I-TASSER results

Input Sequence in FASTA format

>protein (97 residues)
MPRAARGIRACRGRWVDRLAHQHASGRAAGIRPREVGGAHQSQAQKPYHDATEPLGESLR
YRPAHGDSCINGHRDNPSARESSQFTAGSTAKAVTKL

Predicted Secondary Structure

Sequence	20 40 60 80 \| \| \| \| MPRAARGIRACRGRWVDRLAHQHASGRAAGIRPREVGGAHQSQAQKPYHDATEPLGESLRYRPAHGDSCINGHRDNPSARESSQFTAGSTAKAVTKL
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHCC
Conf.Score	9855666667655788899988655665678755467745665567887655655653454678887665577788655444555667544444449
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 \| \| \| \| MPRAARGIRACRGRWVDRLAHQHASGRAAGIRPREVGGAHQSQAQKPYHDATEPLGESLRYRPAHGDSCINGHRDNPSARESSQFTAGSTAKAVTKL
Prediction	6543354143144421341145345443341445624444565355434423532365153434446412533574453565451443443533477
	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

                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHCC
MPRAARGIRACRGRWVDRLAHQHASGRAAGIRPREVGGAHQSQAQKPYHDATEPLGESLRYRPAHGDSCINGHRDNPSARESSQFTAGSTAKAVTKL

3g06A6

0.19

0.15

0.82

0.78

MUSTER

LAAVATGREMFRLGKLEQIAREKV-RTLALVDEIEVWLAYQNKLKKSLGLTSVT--SEMRFFDVSGVTDLQDAELQVKAAEKS--------------

3g06A6

0.19

0.15

0.82

0.74

dPPAS

AALVATGREMFRLGKLEQIAREKV-RTLALVDEIEVWLAYQNKLKKSLGLTSVT--SEMRFFDVSGVTDLQDAELQVKAAEKS--------------

2kl7A

0.29

0.18

0.60

0.69

wdPPAS

IPEACKGEMKC----IN-----HYGGRSAAV----INDLHGEGPPPPVPPAQHPNPCPPGYEPDDQDSCVD--------------------------

4lm8A

0.19

0.99

0.82

wMUSTER

TQEFADGRGKPHVAFSHLIHNVHNANKAWG-KDNKIPTVAQNIVQDNCHVESDMLTEAKNWRIPTMEVCSSCHVDIDAGKGHSQQLDNSNCIACHNS

2kl7A

0.32

0.19

0.58

0.53

wPPAS

IPEA------CKGKCIN-----HYGGRSAAV----INDLHGEGPPPPVPPAQHPNPCPPGYEPDDQDSCV----D----------------------

2zkrc2

0.38

0.19

0.48

0.79

dPPAS2

--------------AVSELAHQTSTGRAVARIPRVRGG-----------------GTHRSGQGAFGNMCRGGRMFAPT-------------------

3g06A6

0.18

0.15

0.85

0.80

PPAS

LAAVATGREMFRLGKLEQIAREKV-RTLALVDEIEVWLAYQNKLKKSLGLTSVT--SEMRFF---DVSGV-TVTDLQDAELQVK-AAEKS-------

3g06A6

0.18

0.15

0.85

1.00

Env-PPAS

LAAVATGREMFRLGKLEQIAREKV-RTLALVDEIEVWLAYQNKLKKSLGLTSVT--SEMRFF---DVSGV-TVTDLQDAELQVK-AAEKS-------

4jkzA2

0.23

0.22

0.95

0.74

MUSTER

MPKTDD-VTADLASWAGTLAAALTTRRGAMLKTLMAASLHEDTAARLREGFSRPLIESVRDRQAAADALLGA---NAVLSEGRSYSR-QRAETSARI

2rn7A

0.17

0.16

0.97

0.73

dPPAS

RQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVQHERDTGGDDGGLTTAERQRLK-EPERENRELRRSNDIL--RLASAYFAKAEFDRLWKK

(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=-2.22

Estimated TM-score = 0.45±0.15

Estimated RMSD = 8.6±4.5Å

Download Model 2

C-score=-3.03

Download Model 3

C-score=-4.97

Download Model 4

C-score=-4.49

Download Model 5

C-score=-3.43

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	3g06A6	0.666	2.28	0.150	0.825
2	4pufA	0.647	3.23	0.140	0.959
3	3cvrA2	0.605	3.01	0.143	0.866
4	2di4A	0.575	3.54	0.032	0.897
5	4ww0A	0.572	3.60	0.032	0.897
6	2akcB	0.566	3.61	0.067	0.876
7	4ce4c2	0.565	3.39	0.023	0.825
8	1gwxB	0.564	3.81	0.042	0.938
9	1xvpD	0.558	3.73	0.043	0.928
10	4cz8A2	0.556	3.96	0.011	0.907

