I-TASSER results

Input Sequence in FASTA format

>protein (108 residues)
MLLPLGPPLPPDAVVAKRAESGMLGGLSVPLSWGVAVPPDDYDHWAPAPEDGADVDVQAA
EGADAEAAAMDEWDEWQAWNEWVAENAEPRFEVPRSSSSVIPHSPAAG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MLLPLGPPLPPDAVVAKRAESGMLGGLSVPLSWGVAVPPDDYDHWAPAPEDGADVDVQAAEGADAEAAAMDEWDEWQAWNEWVAENAEPRFEVPRSSSSVIPHSPAAG
Prediction	CCCCCCCCCCCCCEEEEHCCCCCHCCCEHCCCCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	988889999986555554566755575555655655799887788889866677766556789876567787646777777676556776667888888888998899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MLLPLGPPLPPDAVVAKRAESGMLGGLSVPLSWGVAVPPDDYDHWAPAPEDGADVDVQAAEGADAEAAAMDEWDEWQAWNEWVAENAEPRFEVPRSSSSVIPHSPAAG
Prediction	742444442366324244354211121323242133133742642245465666345635643634434564155164255244664544252454443224444668
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCEEEEHCCCCCHCCCEHCCCCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
MLLPLGPPLPPDAVVAKRAESGMLGGLSVPLSWGVAVPPDDYDHWAPAPEDGADVDVQAAEGADAEAAAMDEWDEWQAWNEWVAENAEPRFEVPRSSSSVIPHSPAAG

