I-TASSER results

I-TASSER results for job id Rv2261c

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

Input Sequence in FASTA format

>protein (140 residues)
MHIAPLISYEMTFSDLTRHAARLGAALLVYQSSTSTFQGSWAQPQLAAQPAVRAVEAGIP
AVHASLSGDSSAFDTRGRRLAWCSAEFNGAIVVNVPLASNVTLYLRLGDWVPVTAFVVMG
AGFAVFLRRSLARVSDCADK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MHIAPLISYEMTFSDLTRHAARLGAALLVYQSSTSTFQGSWAQPQLAAQPAVRAVEAGIPAVHASLSGDSSAFDTRGRRLAWCSAEFNGAIVVNVPLASNVTLYLRLGDWVPVTAFVVMGAGFAVFLRRSLARVSDCADK
Prediction	CCEEEEEEEHHHCHHHHHHHHHHCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEHCCCCCEEEHCCCCCEEEEHCCCCCEEEEEEHCCCCCCCHEHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	96788776445555999999998996999984888999987689999999999999899699977987559988999599985899758999998589999735544568999999999999999998655678877789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MHIAPLISYEMTFSDLTRHAARLGAALLVYQSSTSTFQGSWAQPQLAAQPAVRAVEAGIPAVHASLSGDSSAFDTRGRRLAWCSAEFNGAIVVNVPLASNVTLYLRLGDWVPVTAFVVMGAGFAVFLRRSLARVSDCADK
Prediction	44002001032311420241045404000000020115544233112220211010232010112433200001244412240455331203030426644110223233322312333333322233344444564688
	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

CCEEEEEEEHHHCHHHHHHHHHHCCCEEEEHCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEHCCCCCEEEHCCCCCEEEEHCCCCCEEEEEEHCCCCCCCHEHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
MHIAPLISYEMTFSDLTRHAARLGAALLVYQSSTSTFQGSWAQPQLAAQPAVRAVEAGIPAVHASLSGDSSAFDTRGRRLAWCSAEFNGAIVVNVPLASNVTLYLRLGDWVPVTAFVVMGAGFAVFLRRSLARVSDCADK

2mr6A

0.13

0.12

0.91

0.83

MUSTER

MGVVILVLTERIAEELRKEVQKHDPNVKTVPTKDK---------EKVKEEIEKARKQGRPIVVFVRGGDDERAK---DIAEYAQKEGLRVIVIIVSLRKGYEDKKKKGYDVYTSRNEDEAKKKLKEALEKSGSLEHHHHH

2dyvA

0.16

0.14

0.87

1.25

dPPAS

SKLAVCICHDGMIPELAREAAYKGCNVYIRISGYST----QVNDQWILTNRSNAWHNLMYTVSVNLAGYGQICNFDGTTLVQGHRNPWEIVTGEIY--------------PKMADNARLSWGLENNIYNLGHRGYVAKPG

2w1vA

0.21

0.18

0.84

1.52

wdPPAS

CKVGLGICYDMRFAELAQIYAQRGCQLLVYPGA---FNLTTGPAHWELLQRARAVDNQVYVATASPAGHSTVVDPWGQVLTKAGT-EETILYSDIDLKKLAEIRQQIP-------------------ILKQKRADTVESK

2w1vA

0.21

0.18

0.84

1.03

wMUSTER

CKVGLGICYDMRFAELAQIYAQRGCQLLVYPGA---FNLTTGPAHWELLQRARAVDNQVYVATASPARDSTVVDPWGQVLTKAGT-EETILYSDIDLKKLAEIRQQIP-------------------ILKQKRADTVESK

2w1vA

0.21

0.18

0.84

1.19

wPPAS

CKVGLGICYDMRFAELAQIYAQRGCQLLVYPG--A-FNLTTGPAHWELLQRARAVDNQVYVATASPARDSTVVDPWGQVLTKAGT-EETILYSDIDLKKLAEIRQQIP-------------------ILKQKRADTVESK

2dyvA

0.14

0.12

0.87

2.90

dPPAS2

SKLAVCICHDGMIPELAREAAYKGCNVYIRIS--GY--STQVNDQWILTNRSNAWHNLMYTVSVNLAGYGQICNFDGTTLVQGHRNPWEIVTGEIY--------------PKMADNARLSWGLENNIYNLGHRGYVAKPG

