I-TASSER results

I-TASSER results for job id Rv1137c

[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)
MLSARCHIRHIGSPGKDARCAHLSATLRPGIGISPTNVGNATVLADGTPAKPIQGAETMQ
RARHTGSCFSANARGPAISSGNPSRAGCGVPSSTTTPSSTPQAIRLLACTDSDALTVTRT
AR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLSARCHIRHIGSPGKDARCAHLSATLRPGIGISPTNVGNATVLADGTPAKPIQGAETMQRARHTGSCFSANARGPAISSGNPSRAGCGVPSSTTTPSSTPQAIRLLACTDSDALTVTRTAR
Prediction	CCCCCEEEEHCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCEEEEHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEEEEEHCC
Conf.Score	98764566656888876544445454578867887766755787588888877656777776546764466677876678998777788888888999986776666536788567766479
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLSARCHIRHIGSPGKDARCAHLSATLRPGIGISPTNVGNATVLADGTPAKPIQGAETMQRARHTGSCFSANARGPAISSGNPSRAGCGVPSSTTTPSSTPQAIRLLACTDSDALTVTRTAR
Prediction	74434030431354455230441433143424143442341312254343542643632541444341243535243155444533213334544446433410201103454214234458
	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

CCCCCEEEEHCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCEEEEHCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEEEEEHCC
MLSARCHIRHIGSPGKDARCAHLSATLRPGIGISPTNVGNATVLADGTPAKPIQGAETMQRARHTGSCFSANARGPAISSGNPSRAGCGVPSSTTTPSSTPQAIRLLACTDSDALTVTRTAR

5ay6A1

0.16

0.97

0.83

MUSTER

AAAVSYKVGTAGSPSKSATNSHNYDVVYSSTGIANPVSGNNEYLVDIKENGVIVATGKVAYDAATNELVSSTIDYKGASP--VT--GSMTTTRINAAGTTVNLADLIVNASGADDAEVVAGK

4cfiA2

0.12

0.10

0.84

0.58

dPPAS

----------MVQTGQTLGTIKVAIDSSWSSGSTGQETTQINVVSDGKGGNQALSSTAVTAVFGSSTAGTGTAASPSFQTLALSTSATSALSATDQANATAMVAQINAVNKP----------

4ruwA2

0.39

0.30

0.75

0.57

wdPPAS

--GAPVAARTVGEDGLDG-WAQLTAS-RPGLRLS-KNRGQAD---DGTAVRAV------------------NRAGVALDSGT-SRDRCTV---ETWRGALPPGARLEACVGADGILASRTET

5ay6A1

0.22

0.20

0.90

0.68

wMUSTER

AAAVSYKVGTAGSP---------SKT---NVVDSATNSHNYDVVYSSTIANPVSGNNEYLDIKENGVIVATAATNELVSSTIDYKGASPVTGSMTTAGTTVNLADLIVNASGADDAEVVAGK

4ruwA2

0.47

0.34

0.72

0.56

wPPAS

--GAPVAARTVGEDGLDG-WAQLTAS-RPGLRLS-KNRGQA----DGTAV----------RAR--------NRAGVALDSGT-SRDRCTV--ETALP---PGA-RLEACVGADGILASRTET

4pgaA2

0.19

0.16

0.80

0.54

dPPAS2

--SPQVDIAY-SYGNVTD--TAYKALAQNGA--------KALIHA-GTGNGSSRVVPALQQLRKNGHVNQ----GGVLRNAEQPDDKNDWVVAHDL---NPEKARILAMV---AMTKTQDSK

4ruwA2

0.40

0.30

0.76

0.57

PPAS

--GAPVAARTVGEDGLDG-WAQLTAS-RPGLRLS-KNRGQAD---DGTAVRAV-------R----------NRAGVALDSGT-SRDRCTV---ETWRGALPPGARLEACVGADGILASRTET

5eiqA1

0.28

0.18

0.66

0.68

Env-PPAS

--------SYHPKP-------WLGAQ--PATVVTPVNVAWRFGLFPG-EIAPLL---FRDVSSELAE-FF-------LEEVTPAQGGCRRPDWGPGVWSQP----------SDVLLVTE---

4cfiA2

0.14

0.12

0.86

0.81

MUSTER

MVQTGQTLGTI-------KVAIDSSGAAWSSGSTGQETTQINVVSDGKQNNQALSSTAVTAVFGSSTAGTGTAASPSFQTLALSTSATSALSATDQANATAMVAQINAVNKP----------

