I-TASSER results

I-TASSER results for job id Rv1209

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

Input Sequence in FASTA format

>protein (122 residues)
MALVLVYLVVLVLVAIVLFAAASLLFGRGEQLPPLPRATTATTLPAFGVTRADVDAVKFT
QVLRGYKTSEVDWVLERLGRELEALRSQLGAIHASSEDAEAESDASNPSRGETVVHYRSD
PA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MALVLVYLVVLVLVAIVLFAAASLLFGRGEQLPPLPRATTATTLPAFGVTRADVDAVKFTQVLRGYKTSEVDWVLERLGRELEALRSQLGAIHASSEDAEAESDASNPSRGETVVHYRSDPA
Prediction	CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	85799999999999999999999985788888888999988788866799888887665644468998999999999999999999999999997655555556677777787777778899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MALVLVYLVVLVLVAIVLFAAASLLFGRGEQLPPLPRATTATTLPAFGVTRADVDAVKFTQVLRGYKTSEVDWVLERLGRELEALRSQLGAIHASSEDAEAESDASNPSRGETVVHYRSDPA
Prediction	43333333333333323333332221143661452467554461476514673055141522344142730240053035315525542562555466474555456575464456746658
	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

CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
MALVLVYLVVLVLVAIVLFAAASLLFGRGEQLPPLPRATTATTLPAFGVTRADVDAVKFTQVLRGYKTSEVDWVLERLGRELEALRSQLGAIHASSEDAEAESDASNPSRGETVVHYRSDPA

4ug1A

0.19

0.11

0.57

1.21

MUSTER

------------------------------------GSHMTSEQFEYHLTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug1A

0.19

0.11

0.57

1.23

dPPAS

------------------------------------GSHMTSEQFEYHLTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug1A

0.19

0.11

0.57

2.00

wdPPAS

------------------------------------GSHMTSEQFEYHLTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug1A

0.19

0.11

0.57

1.57

wMUSTER

-------------------------------------SHMTSEQFEYHLTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug1A

0.20

0.11

0.57

2.31

wPPAS

----------------------------GSHM-----TSEQFEYH---LTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug1A

0.19

0.11

0.57

2.37

dPPAS2

------------------------------------GSHMTSEQFEYHLTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug1A

0.19

0.11

0.57

1.73

PPAS

------------------------------------GSHMTSEQFEYHLTGKEILEKEFKTGLRGYSPEDVDEFLDMVIKDYSTFTQEIEALQAENIRLVQELDNA----------------

4ug3A

0.14

0.07

0.54

1.52

Env-PPAS

---------------------------------------SHMLADKVKLSAKEILEKEFKTGVRGYKQEDVDKFLDMIIKDYETFHQEIEELQQENLQLKKQLEE-----------------

4ug3A

0.14

0.07

0.54

1.19

MUSTER

---------------------------------------SHMLADKVKLSAKEILEKEFKTGVRGYKQEDVDKFLDMIIKDYETFHQEIEELQQENLQLKKQLEE-----------------

4ug3A

0.14

0.07

0.54

1.19

dPPAS

---------------------------------------SHMLADKVKLSAKEILEKEFKTGVRGYKQEDVDKFLDMIIKDYETFHQEIEELQQENLQLKKQLEE-----------------

(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=-2.77

Estimated TM-score = 0.40±0.13

Estimated RMSD = 10.5±4.6Å

Download Model 2

C-score=-3.22

Download Model 3

C-score=-3.49

Download Model 4

C-score=-3.76

Download Model 5

C-score=-4.28

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	2d4yA	0.648	3.07	0.091	0.885
2	4ut1A	0.641	3.23	0.116	0.893
3	4uosA	0.598	3.83	0.033	0.893
4	4ui9I	0.593	4.22	0.076	0.926
5	3euhB	0.593	3.66	0.033	0.869
6	4f4cA4	0.586	3.63	0.055	0.869
7	4jkvA	0.586	3.96	0.126	0.918
8	4rnbA	0.580	4.28	0.051	0.910
9	2p7nA	0.578	4.17	0.115	0.902
10	3v0aB	0.577	4.02	0.042	0.877