2w1vA

0.21

0.17

0.84

0.91

PPAS

CKVGLGICYDMRFAELAQIYAQRGCQLLVYPGA---FNLTTGPAHWELLQRARAVDNQVYVATASPARDSTVVDPWGQVLTKAGT-EETILYSDIDLKKLAEIRQQIP-------------------ILKQKRADLYTVE

1wsaB2

0.13

0.10

0.79

1.05

Env-PPAS

PRVDILYAHPDDTDVLVNAALQAGAKGIIHAG----MGNGNPF-PLTQNALEKAAKSGVVVARSSRVG-------SGS----------------TTQEAEVDD-KKLGFVATESLNPQKARVLLMLALTKTSDREAIQKI

2d6fA3

0.17

0.14

0.82

0.83

MUSTER

VRVAFIKSY----PDIIKWHLDEGYRGIVIEG----TGLGHCP-DTLIPVIGEAHDMGVPVAMTSQC-------LNGRV--NMNVYSTGRRLLQAGVIPC-------DDMLPEVAYVKMCWVLGPEMAREMMRENIAGER

1sgvB2

0.19

0.08

0.41

1.24

dPPAS

------------------------------------------ARRDLTAAEASAAANGRSLPAVGIDGVYAACDADGRVIALLRDEGSRTRSVAVLRPAT----------------------------------------

(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=-1.82

Estimated TM-score = 0.50±0.15

Estimated RMSD = 8.5±4.5Å

Download Model 2

C-score=-2.47

Download Model 3

C-score=-2.98

Download Model 4

C-score=-2.17

Download Model 5

C-score=-4.86

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	2dyvA	0.737	2.44	0.126	0.857
2	3dlaD	0.725	2.27	0.175	0.857
3	2w1vA	0.723	2.14	0.193	0.836
4	1emsA	0.723	2.47	0.215	0.857
5	2plqA	0.721	2.67	0.164	0.864
6	2vhhC	0.714	2.44	0.169	0.850
7	2gglA	0.706	2.85	0.105	0.864
8	3p8kA	0.701	1.97	0.188	0.793
9	4h5uA	0.700	2.16	0.157	0.814
10	5h8iA	0.693	2.80	0.127	0.850

(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	0.20	10	3dlaB	ONL	Rep, Mult	8,11,12,32,36,42,46,63
2	0.06	3	4if4A	BEF	Rep, Mult	7,8,9,32,35,36,66
3	0.06	3	1gegF	GLC	Rep, Mult	14,56
4	0.06	3	5c2xB	CO3	Rep, Mult	18,56
5	0.04	2	1fo6A	XE	Rep, Mult	14,15
6	0.02	1	2o011	CLA	Rep, Mult	55,56
7	0.02	1	3i4kG	MG	Rep, Mult	5,29,64,65
8	0.02	1	1emsA	NA	Rep, Mult	6,16,17,20,28,30
9	0.02	1	1zpdA	DPX	Rep, Mult	7,17,52

	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	2dyvA	0.737	2.44	0.126	0.857	3.5.1.49	16,18,45
2	0.060	1ovmC	0.509	4.63	0.099	0.829	4.1.1.74	NA
3	0.060	2vbiA	0.514	4.18	0.092	0.807	4.1.1.1	NA
4	0.060	1ozgA	0.526	4.45	0.107	0.871	2.2.1.6	44
5	0.060	2jlaA	0.530	4.63	0.070	0.879	2.2.1.9	28
6	0.060	2vk1A	0.509	4.52	0.061	0.829	4.1.1.1	NA
7	0.060	1emsA	0.723	2.47	0.215	0.857	3.6.1.29	63
8	0.060	1llwA	0.512	4.52	0.074	0.843	1.4.7.1	NA
9	0.060	2jlcB	0.534	4.56	0.077	0.871	2.2.1.9	NA
10	0.060	2vjyA	0.509	4.56	0.061	0.836	4.1.1.1	NA
11	0.060	2x42A	0.534	4.24	0.093	0.814	3.2.1.21	NA
12	0.060	1ddzA	0.516	4.05	0.050	0.771	4.2.1.1	NA
13	0.060	3ey9A	0.519	4.47	0.099	0.857	1.2.2.2	NA
14	0.060	2ihvA	0.525	4.45	0.084	0.843	2.5.1.66	NA
15	0.060	3lq1A	0.538	4.70	0.083	0.907	2.2.1.9	NA
16	0.060	1ofdA	0.513	4.45	0.083	0.821	1.4.7.1	NA
17	0.060	1zpdA	0.531	4.59	0.071	0.879	4.1.1.1	NA
18	0.060	1ybhA	0.513	4.72	0.091	0.864	2.2.1.6	NA
19	0.060	2vhhC	0.714	2.44	0.169	0.850	3.5.1.6	9,36

