I-TASSER results

I-TASSER results for job id Rv2641

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

Input Sequence in FASTA format

>protein (152 residues)
MSRVQLALNVDDLEAAITFYSRLFNAEPAKRKPGYANFAIADPPLKLVLLENPGTGGTLN
HLGVEVGSSNTVHAEIARLTEAGLVTEKEIGTTCCFATQDKVWVTGPGGERWEVYTVLAD
SETFGSGPRHNDTSDGEASMCCDGQVAVGASG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSRVQLALNVDDLEAAITFYSRLFNAEPAKRKPGYANFAIADPPLKLVLLENPGTGGTLNHLGVEVGSSNTVHAEIARLTEAGLVTEKEIGTTCCFATQDKVWVTGPGGERWEVYTVLADSETFGSGPRHNDTSDGEASMCCDGQVAVGASG
Prediction	CCCEEEEEHCCCHHHHHHHHHHHHCCEEEEEHCCEEEEEHCCCCEEEEEEHCCCCCCCCEEEEEHCCCHHHHHHHHHHHHHHCCCEHCCCCCCCCCCCCEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98668999858799999999999899679997988788867997799999679989986589998599999999999999989954457887777766558999889998899999778766667777666777788887888888888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSRVQLALNVDDLEAAITFYSRLFNAEPAKRKPGYANFAIADPPLKLVLLENPGTGGTLNHLGVEVGSSNTVHAEIARLTEAGLVTEKEIGTTCCFATQDKVWVTGPGGERWEVYTVLADSETFGSGPRHNDTSDGEASMCCDGQVAVGASG
Prediction	43312114327324202410461040423443741020115444020101234655320100001063363044015204734342354542323334333010102442300011236625324644634646655443113343665678
	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

CCCEEEEEHCCCHHHHHHHHHHHHCCEEEEEHCCEEEEEHCCCCEEEEEEHCCCCCCCCEEEEEHCCCHHHHHHHHHHHHHHCCCEHCCCCCCCCCCCCEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MSRVQLALNVDDLEAAITFYSRLFNAEPAKRKPGYANFAIADPPLKLVLLENPGTGGTLNHLGVEVGSSNTVHAEIARLTEAGLVTEKEIGTTCCFATQDKVWVTGPGGERWEVYTVLADSETFGSGPRHNDTSDGEASMCCDGQVAVGASG

5c4pA

0.67

0.48

0.72

2.74

MUSTER

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.67

0.48

0.72

3.31

dPPAS

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.67

0.48

0.72

3.46

wdPPAS

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.67

0.48

0.72

3.32

wMUSTER

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.67

0.48

0.72

3.63

wPPAS

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.67

0.48

0.72

4.64

dPPAS2

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.67

0.48

0.72

3.43

PPAS

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATVEEN--------QDKVWVTGPGGEPWEVYVV-----------------------------------

5c4pA

0.66

0.47

0.72

3.30

Env-PPAS

MSRVQLALRVPDLEASIGFYSKLFGTGPAKVRPGYANFAIAEPPLKLVLIEGAGDATRLDHLGVEVEDSAQVGHAARRLKESGLATV--------EENQDKVWVTGPGGEPWEVYVV-----------------------------------

1mpyA1

0.18

0.16

0.93

2.45

MUSTER

MRPGHVQLRVLDMSKALEHYVELLGLIEMDRDQGRVYLKAWTEVDKFSLVLREADEPGMDFMGFKVVDEDALRQLERDLMAYGCAVEQLPA-GELNSCGRRVRFQAPSGHHFELYA---DKEYTGKWGLNDVNPEA-------PRDLKGMAA

1mpyA1

0.16

0.15

0.94

2.82

dPPAS

MRPGHVQLRVLDMSKALEHYVELLGLIEMDRDQGRVYLKAWTEVDKFSLVLREADEPGMDFMGFKVVDEDALRQLERDLMAYGCAVEQLPA-GELNSCGRRVRFQAPSGHHFELYADKEYTGKWGLNDVNPEAWPRDLKG--MAAV------