(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	5	2z4jA	III	Rep, Mult	17,21,36,37,41,55
2	0.05	3	3sb6A	CU	Rep, Mult	17,21
3	0.05	3	2yloA	YLO	Rep, Mult	18,19,37,69,72,73,76,77
4	0.03	2	3attA	MG	Rep, Mult	71,75
5	0.03	2	3v1vA	MG	Rep, Mult	76,78,81
6	0.03	2	5sy7B	NUC	Rep, Mult	6,14
7	0.03	2	3uanB	SGN	Rep, Mult	22,23,93
8	0.03	2	4bwzA	ZN	Rep, Mult	5,9,51
9	0.02	1	3proC	AES	Rep, Mult	96,97
10	0.02	1	1i95K	WO2	Rep, Mult	47,48
11	0.02	1	2xgfA	FE2	Rep, Mult	21,23
12	0.02	1	3gvkA	UUU	Rep, Mult	41,42
13	0.02	1	2rjrB	295	Rep, Mult	61,62
14	0.02	1	2fkwH	BCL	Rep, Mult	8,11,12,19,22
15	0.02	1	2pixA	FLF	Rep, Mult	72,73,76,77,80
16	0.02	1	4gszA	ZN	Rep, Mult	65,67
17	0.02	1	2i10B	NPO	Rep, Mult	9,10,41