5fmwA

0.14

1.00

0.79

MUSTER

AVNITSENLIDDVVSLIRGTRKYAFELKEKLLRGTVIDVTDFVNWASSINDAPVLISQKLSPPVKMKNAHLKKQNLERAIEDYINEFSVRKCHTCQNGGILMDGKPFK

4cwuT

0.19

0.13

0.67

0.77

dPPAS

-------------------------------APGLGVQTVDVQETQTSPVASAVADAAVQAVAAAASKTSTEVQT-DPWMFRVSAPRRPRGSRKYGAASALLPE----

4cwuT

0.17

0.10

0.61

0.66

wdPPAS

-------------------APGL--GVTVDVQ----ETQTS------PVASAVADAAVQAVAAAASKTSTEVQTD------WMFRVSAPRRPRGSRASALLPE-----

5fj8O

0.14

0.96

0.83

wMUSTER

NVISLGSLTVEDYLSSVTSMKYTISSLFVQLGYLIQISKLHY---TPIEDLWQFLYEKHYKNIPRNSPLSDLKKRSQAKMNAKTDFAK-IINKPNELSQILTVDPKTS

1jhnA3

0.40

0.23

0.57

0.67

wPPAS

---PVNPS-PED----QK-----------PEDWD-AVKPDDWNEDAPA--------------PDEEAQRPMIDNNYKG--KWKP-N--PNYQKPRK----IPN-PD--

2e7iA3

0.19

0.14

0.72

0.84

dPPAS2

VMHSLAK--KDAWVVMDENCVAARAGLNI-----ALVPKTDYPDYAITPENFAQTIEETKKRGEVVLAL---------------------ITYPDGNYGNL--PDVKK

2crzA

0.24

0.19

0.82

0.76

PPAS

SGPP-GPCLPPRLQGRPKAKE-------IQLRWG---PPL-VDGGSPMSPIEKDEPREVYQGSEVECTVSS-----LPGKTYSAANKPFSEKCDITTAPGSG--PSSG

2lwfA

0.23

0.21

0.94

0.72

Env-PPAS

ELLPITEAIPSASVYAVYDKSDELQGISRNIAASVSA------HLKSVPELCGSVKVGIVEEPDKAVL-TQAWKLWIEEHIKVTGKVPPGNKSGNNVKVTLEHHHHHH

5fj8O

0.14

0.96

0.79

MUSTER

NVISLGSLTVEDYLSSVTSMKYTISSLFVQLGYLIQISKLHY---TPIEDLWQFLYEKHYKNIPRNSPLSDLKKRSQAKMNAKTDFAK-IINKPNELSQILTVDPKTS

2mcdA

0.21

0.18

0.83

0.68

dPPAS

------------------MRGSHHHHHHGSVSFGAPSPLEDEINYMTPPEQEAQPGALAAEGPLAGLPVTRSDARVLIFNEWEERKSEPWLRLDMSDKAIFRRYPHLR

(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=-4.17

Estimated TM-score = 0.27±0.08

Estimated RMSD = 13.8±3.9Å

Download Model 2

C-score=-4.33

Download Model 3

C-score=-4.54

Download Model 4

C-score=-4.50

Download Model 5

C-score=-4.85

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	4wwxB	0.483	4.46	0.059	0.870
2	4yh5A	0.456	4.47	0.129	0.843
3	1gntA	0.454	4.26	0.048	0.787
4	3hpgB2	0.453	4.16	0.032	0.759
5	1oa0A	0.452	4.45	0.075	0.806
6	5i32A	0.450	4.42	0.047	0.778
7	2f2bA	0.449	4.39	0.065	0.778
8	2abmA	0.447	4.25	0.037	0.768
9	2bw3A2	0.447	4.69	0.020	0.870
10	3mktA	0.447	4.77	0.020	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	0.11	5	3e7lC	ZN	Rep, Mult	72,75
2	0.07	3	3as0A	SAU	Rep, Mult	43,45,90
3	0.07	3	2a68P	MG	Rep, Mult	75,78
4	0.04	2	1wdc2	III	Rep, Mult	72,73,74,75,76,77,78,79,80,81,82,83,84,85,88,89
5	0.04	2	1c6v1	III	Rep, Mult	15,17,18,25
6	0.04	2	2wsc4	CLA	Rep, Mult	24,29,39,45,46
7	0.02	1	2wsc3	CLA	Rep, Mult	24,28,29,31
8	0.02	1	4jbeA	CA	Rep, Mult	69,72
9	0.02	1	3fy4C	PO4	Rep, Mult	91,92,95
10	0.02	1	1utzA	PF3	Rep, Mult	103,104
11	0.02	1	3gyyA	ZN	Rep, Mult	81,85
12	0.02	1	4a8fA	MG	Rep, Mult	71,108

	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	3hbxA	0.415	4.73	0.067	0.778	4.1.1.15	48
2	0.060	1a6rA	0.424	4.33	0.040	0.732	3.4.22.40,3.4.22.-	NA
3	0.060	1ywgO	0.414	4.34	0.071	0.732	1.2.1.12	NA
4	0.060	2hfuA	0.416	4.37	0.049	0.713	2.7.1.36	NA
5	0.060	1k3uA	0.423	4.49	0.053	0.768	4.2.1.20	NA
6	0.060	1rv8B	0.327	4.84	0.096	0.620	4.1.2.13	NA
7	0.060	2gwdA	0.451	4.69	0.093	0.880	6.3.2.2	NA
8	0.060	2bkwA	0.422	4.31	0.039	0.759	2.6.1.44	NA
9	0.060	1p57A	0.280	4.87	0.013	0.537	3.4.21.106	26,36,50
10	0.060	2jc9A	0.415	4.12	0.050	0.694	3.1.3.5	NA
11	0.060	2hzpA	0.434	4.35	0.058	0.778	3.7.1.3	9,13
12	0.060	1k6yA	0.419	4.10	0.010	0.713	2.7.7.49	59
13	0.060	1bjoA	0.426	4.38	0.058	0.778	2.6.1.52	NA
14	0.060	2a2dA	0.419	4.16	0.022	0.676	2.7.1.157,2.7.1.-	NA
15	0.060	3f9kI	0.445	4.58	0.043	0.806	2.7.7.49	78,80,93
16	0.060	1c7jA	0.364	4.43	0.082	0.685	3.1.1.-	NA
17	0.060	1cb7B	0.416	4.08	0.070	0.722	5.4.99.1	NA
18	0.060	1xizB	0.428	4.82	0.061	0.815	2.7.1.69	27
19	0.060	2hfsA	0.418	4.46	0.049	0.722	2.7.1.36	65

