I-TASSER results

I-TASSER results for job id Rv2120c

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

Input Sequence in FASTA format

>protein (160 residues)
MTHVLVLLLALLIGVVAGLRSLTAPAVVSWAAFLGWINLHGTWASWMGNFVTVVIVSVLA
VAELVNDKRPKTPPRTVTPVFAVRIILGAFAGAVIGTAWGYRWGGLGAGVIGAVLGTMGG
YQARTRLVAARGGHDLPIALLEDSVAVLGGFAIVAAAAAL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTHVLVLLLALLIGVVAGLRSLTAPAVVSWAAFLGWINLHGTWASWMGNFVTVVIVSVLAVAELVNDKRPKTPPRTVTPVFAVRIILGAFAGAVIGTAWGYRWGGLGAGVIGAVLGTMGGYQARTRLVAARGGHDLPIALLEDSVAVLGGFAIVAAAAAL
Prediction	CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	9857799999999999987787799999999998988889974666467589999999999999975589999887755789999999778887546778747899999999999999999999998876478875678999999999999999997549
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTHVLVLLLALLIGVVAGLRSLTAPAVVSWAAFLGWINLHGTWASWMGNFVTVVIVSVLAVAELVNDKRPKTPPRTVTPVFAVRIILGAFAGAVIGTAWGYRWGGLGAGVIGAVLGTMGGYQARTRLVAARGGHDLPIALLEDSVAVLGGFAIVAAAAAL
Prediction	6421133331331131013221301000011133331637432132133330330022101111223424633634333310321212120111013454331100000000020002102311332254451441210000100011111311332336
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC
MTHVLVLLLALLIGVVAGLRSLTAPAVVSWAAFLGWINLHGTWASWMGNFVTVVIVSVLAVAELVNDKRPKTPPRTVTPVFAVRIILGAFAGAVIGTAWGYRWGGLGAGVIGAVLGTMGGYQARTRLVAARGGHDLPIALLEDSVAVLGGFAIVAAAAAL

4hzuS

0.16

0.14

0.86

1.00

wPPAS

MTKKENTIAAVLIAMTVALSILLCEVGIYTSAILGRR----------------MGLLVGGASGFLIDILGYPV---CLFSLVIHGTQGLVVGWLLPRHHKGILLPLLVGSLVMVIGYCLATTLLFGWPAG----SIFGNVVQVGFGAGVTLSIVGPLTRL

4ke2A

0.13

0.99

1.10

dPPAS2

AATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKA--LETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAA

4hzuS

0.16

0.96

0.95

MUSTER

MSLKENTIAAVLIAMTVALSILV---VIPIPATKGIVTLCEVGSAILYGRR--MGLLVGGASGFLIDILTGYPV-WCLFSLVIHGTQGLVVGWLLPRHHKGIRSMLLPLLVGSLVMVIGYCLATTLLFGWPAGASIFGNVVQVGFGAGVTLSIVGPLTRL

4ke2A

0.13

0.99

0.70

dPPAS

AATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKA--LETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAA

4hzuS

0.15

0.13

0.88

0.78

wdPPAS

MTKKENTIAAVLIAMTVALSILLCEVGIYTSAIL------GRRMGLLVGGASGFLIDILTGYPVWC-----------LFSLVIHGTQGLVVGWLLPRHHKGILLPLLVGSLVMVIGYCLATTLLFGWPAGLAS--IFGNVVQVGFGAGVTLSIVGPLTRL

4hzuS

0.16

0.14

0.89

0.95

wMUSTER

GSLKENTIAAVLIAMTVALSILLCEVGIYTSAILGRR----------------MGLLVGGASGFLIDILTGYPV-WCLFSLVIHGTQGLVVGWLLPRHHKGIRSMLLPLLVGSLVMVIGYCLATTLLFGWPAGASIFGNVVQVGFGAGVTLSIVGPLTRL

5a43A

0.19

0.14

0.72

0.85

wPPAS

I--KSLFAVIIGGSVGCTLRWLLSTKFNSLF--------------------------------------PNLPPGTLVVNLLAGLIIGTLAYFLRQPHLDPFWKLITTGLCGGL--TFSTFSVEVFALLQAG--NYIWALTSVLVHVIGSLITALGFFII

4hzuS

0.15

0.13

0.86

1.00

dPPAS2

MTKKENTIAAVLIAMTVALSILLCEVGIYTSAIL-----YGRRMGLLVGGASGFLIDILTGYPVWC-----------LFSLVIHGTQGLVVGWLLPRHHKGILLPLLVGSLVMVIGYCLATTLLFGWPAG------LASIFGNVVQVGFGAGVTLSIVGP