3zifN

0.13

0.11

0.81

0.54

dPPAS

--------------EGRIYVPYVTARLPKWSGSVQDKTGSNM---LGGVVLPPNS------QAHRTETVGTEATRDNLHAEGARRPEDQTPYMILVEDSLGGLKRRMDLLEESNQQLLATLN

(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=-3.73

Estimated TM-score = 0.31±0.10

Estimated RMSD = 12.9±4.2Å

Download Model 2

C-score=-4.46

Download Model 3

C-score=-4.62

Download Model 4

C-score=-4.50

Download Model 5

C-score=-5.00

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	4d9gA	0.542	4.30	0.044	0.926
2	2efyA	0.542	3.85	0.066	0.869
3	4aecA	0.542	3.86	0.047	0.869
4	2isqA	0.541	3.89	0.037	0.877
5	2d1fA	0.540	4.21	0.044	0.910
6	2q3dA	0.539	3.96	0.085	0.869
7	2rkbA	0.539	4.33	0.097	0.926
8	4lmaA	0.538	3.95	0.057	0.869
9	3vbeA	0.538	3.92	0.057	0.869
10	1d6sA	0.537	3.92	0.046	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	0.13	9	4m0kC	CA	Rep, Mult	57,61
2	0.06	4	3d4vD	NUC	Rep, Mult	9,100,102
3	0.04	3	4kt0J	CLA	Rep, Mult	107,110
4	0.03	2	5cy4A	CA	Rep, Mult	2,3,4,112
5	0.03	2	1rmgA	GLC	Rep, Mult	95,97
6	0.03	2	3f1fW	MG	Rep, Mult	63,65
7	0.03	2	1comA	PRE	Rep, Mult	6,73,105
8	0.01	1	2vn4A	MAN	Rep, Mult	80,81
9	0.01	1	2o01L	CLA	Rep, Mult	48,49
10	0.01	1	3eukA	MG	Rep, Mult	99,100
11	0.01	1	2g0yA	CA	Rep, Mult	13,34
12	0.01	1	1esqB	TZP	Rep, Mult	34,41,43,44
13	0.01	1	4fevD	KAN	Rep, Mult	3,7
14	0.01	1	1fcjA	SO4	Rep, Mult	41,42,65,121
15	0.01	1	3gvdB	CYS	Rep, Mult	47,63,64
16	0.01	1	3pgqB	GY3	Rep, Mult	78,98,103
17	0.01	1	3ff6B	RCP	Rep, Mult	45,71,82

	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	1xnvA	0.521	4.18	0.063	0.902	6.4.1.3	47
2	0.060	1v8zB	0.534	4.09	0.090	0.893	4.2.1.20	NA
3	0.060	1on3E	0.523	4.10	0.064	0.885	2.1.3.1	47
4	0.060	1onxA	0.533	4.38	0.125	0.918	3.4.19.-	NA
5	0.060	1uyrA	0.532	3.88	0.085	0.861	6.4.1.2,6.3.4.14	NA
6	0.060	2efyA	0.542	3.85	0.066	0.869	2.5.1.47	NA
7	0.060	2rkbA	0.539	4.33	0.097	0.926	4.3.1.19,4.3.1.17	NA
8	0.060	1k39B	0.521	4.35	0.063	0.885	5.3.3.8	NA
9	0.060	1m54A	0.531	3.84	0.029	0.853	4.2.1.22	NA
10	0.060	3ff6A	0.533	3.83	0.095	0.853	6.4.1.2,6.3.4.14	47
11	0.060	1j33A	0.516	4.59	0.068	0.926	2.4.2.21	NA
12	0.060	3f98A	0.524	4.36	0.086	0.902	3.1.1.47	61,63,91
13	0.060	2a7sA	0.531	3.96	0.075	0.869	6.4.1.3	47
14	0.060	2f9iA	0.532	4.11	0.056	0.877	6.4.1.2	NA
15	0.060	3iauA	0.530	4.24	0.055	0.893	4.3.1.19	NA
16	0.060	3dnyT	0.529	4.25	0.045	0.893	3.6.5.3	NA
17	0.060	1ve5D	0.513	4.35	0.080	0.885	4.3.1.19	NA
18	0.060	1p5jA	0.518	4.42	0.088	0.926	4.3.1.17	NA
19	0.060	1ybqA	0.518	4.47	0.106	0.926	3.4.19.1	12,47