(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	4	3l26A	MG	Rep, Mult	63,64,65,66
2	0.08	3	3oe6A	OLC	Rep, Mult	79,80,83,84,87
3	0.06	2	3oe6A	OLC	Rep, Mult	72,75,76,79
4	0.06	2	2i37A	UUU	Rep, Mult	69,70,71,75,76
5	0.06	2	1sumB	FE	Rep, Mult	51,55,76,80
6	0.03	1	2vrzA	ZN	Rep, Mult	83,86
7	0.03	1	1fbmD	RTL	Rep, Mult	85,92
8	0.03	1	3uctA	MN	Rep, Mult	59,70
9	0.03	1	1kejA	CO	Rep, Mult	53,55
10	0.03	1	1pnkA	CA	Rep, Mult	68,70

	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	3no9A	0.522	4.23	0.062	0.811	4.2.1.2	49
2	0.060	1qleC	0.512	4.18	0.065	0.828	1.9.3.1	17
3	0.060	1qd1B	0.329	5.28	0.111	0.680	2.1.2.5,4.3.1.4	NA
4	0.060	1h2aL	0.491	4.15	0.107	0.779	1.12.2.1	NA
5	0.060	1krqA	0.494	4.45	0.055	0.803	1.16.3.1	50
6	0.060	3mddA	0.501	4.34	0.075	0.811	1.3.99.3	52,55,86
7	0.060	1w27A	0.499	3.67	0.078	0.738	4.3.1.24	NA
8	0.060	2vuaA	0.317	5.52	0.034	0.656	3.4.24.69	75,76,82
9	0.060	1vdkA	0.519	4.07	0.052	0.787	4.2.1.2	NA
10	0.060	1udyA	0.505	4.51	0.074	0.820	1.3.99.3	50,76
11	0.060	3b8cA	0.529	3.81	0.033	0.762	3.6.3.6	NA
12	0.060	1eumE	0.497	4.24	0.077	0.795	1.16.3.1	NA
13	0.060	3e04D	0.507	4.15	0.068	0.787	4.2.1.2	84
14	0.060	1jqiA	0.499	4.49	0.109	0.803	1.3.99.2	76
15	0.060	3btaA	0.513	4.22	0.051	0.844	3.4.24.69	NA
16	0.060	1bucA	0.503	4.59	0.091	0.811	1.3.99.2	81
17	0.060	1b8fA	0.516	4.08	0.105	0.779	4.3.1.3	NA
18	0.060	1h2rL	0.491	4.29	0.107	0.787	1.12.2.1	28,49
19	0.060	1yfeA	0.510	4.24	0.112	0.787	4.2.1.2	67

