I-TASSER results

I-TASSER results for job id Rv2705c

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

Input Sequence in FASTA format

>protein (129 residues)
MRMTPDPAMLVHLCGVQEWSHARERGGIYPESDKTGYIHLSTLEQVHLPANRLYRGRADL
VLLYIDPAALDSPVRWEPGVPTDPRSMLFPHLYGPLPVRAVIGAAAYPPAGDGSFGPAPE
FRSATADPT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRMTPDPAMLVHLCGVQEWSHARERGGIYPESDKTGYIHLSTLEQVHLPANRLYRGRADLVLLYIDPAALDSPVRWEPGVPTDPRSMLFPHLYGPLPVRAVIGAAAYPPAGDGSFGPAPEFRSATADPT
Prediction	CCCCCCCCEEEEEHCHHHHHHHHHHCCCCCCCCCCCCEHCCCHHHHHHHHHHHHCCCCCEEEEEHCHHHCCCCEEHCCCCCCCCCCCCCCCHCCCCCHHHEEEEEEEHCCCCCCCCCCHHHHHHCCCCC
Conf.Score	999999977999859789999998799889877778577799999999999985999978999985676688868758999999987666544799977646767765689997678867776556889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MRMTPDPAMLVHLCGVQEWSHARERGGIYPESDKTGYIHLSTLEQVHLPANRLYRGRADLVLLYIDPAALDSPVRWEPGVPTDPRSMLFPHLYGPLPVRAVIGAAAYPPAGDGSFGPAPEFRSATADPT
Prediction	864455231001003473155047545144434630000003461044005411563540000102274156503022454666733200002251426203403604347613142174047345668
	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

CCCCCCCCEEEEEHCHHHHHHHHHHCCCCCCCCCCCCEHCCCHHHHHHHHHHHHCCCCCEEEEEHCHHHCCCCEEHCCCCCCCCCCCCCCCHCCCCCHHHEEEEEEEHCCCCCCCCCCHHHHHHCCCCC
MRMTPDPAMLVHLCGVQEWSHARERGGIYPESDKTGYIHLSTLEQVHLPANRLYRGRADLVLLYIDPAALDSPVRWEPGVPTDPRSMLFPHLYGPLPVRAVIGAAAYPPAGDGSFGPAPEFRSATADPT

2jqnA

0.31

0.27

0.88

3.76

MUSTER

MT------LIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHL---ALE--

2jqnA

0.30

0.26

0.88

9.56

dPPAS

------MTLIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHLALE-----

2jqnA

0.31

0.27

0.88

7.14

wdPPAS

MT------LIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHL---ALE--

2jqnA

0.30

0.26

0.88

4.38

wMUSTER

-------TLIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHL---ALE--

2jqnA

0.31

0.27

0.88

5.45

wPPAS

MT------LIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHL---ALE--

2jqnA

0.30

0.26

0.88

16.12

dPPAS2

------MTLIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHLALE-----

2jqnA

0.31

0.27

0.88

4.96

PPAS

MT------LIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHL---ALE--

2jqnA

0.31

0.27

0.88

5.24

Env-PPAS

MT------LIYKILSRAEWDAAKAQGRFEGSDLADGFIHLSAGEQAQETAAKWFRGQANLVLLAVEAEPLGEDLKWEAS----RGGARFPHLYRPLLVSEVTREADLDLDADGVPQLGDHL---ALE--

1wfxA2

0.15

0.11

0.71

0.83

MUSTER

PLPGEPPPILYHGTTEEALPLIER---IRGRRL---KVHLTSLEDAVSTGRRH---GNLVAVLLVDVECLRRGLKVERSKTV---------TVDWVPPECIAEVRRESL--------------------

1wfxA2

0.14

0.10

0.73

1.24

dPPAS

PLPGEPPPILYHGTTEEALPLIERGIRGRRL-----KVHLTSLEDAVSTGRRH---GNLVAVLLVDVECLRRR-----GLKVERSKTVY--TVDWVPPECIAEVRRESL--------------------

