.8	NA
7	0.060	3ecrA	0.431	4.20	0.078	0.725	2.5.1.61	14
8	0.060	2h6jH	0.410	4.95	0.080	0.775	3.4.25.1	NA
9	0.060	1nh7A	0.417	4.24	0.030	0.675	2.4.2.17	NA
10	0.060	1txgA	0.425	4.47	0.052	0.758	1.1.1.94	NA
11	0.060	1q5rN	0.412	4.82	0.072	0.775	3.4.25.1	NA
12	0.060	3a1kA	0.422	4.88	0.048	0.800	3.5.1.4	NA
13	0.060	1h3dA	0.434	3.90	0.082	0.675	2.4.2.17	86
14	0.060	2iukB	0.430	4.94	0.045	0.817	1.13.11.12	NA
15	0.060	1yj8A	0.457	4.26	0.043	0.775	1.1.1.8	NA
16	0.060	1wppA	0.427	4.89	0.055	0.792	3.6.1.1	14,47,49,61
17	0.060	1bdgA	0.412	4.55	0.074	0.758	2.7.1.1	NA
18	0.060	2nsyB	0.374	4.88	0.054	0.683	6.3.1.5	47,101
19	0.060	2qb7A	0.435	4.95	0.055	0.833	3.6.1.11	48,112

(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	0.479	4.28	0.06	0.82	3csbA	GO:0005215 GO:0005363 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
1	0.07	0.347	4.63	0.04	0.62	2xz3A	GO:0005215 GO:0005363 GO:0006810 GO:0015768 GO:0016020 GO:0016021 GO:0019031
2	0.07	0.485	3.76	0.04	0.77	4hs7A	GO:0005363 GO:0015768
3	0.07	0.377	4.18	0.05	0.62	4r0yB	GO:0005215 GO:0005363 GO:0005886 GO:0006810 GO:0006974 GO:0007268 GO:0008643 GO:0014069 GO:0015768 GO:0016020 GO:0019904 GO:0023052 GO:0030054 GO:0030288 GO:0032403 GO:0034289 GO:0035418 GO:0042597 GO:0042956 GO:0043190 GO:0045202 GO:0045211 GO:0055052 GO:0060326 GO:0061136 GO:0070842 GO:1901982 GO:1990060
4	0.07	0.473	4.02	0.04	0.79	1eu8A	GO:0005215 GO:0005886 GO:0006810 GO:0008643 GO:0016020
5	0.07	0.352	5.11	0.01	0.68	4irlB	GO:0000166 GO:0003924 GO:0005215 GO:0005363 GO:0005525 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0042981 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
6	0.07	0.434	4.77	0.08	0.82	4elqA	GO:0046872
7	0.07	0.383	4.53	0.04	0.68	3k01A
8	0.07	0.467	4.08	0.03	0.77	2zyoA	GO:0005363 GO:0015768
9	0.07	0.430	4.70	0.04	0.80	4ryaA	GO:0005215 GO:0006810
10	0.06	0.396	4.68	0.06	0.73	1iruD	GO:0000502 GO:0004175 GO:0004298 GO:0005634 GO:0005737 GO:0005839 GO:0006508 GO:0006511 GO:0008233 GO:0016787 GO:0019773 GO:0042802 GO:0051603 GO:0070062
11	0.06	0.401	4.74	0.07	0.72	2ku1A	GO:0000502 GO:0004175 GO:0004298 GO:0005737 GO:0005839 GO:0006508 GO:0006511 GO:0008233 GO:0010498 GO:0016787 GO:0019773 GO:0051603
12	0.06	0.478	4.17	0.05	0.80	4blbB	GO:0000122 GO:0001501 GO:0001843 GO:0001947 GO:0003281 GO:0003714 GO:0004871 GO:0005215 GO:0005363 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005929 GO:0006355 GO:0006508 GO:0006810 GO:0006974 GO:0007165 GO:0007275 GO:0007368 GO:0008013 GO:0008134 GO:0008643 GO:0015768 GO:0019901 GO:0021513 GO:0021775 GO:0021776 GO:0030288 GO:0034289 GO:0035904 GO:0042597 GO:0042956 GO:0042992 GO:0042994 GO:0043190 GO:0043433 GO:0043588 GO:0045668 GO:0045879 GO:0055052 GO:0060326 GO:0060976 GO:0072372 GO:0097542 GO:0097546 GO:1901621 GO:1901982 GO:1990060 GO:2000059
13	0.06	0.356	5.05	0.04	0.68	1y4cA	GO:0005215 GO:0005363 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
14	0.06	0.411	4.48	0.10	0.71	5a5bD	GO:0000502 GO:0004175 GO:0004298 GO:0005634 GO:0005737 GO:0005739 GO:0005839 GO:0006508 GO:0006511 GO:0008233 GO:0010499 GO:0016787 GO:0019773 GO:0034515 GO:0042175 GO:0043161 GO:0051603
15	0.06	0.368	5.47	0.07	0.75	4ozqB	GO:0000166 GO:0001558 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005819 GO:0005856 GO:0005874 GO:0005886 GO:0007018 GO:0007019 GO:0007080 GO:0008017 GO:0008284 GO:0008574 GO:0010389 GO:0015631 GO:0016020 GO:0016887 GO:0019901 GO:0021685 GO:0021693 GO:0021695 GO:0021766 GO:0021772 GO:0021846 GO:0021987 GO:0030155 GO:0030165 GO:0030334 GO:0030496 GO:0031146 GO:0031641 GO:0032147 GO:0032467 GO:0032487 GO:0033624 GO:0034446 GO:0043066 GO:0043161 GO:0043523 GO:0043524 GO:0045184 GO:0051233 GO:0051301 GO:1902519 GO:1903047 GO:1903429 GO:2000045
16	0.06	0.459	4.34	0.04	0.79	2gh9A	GO:0005363 GO:0015768
17	0.06	0.340	4.85	0.03	0.63	1r6zZ	GO:0003676 GO:0003723 GO:0004521 GO:0005215 GO:0005363 GO:0005737 GO:0005829 GO:0006810 GO:0006974 GO:0007279 GO:0007349 GO:0007367 GO:0008643 GO:0009047 GO:0010526 GO:0015768 GO:0016032 GO:0016246 GO:0016442 GO:0030288 GO:0030422 GO:0030423 GO:0031047 GO:0033227 GO:0034289 GO:0035071 GO:0035087 GO:0035190 GO:0035195 GO:0035197 GO:0042597 GO:0042956 GO:0043190 GO:0045071 GO:0046872 GO:0048102 GO:0051607 GO:0055052 GO:0060326 GO:0070578 GO:0070868 GO:0090502 GO:0098586 GO:1901982 GO:1990060
18	0.06	0.480	4.03	0.06	0.79	3woaA	GO:0003677 GO:0005215 GO:0005363 GO:0006351 GO:0006355 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0043565 GO:0055052 GO:0060326 GO:1901982 GO:1990060

Consensus prediction of GO terms

Molecular Function	GO:0015154
GO-Score	0.48
Biological Processes	GO:0015766
GO-Score	0.48
Cellular Component	GO:0030288	GO:0055052	GO:1990060	GO:0019031	GO:0014069	GO:0030054	GO:0045211
GO-Score	0.13	0.13	0.13	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.

I-TASSER results for job id Rv3424c

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

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