(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	0.13	0.285	5.38	0.05	0.60	1yl5A	GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0008652 GO:0008839 GO:0009085 GO:0009089 GO:0016491 GO:0016726 GO:0019877 GO:0050661 GO:0051287 GO:0055114 GO:0070402 GO:0070404
1	0.07	0.452	4.30	0.05	0.79	1e1dA	GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
2	0.06	0.378	4.60	0.07	0.73	2ivnA	GO:0000049 GO:0000408 GO:0002949 GO:0003727 GO:0005737 GO:0008033 GO:0016740 GO:0016746 GO:0046872 GO:0061711
3	0.06	0.366	4.76	0.04	0.66	3pasB	GO:0003677 GO:0006351 GO:0006355
4	0.06	0.368	4.21	0.05	0.67	4gq0A	GO:0001523 GO:0001758 GO:0004033 GO:0005576 GO:0005764 GO:0005829 GO:0006081 GO:0007586 GO:0008202 GO:0016488 GO:0016491 GO:0044597 GO:0044598 GO:0045550 GO:0047718 GO:0055114 GO:0070062
5	0.06	0.350	4.58	0.05	0.69	4bgaC	GO:0000166 GO:0005524 GO:0006040 GO:0006508 GO:0008233 GO:0008237 GO:0009254 GO:0016773 GO:0046872
6	0.06	0.343	4.81	0.05	0.66	3b8bA	GO:0000103 GO:0000287 GO:0005737 GO:0008441 GO:0016020 GO:0016311 GO:0046854
7	0.06	0.336	5.01	0.01	0.66	3bubA	GO:0000139 GO:0003824 GO:0004553 GO:0004559 GO:0004572 GO:0005783 GO:0005794 GO:0005795 GO:0005975 GO:0006013 GO:0006486 GO:0006487 GO:0006491 GO:0006517 GO:0008152 GO:0008270 GO:0015923 GO:0016020 GO:0016021 GO:0016063 GO:0016787 GO:0016798 GO:0030246 GO:0035010 GO:0046872
8	0.06	0.449	4.39	0.07	0.80	1gnlA	GO:0003824 GO:0005737 GO:0016491 GO:0016661 GO:0046872 GO:0050418 GO:0051536 GO:0051539 GO:0055114
9	0.06	0.284	5.16	0.09	0.62	2aizP	GO:0009279 GO:0016020 GO:0016021
10	0.06	0.318	4.97	0.05	0.62	1qzmA	GO:0000166 GO:0003677 GO:0004176 GO:0004252 GO:0005524 GO:0005737 GO:0005829 GO:0006508 GO:0006515 GO:0008233 GO:0008236 GO:0009408 GO:0016787 GO:0016887 GO:0030163 GO:0033554 GO:0043565
11	0.06	0.351	5.00	0.06	0.73	4mo5A	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
12	0.06	0.314	4.61	0.06	0.57	2krkA	GO:0000165 GO:0000166 GO:0000209 GO:0000502 GO:0002223 GO:0002479 GO:0003712 GO:0005102 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005838 GO:0006366 GO:0006521 GO:0008134 GO:0008540 GO:0016020 GO:0016234 GO:0016787 GO:0016887 GO:0017025 GO:0022624 GO:0030163 GO:0030433 GO:0031145 GO:0031410 GO:0031531 GO:0031595 GO:0031597 GO:0033209 GO:0036402 GO:0038061 GO:0038095 GO:0043069 GO:0043161 GO:0043488 GO:0045892 GO:0045893 GO:0045899 GO:0050852 GO:0051436 GO:0051437 GO:0060071 GO:0070062 GO:0072562 GO:0090090 GO:0090261 GO:0090263 GO:1901800
13	0.06	0.450	4.86	0.05	0.87	4zfvA	GO:0005524 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773
14	0.06	0.327	4.89	0.06	0.65	4tlxA	GO:0000166 GO:0004497 GO:0016491 GO:0055114
15	0.06	0.402	5.04	0.03	0.80	3qbxB	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
16	0.06	0.380	4.69	0.06	0.73	2pizA	GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
17	0.06	0.311	5.44	0.05	0.69	3cqyA	GO:0000166 GO:0005524 GO:0005975 GO:0006040 GO:0009254 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0097175
18	0.06	0.304	4.77	0.03	0.59	3ktbA	GO:0003677 GO:0045892 GO:0046685

Consensus prediction of GO terms

Molecular Function	GO:0003824
GO-Score	0.33
Biological Processes	GO:0044710
GO-Score	0.47
Cellular Component	GO:0044444
GO-Score	0.36

(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 Rv2348c

[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]