(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=1.25

Estimated TM-score = 0.89±0.07

Estimated RMSD = 2.1±1.7Å

Download Model 2

C-score=-2.08

Download Model 3

C-score=-0.14

Download Model 4

C-score=-1.60

Download Model 5

C-score=-4.30

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	2jqnA	0.845	1.30	0.298	0.884
2	1tiiA	0.622	2.75	0.147	0.783
3	1lt4A	0.621	2.84	0.147	0.783
4	4tlvA1	0.605	3.39	0.099	0.822
5	4k6lG	0.603	3.18	0.087	0.806
6	1ikqA3	0.589	3.83	0.115	0.899
7	1prtA	0.587	3.63	0.068	0.814
8	4z9cA	0.583	3.36	0.085	0.806
9	2vseA	0.582	4.21	0.066	0.853
10	2q5tA2	0.581	3.85	0.099	0.876

(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	0.33	24	4hyfA	NCA	Rep, Mult	12,13,39,40,41,89
2	0.06	4	3tj9B	ZN	Rep, Mult	39,91
3	0.03	2	2a5fB	NAD	Rep, Mult	12,13,14,15,16,29,30,31,39,40,41,49,54,89
4	0.03	2	3dgdA	ZN	Rep, Mult	12,65
5	0.01	1	3e2vA	MG	Rep, Mult	39,71
6	0.01	1	2jfsA	MN	Rep, Mult	91,112
7	0.01	1	1f5fA	ZN	Rep, Mult	39,66
8	0.01	1	4h03A	EDO	Rep, Mult	1,86,87

	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	1dtpA	0.556	4.14	0.059	0.891	2.4.2.36	NA
2	0.060	1ddtA	0.546	4.15	0.057	0.876	2.4.2.36	NA
3	0.060	3hhsB	0.429	4.52	0.038	0.705	1.14.18.1	NA
4	0.060	1og1A	0.457	3.47	0.069	0.659	2.4.2.31	NA
5	0.060	1zxvA	0.453	3.82	0.040	0.705	3.4.24.83	NA
6	0.060	1ikpA	0.588	3.85	0.115	0.899	2.4.2.-	NA
7	0.060	1a26A	0.547	3.73	0.100	0.791	2.4.2.30	NA
8	0.060	1f1hA	0.422	3.82	0.072	0.620	6.3.1.2	NA
9	0.060	1g24A	0.487	4.06	0.085	0.752	2.4.2.-	NA
10	0.060	2rf5A	0.523	3.49	0.087	0.752	2.4.2.30	NA
11	0.060	3ikmD	0.442	5.01	0.032	0.830	2.7.7.7	NA
12	0.060	3cjcA	0.425	4.05	0.037	0.690	3.1.21.1	NA
13	0.060	2hw2A	0.476	4.29	0.096	0.744	2.4.2.30	12,67
14	0.060	1iu4A	0.442	4.03	0.058	0.682	2.3.2.13	NA
15	0.060	1s5bA	0.618	2.91	0.145	0.791	2.4.2.36	NA
16	0.060	2wb8A	0.444	4.80	0.058	0.752	2.7.11.1	NA
17	0.060	1f0xA	0.439	4.57	0.085	0.736	1.1.1.28	38
18	0.060	1a59A	0.427	4.67	0.064	0.713	2.3.3.1	NA
19	0.060	2pqfA	0.512	3.26	0.050	0.713	2.4.2.30	NA