(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	0.38	0.510	2.31	0.18	0.59	4ug1B	GO:0005737 GO:0007049 GO:0008360 GO:0051301
1	0.19	0.472	1.90	0.14	0.52	4ug3A	GO:0005737 GO:0007049 GO:0008360 GO:0051301
2	0.09	0.641	3.23	0.12	0.89	4ut1A	GO:0005198 GO:0009424 GO:0044780
3	0.09	0.648	3.07	0.09	0.89	2d4yA	GO:0005198 GO:0005576 GO:0009288 GO:0009424 GO:0044780 GO:0071973
4	0.07	0.610	3.82	0.05	0.93	5bpwA	GO:0004842 GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
5	0.07	0.593	4.22	0.08	0.93	5a31I	GO:0004842 GO:0005634 GO:0005654 GO:0005680 GO:0005829 GO:0007049 GO:0007067 GO:0016567 GO:0019903 GO:0030071 GO:0031145 GO:0042787 GO:0043161 GO:0051301 GO:0051436 GO:0051437 GO:0051439 GO:0070979
6	0.07	0.568	4.06	0.05	0.89	5bptA	GO:0005680 GO:0030071 GO:0031145
7	0.06	0.421	4.28	0.02	0.69	3peiA	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
8	0.06	0.460	3.67	0.04	0.62	3g9gA	GO:0000144 GO:0000147 GO:0001400 GO:0004857 GO:0005934 GO:0005935 GO:0006897 GO:0007049 GO:0032185 GO:0042802 GO:0043086 GO:0061645
9	0.06	0.359	4.49	0.07	0.61	1pmtA	GO:0004364 GO:0005737 GO:0016740
10	0.06	0.378	5.22	0.08	0.68	1n8pA	GO:0003824 GO:0003962 GO:0004123 GO:0005737 GO:0008652 GO:0016829 GO:0019343 GO:0019344 GO:0019346 GO:0030170 GO:0042802 GO:0044540 GO:0071266 GO:0080146
11	0.06	0.350	4.69	0.05	0.61	4g9hA	GO:0016740
12	0.06	0.368	4.63	0.06	0.60	4b8cB	GO:0000288 GO:0000289 GO:0000749 GO:0000932 GO:0005634 GO:0005737 GO:0006351 GO:0006355 GO:0006357 GO:0006368 GO:0007124 GO:0017148 GO:0030015 GO:0032947 GO:0032968 GO:0051726
13	0.06	0.439	3.90	0.06	0.67	3s84B	GO:0001523 GO:0002227 GO:0005319 GO:0005507 GO:0005576 GO:0005615 GO:0005769 GO:0005788 GO:0005829 GO:0006695 GO:0006810 GO:0006869 GO:0006982 GO:0007159 GO:0008203 GO:0008289 GO:0009986 GO:0010873 GO:0010898 GO:0015485 GO:0016209 GO:0017127 GO:0019430 GO:0030300 GO:0031102 GO:0031210 GO:0032374 GO:0033344 GO:0033700 GO:0034361 GO:0034364 GO:0034371 GO:0034372 GO:0034375 GO:0034378 GO:0034380 GO:0034445 GO:0035634 GO:0042157 GO:0042158 GO:0042627 GO:0042632 GO:0042744 GO:0042803 GO:0043691 GO:0044240 GO:0044267 GO:0045723 GO:0046470 GO:0051006 GO:0055088 GO:0060228 GO:0065005 GO:0070062 GO:0070328 GO:0072562
14	0.06	0.392	5.09	0.04	0.73	2aekA	GO:0016106 GO:0016829 GO:0045482
15	0.06	0.364	4.57	0.05	0.63	3drwA	GO:0000287 GO:0005737 GO:0005975 GO:0006000 GO:0006096 GO:0008443 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0043844 GO:0046835 GO:0046872
16	0.06	0.300	4.85	0.08	0.55	2v9qA	GO:0002042 GO:0005737 GO:0005886 GO:0005887 GO:0006919 GO:0006935 GO:0007155 GO:0007156 GO:0007275 GO:0007399 GO:0007411 GO:0007507 GO:0008046 GO:0009986 GO:0016020 GO:0016021 GO:0016199 GO:0021836 GO:0030154 GO:0030275 GO:0030336 GO:0030424 GO:0033600 GO:0035025 GO:0035385 GO:0042802 GO:0042995 GO:0050772 GO:0050925 GO:0070100
17	0.06	0.337	5.21	0.05	0.64	1o7dA	GO:0003824 GO:0004553 GO:0004559 GO:0005764 GO:0005975 GO:0006013 GO:0006517 GO:0007611 GO:0008152 GO:0008270 GO:0015923 GO:0016787 GO:0016798 GO:0030246 GO:0046872
18	0.06	0.386	4.63	0.03	0.72	4n0rA	GO:0005975
19	0.06	0.374	4.05	0.03	0.61	3mydA	GO:0005886 GO:0006810 GO:0009306 GO:0015031 GO:0016020 GO:0016021 GO:0044780 GO:0044781
20	0.06	0.294	5.09	0.00	0.59	2cv6A	GO:0045735

Consensus prediction of GO terms

Molecular Function	GO:0005198	GO:0019903	GO:0004842
GO-Score	0.17	0.07	0.07
Biological Processes	GO:0051301	GO:0007049	GO:0008360	GO:0030031	GO:0070925	GO:0044781
GO-Score	0.54	0.54	0.50	0.35	0.35	0.35
Cellular Component	GO:0005737	GO:0044461
GO-Score	0.50	0.35

(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.