(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	0.29	0.721	2.67	0.16	0.86	4gylA	GO:0004040 GO:0006807 GO:0016787 GO:0016810
1	0.25	0.723	2.47	0.21	0.86	1emsA	GO:0000166 GO:0003824 GO:0006139 GO:0006807 GO:0008152 GO:0016787 GO:0016810 GO:0047710
2	0.23	0.697	2.79	0.14	0.86	5h8iC	GO:0006596 GO:0006807 GO:0016787 GO:0016810 GO:0050126
3	0.22	0.715	2.68	0.17	0.86	2uxyA	GO:0004040 GO:0006807 GO:0015976 GO:0016787 GO:0016810 GO:0043605
4	0.18	0.665	2.69	0.17	0.80	3ivzA	GO:0000257 GO:0006807 GO:0016787 GO:0016810
5	0.18	0.710	2.05	0.18	0.81	3p8kA	GO:0006807 GO:0016787 GO:0016810
6	0.17	0.713	2.44	0.17	0.85	2vhiA	GO:0003837 GO:0006207 GO:0006208 GO:0006807 GO:0016787 GO:0016810
7	0.13	0.723	2.14	0.19	0.84	2w1vA	GO:0005737 GO:0005739 GO:0005813 GO:0006107 GO:0006528 GO:0006541 GO:0006807 GO:0016787 GO:0016810 GO:0050152 GO:0070062
8	0.12	0.737	2.44	0.13	0.86	2dyuA	GO:0004328 GO:0006807 GO:0016787 GO:0016810
9	0.12	0.708	2.96	0.11	0.87	1erzA	GO:0006807 GO:0016787 GO:0016810 GO:0047417
10	0.12	0.726	2.27	0.17	0.86	3seqA	GO:0000166 GO:0003952 GO:0005524 GO:0005618 GO:0005737 GO:0005886 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874 GO:0040007
11	0.10	0.714	2.44	0.17	0.85	2vhhC	GO:0003837 GO:0006207 GO:0006208 GO:0006807 GO:0016787 GO:0016810
12	0.09	0.676	2.58	0.16	0.81	1j31A	GO:0006807 GO:0016810
13	0.09	0.682	2.24	0.21	0.79	1f89A	GO:0006807 GO:0016787 GO:0016810
14	0.07	0.633	2.24	0.25	0.74	3hkxA	GO:0004040 GO:0006807 GO:0016810
15	0.07	0.593	2.17	0.14	0.70	4f4hB	GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0008795 GO:0009435 GO:0016810 GO:0016874
16	0.07	0.708	2.15	0.15	0.82	4hg3A	GO:0006807 GO:0016787 GO:0016810
17	0.07	0.626	2.90	0.21	0.77	3n05A	GO:0000166 GO:0003952 GO:0005524 GO:0006807 GO:0009435 GO:0016810 GO:0016874
18	0.07	0.639	2.44	0.14	0.77	3wuyA	GO:0006807 GO:0016810

Consensus prediction of GO terms

Molecular Function	GO:0004551	GO:0036094	GO:1901265	GO:0004040	GO:0016815
GO-Score	0.50	0.50	0.50	0.45	0.37
Biological Processes	GO:1901360	GO:0006725	GO:0046483	GO:0006595	GO:0042401	GO:0044270	GO:0043603	GO:0044238	GO:0044699
GO-Score	0.50	0.50	0.50	0.46	0.46	0.44	0.44	0.43	0.38
Cellular Component
GO-Score

(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.