4hzuS

0.17

0.15

0.91

0.97

PPAS

MTKKENTIAAVLIAMTVALSILV---VIPIPATKGIVTLCEVGIYTSA----RMGLLVGGASGFLIDILTGYPV--CLFSLVIHGTQGLVVGWLLPRHHKGILLPLLVGSLVMVIGYCLATTLLFGWPAG------LASIFGNVVQVGFGAGVTLSIVGP

1n0eB

0.11

0.09

0.84

0.70

Env-PPAS

TTENLYFQGHMLLGTFNN-R-ISLPAKLRAFFEGSIVINRGFENCLEVRK--------PQDFQKYFEQFNSFPSTQKDTRTLKRLIFANANFVDVDTAGRVLIPNNLINDAKVLIGQFDHLEIKKLYEDYLANSESLETVAERM----------------

(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=-1.57

Estimated TM-score = 0.52±0.15

Estimated RMSD = 8.3±4.5Å

Download Model 2

C-score=-3.37

Download Model 3

C-score=-2.56

Download Model 4

C-score=-2.24

Download Model 5

C-score=-3.78

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	4hzuS	0.813	1.70	0.146	0.900
2	4rfsS	0.737	2.60	0.125	0.900
3	4tkrA	0.720	2.57	0.146	0.900
4	3rlbA	0.708	2.69	0.112	0.894
5	5kbwA	0.703	3.04	0.097	0.900
6	3p5nA	0.699	2.82	0.139	0.900
7	4m58A	0.698	2.97	0.083	0.900
8	4huqS	0.682	3.02	0.120	0.887
9	5d0yA	0.664	2.87	0.094	0.863
10	4z7fA	0.663	3.26	0.155	0.875

(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	0.07	4	1x92B	M7P	Rep, Mult	63,66
2	0.06	3	3ar7A	PTY	Rep, Mult	57,85,89,92
3	0.06	3	5kc0A	RBF	Rep, Mult	73,76,77,83,120,124,135,138,139,142,143
4	0.04	2	3retB	PYR	Rep, Mult	32,108,150
5	0.04	2	4xk8L	CLA	Rep, Mult	59,91
6	0.04	2	3aqtB	RCO	Rep, Mult	12,25,28,29,32,58,59,62,90
7	0.04	2	1bjyB	CTC	Rep, Mult	141,145,148
8	0.02	1	3ar2A	NA	Rep, Mult	12,13,15,16,63
9	0.02	1	3p5nA	RBF	Rep, Mult	19,82,84,87,116,120,142,143,146
10	0.02	1	3e3gD	SO4	Rep, Mult	73,75
11	0.02	1	5d92A	8K6	Rep, Mult	28,143
12	0.02	1	2h2sA	SEK	Rep, Mult	30,34,157
13	0.02	1	2yxhA	MG	Rep, Mult	117,143
14	0.02	1	2a1oA	OXY	Rep, Mult	109,113
15	0.02	1	3dhdA	POP	Rep, Mult	20,135
16	0.02	1	1b5dA	DCM	Rep, Mult	75,84

	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	1rqiA	0.516	5.22	0.045	0.912	2.5.1.10	NA
2	0.060	1ffuB	0.492	4.31	0.082	0.794	1.2.99.2	NA
3	0.060	1z11A	0.481	4.98	0.054	0.812	1.14.14.1	NA
4	0.060	2pywA	0.512	4.64	0.052	0.812	2.7.1.100	NA
5	0.060	3b8cB	0.518	4.53	0.103	0.838	3.6.3.6	62,82,85
6	0.060	2vn0A	0.491	4.67	0.045	0.806	1.14.14.1	NA
7	0.060	1n6bA	0.483	4.66	0.045	0.800	1.14.14.1	NA
8	0.060	3b8eA	0.497	4.50	0.057	0.794	3.6.3.9	NA
9	0.060	3b8eC	0.518	4.35	0.044	0.825	3.6.3.9	20,82,109
10	0.060	2f89F	0.501	5.15	0.038	0.831	2.5.1.1,2.5.1.10	NA
11	0.060	3ixzA	0.496	4.32	0.082	0.787	3.6.3.10	NA
12	0.060	1hm7B	0.489	5.07	0.072	0.850	4.2.3.7,4.6.1.5	NA
13	0.060	2j1pB	0.477	5.62	0.064	0.887	2.5.1.1,2.5.1.10,2.5.1.29	NA
14	0.060	3b8cA	0.518	4.55	0.096	0.844	3.6.3.6	NA
15	0.060	7reqB	0.524	4.26	0.075	0.756	5.4.99.2	NA
16	0.060	2ve3A	0.491	4.75	0.038	0.781	1.14.-.-	NA
17	0.060	2i2xA	0.492	4.99	0.072	0.856	2.1.1.90	114,116
18	0.060	3dbmA	0.402	5.13	0.032	0.706	4.2.1.92	61,64,79
19	0.060	7reqD	0.524	4.26	0.075	0.756	5.4.99.2	59