(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	0.14	0.519	3.38	0.11	0.74	3c49A	GO:0000723 GO:0003824 GO:0003910 GO:0003950 GO:0005634 GO:0005737 GO:0005814 GO:0005815 GO:0005856 GO:0006273 GO:0006281 GO:0006302 GO:0006471 GO:0016740 GO:0016757 GO:0035861 GO:0051103 GO:0051106 GO:0060236 GO:1990166
1	0.11	0.622	2.75	0.15	0.78	1tiiA	GO:0003824 GO:0005576 GO:0009405
2	0.07	0.324	5.51	0.03	0.67	4tlvA	GO:0003950 GO:0005576 GO:0005886 GO:0009405 GO:0016020 GO:0016740 GO:0016757
3	0.07	0.626	3.00	0.16	0.80	1s5eA	GO:0003824 GO:0003950 GO:0005576 GO:0006471 GO:0009405 GO:0016740 GO:0016757 GO:0030819 GO:0031640 GO:0042517
4	0.07	0.618	2.91	0.14	0.79	1s5bA	GO:0003824 GO:0003950 GO:0005576 GO:0006471 GO:0009405 GO:0016740 GO:0016757 GO:0030819 GO:0031640 GO:0042517
5	0.07	0.622	2.75	0.15	0.78	1lt3A	GO:0003824 GO:0005576 GO:0009405
6	0.07	0.580	3.58	0.07	0.81	1bcpA	GO:0003950 GO:0005576 GO:0009405 GO:0016740 GO:0016757
7	0.07	0.603	3.18	0.09	0.81	4k6lG	GO:0003950 GO:0005576 GO:0009405 GO:0016740 GO:0016757
8	0.07	0.581	3.85	0.10	0.88	2q5tA	GO:0016740 GO:0016757 GO:0047286
9	0.07	0.556	4.14	0.06	0.89	1dtpA	GO:0005576 GO:0005829 GO:0005886 GO:0008320 GO:0009405 GO:0016740 GO:0016757 GO:0030666 GO:0030669 GO:0047286 GO:0071806
10	0.07	0.546	4.15	0.06	0.88	1ddtA	GO:0005576 GO:0005829 GO:0005886 GO:0008320 GO:0009405 GO:0016740 GO:0016757 GO:0030666 GO:0030669 GO:0047286 GO:0071806
11	0.07	0.543	4.02	0.06	0.86	4ow6B	GO:0005576 GO:0009405 GO:0016740 GO:0016757 GO:0047286
12	0.06	0.353	5.31	0.04	0.70	1kfdA	GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0004527 GO:0005737 GO:0005829 GO:0006139 GO:0006260 GO:0006261 GO:0006281 GO:0006284 GO:0006974 GO:0008408 GO:0008409 GO:0016740 GO:0016779 GO:0016787 GO:0071897 GO:0090305
13	0.06	0.317	5.13	0.05	0.58	2zsiA	GO:0005634 GO:0005737 GO:0008152 GO:0009739 GO:0009740 GO:0009939 GO:0010331 GO:0010476 GO:0016787 GO:0048444
14	0.06	0.356	4.60	0.06	0.60	4q05A	GO:0008152 GO:0016787
15	0.06	0.588	3.85	0.12	0.90	1ikpA	GO:0016740 GO:0016757 GO:0047286
16	0.06	0.318	4.30	0.05	0.51	1czsA	GO:0000139 GO:0002576 GO:0005507 GO:0005576 GO:0005615 GO:0005788 GO:0005886 GO:0006888 GO:0007596 GO:0007599 GO:0008015 GO:0016020 GO:0030134 GO:0030168 GO:0031091 GO:0031093 GO:0033116 GO:0046872 GO:0048208 GO:1903561
17	0.06	0.398	4.86	0.05	0.71	2yheA	GO:0046872 GO:0046983
18	0.06	0.295	5.19	0.09	0.55	4hd1A	GO:0009058 GO:0016740 GO:0016767

Consensus prediction of GO terms

Molecular Function	GO:0003950
GO-Score	0.30
Biological Processes	GO:0051704	GO:0006486
GO-Score	0.56	0.50
Cellular Component	GO:0005576	GO:0035861	GO:0005814	GO:0005634	GO:0005886
GO-Score	0.28	0.14	0.14	0.14	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.