(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	0.07	0.536	3.94	0.05	0.87	4lmbA	GO:0004124 GO:0006535 GO:0008652 GO:0016740 GO:0019344
1	0.07	0.541	3.89	0.04	0.88	2isqA	GO:0004124 GO:0005634 GO:0005737 GO:0005774 GO:0005777 GO:0005829 GO:0005886 GO:0006535 GO:0007568 GO:0008652 GO:0009507 GO:0009567 GO:0009570 GO:0009860 GO:0016020 GO:0016740 GO:0019344 GO:0030170 GO:0046686 GO:0048046
2	0.07	0.536	4.13	0.11	0.89	5hbgA	GO:0004124 GO:0006535 GO:0008652 GO:0016740 GO:0019344
3	0.07	0.513	4.38	0.07	0.90	1tdjA	GO:0003824 GO:0004794 GO:0005737 GO:0006520 GO:0006566 GO:0008152 GO:0008652 GO:0009082 GO:0009097 GO:0016597 GO:0016829 GO:0030170
4	0.07	0.535	4.09	0.09	0.89	5dw0A	GO:0000162 GO:0004834 GO:0006568 GO:0008652 GO:0009073 GO:0016829
5	0.07	0.532	4.14	0.04	0.88	3bm5A	GO:0004124 GO:0006535
6	0.07	0.536	3.81	0.06	0.85	3pc3A	GO:0004122 GO:0004124 GO:0005737 GO:0006535 GO:0008340 GO:0008652 GO:0016829 GO:0019343 GO:0019344 GO:0030170 GO:0034976 GO:0046872
7	0.07	0.519	4.11	0.07	0.84	4i1yD	GO:0004124 GO:0006535 GO:0008652 GO:0016740 GO:0019344
8	0.07	0.532	4.05	0.07	0.89	3hmkB	GO:0000166 GO:0000287 GO:0003824 GO:0003941 GO:0005509 GO:0005524 GO:0005737 GO:0005886 GO:0006520 GO:0006563 GO:0007420 GO:0007568 GO:0008152 GO:0008721 GO:0009069 GO:0014070 GO:0016594 GO:0016829 GO:0016853 GO:0018114 GO:0030165 GO:0030170 GO:0030378 GO:0032496 GO:0042493 GO:0042803 GO:0042866 GO:0043025 GO:0043278 GO:0045177 GO:0046872 GO:0051289 GO:0070178 GO:0070179
9	0.07	0.528	3.98	0.08	0.87	1o58C	GO:0004124 GO:0005737 GO:0006535 GO:0008652 GO:0016740 GO:0019344 GO:0030170 GO:0080146
10	0.07	0.541	4.02	0.09	0.87	2ecoA	GO:0004124 GO:0006535 GO:0008652 GO:0016740 GO:0016829 GO:0019344
11	0.07	0.523	4.17	0.06	0.88	5i7wA	GO:0004124 GO:0006535 GO:0016740
12	0.07	0.513	4.35	0.08	0.89	1ve5D	GO:0006520 GO:0030170 GO:0046872
13	0.07	0.536	4.07	0.06	0.88	5dbhX	GO:0003824 GO:0004124 GO:0005737 GO:0006535 GO:0008152 GO:0008652 GO:0016740 GO:0019344 GO:0030170 GO:0080146
14	0.07	0.542	3.86	0.05	0.87	4aecA	GO:0004124 GO:0005739 GO:0006535 GO:0008652 GO:0016740 GO:0019344 GO:0030170
15	0.07	0.521	4.35	0.04	0.90	5d84A	GO:0006535
16	0.07	0.537	3.92	0.05	0.86	1d6sA	GO:0003824 GO:0004124 GO:0005737 GO:0006535 GO:0008152 GO:0008652 GO:0016740 GO:0019344 GO:0030170 GO:0080146
17	0.07	0.530	4.24	0.06	0.89	3iauA	GO:0003824 GO:0004794 GO:0005737 GO:0006520 GO:0008152 GO:0008652 GO:0009082 GO:0009097 GO:0009507 GO:0009536 GO:0016829 GO:0030170
18	0.07	0.530	4.18	0.07	0.88	1o58A	GO:0004124 GO:0005737 GO:0006535 GO:0008652 GO:0016740 GO:0019344 GO:0030170 GO:0080146

Consensus prediction of GO terms

Molecular Function	GO:0016835
GO-Score	0.37
Biological Processes	GO:0046394	GO:0006563	GO:0019344
GO-Score	0.58	0.37	0.37
Cellular Component	GO:0048046	GO:0005634	GO:0005774	GO:0009570	GO:0005829	GO:0005777	GO:0005886
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07	0.07

(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.