(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	0.34	0.813	1.70	0.15	0.90	4hzuS	GO:0016020 GO:0016021
1	0.29	0.717	2.64	0.15	0.90	4tkrB	GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
2	0.25	0.709	2.73	0.11	0.90	4muuA	GO:0005886 GO:0015234 GO:0015888 GO:0016020 GO:0016021 GO:0071934
3	0.24	0.682	3.02	0.12	0.89	4huqS	GO:0005215 GO:0006810 GO:0016020 GO:0016021
4	0.24	0.667	3.29	0.15	0.89	4z7fB	GO:0005215 GO:0006810 GO:0016020 GO:0016021
5	0.24	0.675	2.97	0.10	0.89	5d3mC	GO:0005215 GO:0006810 GO:0016020 GO:0016021
6	0.23	0.737	2.60	0.12	0.90	4rfsS	GO:0005215 GO:0006810 GO:0016020 GO:0016021
7	0.18	0.696	3.13	0.10	0.90	4dveA	GO:0005886 GO:0006810 GO:0015225 GO:0015878 GO:0016020 GO:0016021
8	0.11	0.699	2.82	0.14	0.90	3p5nA	GO:0005215 GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0032217 GO:0032218
9	0.09	0.698	2.97	0.08	0.90	4m58A	GO:0000041 GO:0016020 GO:0016021
10	0.07	0.576	3.51	0.08	0.81	5do7A	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010212 GO:0010949 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045177 GO:0045796 GO:0046982 GO:0055085
11	0.07	0.613	3.41	0.06	0.84	5do7D	GO:0005524 GO:0005886 GO:0006810 GO:0007584 GO:0007588 GO:0010949 GO:0015248 GO:0015914 GO:0015918 GO:0016020 GO:0016021 GO:0016324 GO:0016887 GO:0017127 GO:0030299 GO:0033344 GO:0042493 GO:0042626 GO:0042632 GO:0043190 GO:0043235 GO:0045796 GO:0046982 GO:0055085 GO:0055092
12	0.07	0.524	4.23	0.05	0.78	4f4cA	GO:0000166 GO:0005524 GO:0006810 GO:0006855 GO:0008559 GO:0010038 GO:0015562 GO:0016020 GO:0016021 GO:0016324 GO:0016787 GO:0016887 GO:0042626 GO:0042908 GO:0045087 GO:0050829 GO:0055085 GO:0093002
13	0.07	0.357	4.68	0.06	0.59	3qf7A	GO:0000166 GO:0005524 GO:0006281 GO:0006974 GO:0016787 GO:0046872
14	0.07	0.375	5.49	0.06	0.69	4pl0B	GO:0000166 GO:0005524 GO:0005886 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0016887 GO:0030153 GO:0042626 GO:0043213 GO:0055085
15	0.06	0.416	3.16	0.08	0.54	3b5wA	GO:0000166 GO:0005319 GO:0005524 GO:0005886 GO:0006810 GO:0006869 GO:0008144 GO:0008289 GO:0015437 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0034040 GO:0042626 GO:0043190 GO:0055085 GO:1901264
16	0.06	0.425	4.56	0.06	0.64	5c73A	GO:0000166 GO:0005524 GO:0006810 GO:0016021 GO:0016887 GO:0042626 GO:0055085
17	0.06	0.396	5.82	0.06	0.78	2vbfA	GO:0000287 GO:0003824 GO:0009082 GO:0016831 GO:0030976 GO:0046872 GO:0047433
18	0.06	0.367	5.51	0.07	0.68	3wmgA	GO:0000166 GO:0005524 GO:0006810 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085

Consensus prediction of GO terms

Molecular Function	GO:0015234
GO-Score	0.47
Biological Processes	GO:0071934
GO-Score	0.47
Cellular Component	GO:0016021	GO:0005886
GO-Score	0.80	0.47

(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.