	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	3iw0A	0.517	3.54	0.046	0.783	1.14.-.-	NA
2	0.060	1q2lA	0.512	3.79	0.058	0.835	3.4.24.55	NA
3	0.060	1be3A	0.532	3.50	0.049	0.835	1.10.2.2	NA
4	0.060	2ouyA	0.511	4.07	0.045	0.866	3.1.4.17	NA
5	0.060	3hvlB	0.524	3.81	0.031	0.917	2.3.1.48	NA
6	0.060	3no9A	0.525	4.03	0.077	0.856	4.2.1.2	39
7	0.060	1sqbB	0.526	3.52	0.071	0.835	1.10.2.2	18
8	0.060	3lwdA	0.520	3.21	0.014	0.742	3.1.1.31	19,44
9	0.060	2fyuA	0.530	3.49	0.048	0.835	1.10.2.2	NA
10	0.060	1bucA	0.515	4.22	0.067	0.907	1.3.99.2	NA
11	0.060	3evtA	0.514	3.81	0.011	0.835	1.1.1.95	NA
12	0.060	1kb9A	0.510	3.92	0.047	0.856	1.10.2.2	NA
13	0.060	1tkyA	0.443	4.14	0.074	0.835	6.1.1.3	NA
14	0.060	1bucB	0.514	4.22	0.067	0.907	1.3.99.2	NA
15	0.060	1up8A	0.385	5.05	0.021	0.711	1.11.1.18	NA
16	0.060	2p4qA	0.528	3.59	0.022	0.804	1.1.1.44	NA
17	0.060	3hz3A	0.511	4.16	0.118	0.876	2.4.1.5	NA
18	0.060	3gvxB	0.522	3.89	0.080	0.856	1.1.1.2	NA
19	0.060	1vncA	0.538	4.30	0.108	0.928	1.11.1.10	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	0.09	0.650	2.87	0.16	0.91	3g06A	GO:0003824 GO:0004842 GO:0005576 GO:0009405 GO:0016020 GO:0016567 GO:0016874 GO:0020002 GO:0030254 GO:0030430 GO:0033644 GO:0034052 GO:0061630 GO:0070430 GO:2000484
1	0.08	0.647	3.23	0.14	0.96	4pufA	GO:0004842 GO:0005576 GO:0009405 GO:0010942 GO:0016567 GO:0016874 GO:0030254 GO:0030430 GO:0061630 GO:1903124
2	0.07	0.649	3.02	0.15	0.89	3cvrA	GO:0004842 GO:0005576 GO:0009405 GO:0016567 GO:0016874 GO:0030430
3	0.07	0.594	2.71	0.13	0.81	3ckdC	GO:0004842 GO:0005576 GO:0009405 GO:0016567 GO:0016874 GO:0030430
4	0.06	0.422	4.48	0.09	0.82	4pz0A	GO:0008643 GO:0015608 GO:0034219 GO:0043190
5	0.06	0.358	4.45	0.07	0.63	1tplA	GO:0003824 GO:0006520 GO:0006570 GO:0009072 GO:0016829 GO:0016830 GO:0050371
6	0.06	0.362	3.64	0.03	0.57	1g9uA	GO:0005576 GO:0009279 GO:0016020 GO:0046872
7	0.06	0.351	3.88	0.03	0.59	4e4wB	GO:0000404 GO:0000710 GO:0003690 GO:0003697 GO:0005524 GO:0005634 GO:0006281 GO:0006298 GO:0006974 GO:0016887 GO:0030983 GO:0032135 GO:0032139 GO:0032300 GO:0032389
8	0.06	0.351	3.91	0.05	0.59	2wssS	GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0043209 GO:0046933
9	0.06	0.280	4.39	0.04	0.54	4nkhE	GO:0004842 GO:0005576 GO:0009405 GO:0016567 GO:0016874 GO:0030254 GO:0030430 GO:0042025
10	0.06	0.545	3.27	0.05	0.79	3ckdB	GO:0004842 GO:0005576 GO:0009405 GO:0016567 GO:0016874 GO:0030430
11	0.06	0.314	4.16	0.03	0.53	3a79B	GO:0002224 GO:0002376 GO:0002755 GO:0004888 GO:0005794 GO:0005886 GO:0005887 GO:0006954 GO:0006955 GO:0007165 GO:0016020 GO:0016021 GO:0030670 GO:0031410 GO:0034150 GO:0035355 GO:0035663 GO:0042088 GO:0042496 GO:0042498 GO:0042742 GO:0043123 GO:0043507 GO:0045084 GO:0045087 GO:0045121 GO:0045410 GO:0046982 GO:0050702 GO:0050707 GO:0071723 GO:0071726 GO:1900227
12	0.06	0.331	3.57	0.08	0.53	5b0tA	GO:0004842 GO:0005576 GO:0009405 GO:0016567 GO:0016874 GO:0030430 GO:0042025 GO:0042802 GO:0044164 GO:0044314 GO:0085032
13	0.06	0.327	4.67	0.07	0.63	4b8cD	GO:0000076 GO:0000175 GO:0000288 GO:0000289 GO:0000932 GO:0003723 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0006260 GO:0006351 GO:0006355 GO:0006357 GO:0006368 GO:0007089 GO:0016593 GO:0016787 GO:0030015 GO:0032968 GO:0046872 GO:0048478 GO:0090305 GO:0090503
14	0.06	0.287	4.58	0.05	0.53	4uipB	GO:0016020 GO:0016021
15	0.06	0.282	3.97	0.05	0.48	5il7A	GO:0005525 GO:0005622 GO:0007264 GO:0042802
16	0.06	0.282	4.64	0.06	0.52	4ew5A	GO:0016020 GO:0016021
17	0.06	0.276	4.73	0.05	0.54	1ookG	GO:0000902 GO:0004860 GO:0005737 GO:0005886 GO:0005887 GO:0006469 GO:0007155 GO:0007166 GO:0007596 GO:0007597 GO:0007599 GO:0009986 GO:0015057 GO:0016020 GO:0016021 GO:0019221 GO:0030168 GO:0030193 GO:0031362 GO:0042730 GO:0046426 GO:0070062 GO:0070493
18	0.06	0.297	4.79	0.04	0.56	3m18A

Consensus prediction of GO terms

Molecular Function	GO:0061659
GO-Score	0.32
Biological Processes	GO:0051704	GO:0032446	GO:0009306	GO:0071806
GO-Score	0.54	0.54	0.32	0.32
Cellular Component	GO:0033646
GO-Score	0.54

(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 Rv1012

[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]