(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=0.07

Estimated TM-score = 0.72±0.11

Estimated RMSD = 4.6±3.0Å

Download Model 2

C-score=-1.66

Download Model 3

C-score=-2.64

Download Model 4

C-score=-2.75

Download Model 5

C-score=-1.28

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	1kmyA	0.646	3.25	0.148	0.868
2	1eiqA	0.645	3.23	0.148	0.868
3	3lm4D1	0.643	3.46	0.124	0.875
4	2zt6A3	0.446	4.96	0.039	0.743
5	1wsrA	0.445	5.45	0.073	0.855
6	3hwoA	0.444	5.23	0.036	0.776
7	1htoX	0.440	4.32	0.060	0.684
8	1f1hL	0.440	4.15	0.027	0.671
9	1hbnB2	0.432	4.89	0.118	0.724
10	1tkjA	0.429	4.77	0.098	0.711

(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	0.63	73	2ehzA	FE2	Rep, Mult	5,61,103,113
2	0.07	12	1cjxC	FE2	Rep, Mult	5,61,101,103,113
3	0.04	7	3lm4A	PEO	Rep, Mult	5,7,37,61
4	0.01	1	2wl3A	CA	Rep, Mult	107,151
5	0.01	2	1lqoB	PO4	Rep, Mult	59,61
6	0.01	1	2ei3A	BPY	Rep, Mult	15,19,23
7	0.01	2	3m2rB	TP7	Rep, Mult	19,20,24,48
8	0.01	1	2zyqB	TAR	Rep, Mult	51,54
9	0.00	1	3sk2A	GRI	Rep, Mult	95,96

	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	2zt5A	0.433	4.92	0.015	0.730	6.1.1.14	NA
2	0.060	1kmyA	0.646	3.25	0.148	0.868	1.13.11.39	NA
3	0.060	3kt8D	0.411	5.53	0.021	0.789	6.1.1.2	NA
4	0.060	2pffD	0.406	5.31	0.067	0.737	2.3.1.86	NA
5	0.060	1ftrD	0.419	5.31	0.087	0.763	2.3.1.101	36,51
6	0.060	1htoA	0.440	4.32	0.060	0.684	6.3.1.2	NA
7	0.060	1f2oA	0.426	4.89	0.098	0.717	3.4.11.24	NA
8	0.060	3hwoA	0.444	5.23	0.036	0.776	5.4.4.2	16
9	0.060	1mroB	0.431	5.37	0.088	0.776	2.8.4.1	21,48
10	0.060	3l84A	0.394	5.04	0.056	0.697	2.2.1.1	38,63
11	0.060	1kr2A	0.408	4.62	0.063	0.658	2.7.7.1,2.7.7.18	23
12	0.060	2ib7D	0.393	4.87	0.050	0.638	2.3.1.9	NA
13	0.060	1jrpB	0.385	5.07	0.064	0.691	1.17.1.4	NA
14	0.060	3hxxA	0.407	5.09	0.059	0.704	6.1.1.7	76
15	0.060	1lgrA	0.304	5.43	0.060	0.579	6.3.1.2	31
16	0.060	3eqlM	0.400	5.62	0.035	0.770	2.7.7.6	65
17	0.060	1jroB	0.423	5.17	0.034	0.763	1.1.1.204	NA
18	0.060	1wsvA	0.399	5.58	0.084	0.770	2.1.2.10	141
19	0.060	1eilA	0.643	3.24	0.148	0.868	1.13.11.39	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	0.28	0.660	3.11	0.15	0.87	2wl9A	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
1	0.26	0.693	3.07	0.19	0.89	3hpvA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0046872 GO:0051213 GO:0055114
2	0.24	0.637	3.47	0.16	0.86	3b59A	GO:0046872 GO:0051213 GO:0055114
3	0.24	0.649	3.08	0.14	0.86	2zi8A	GO:0003824 GO:0005506 GO:0006629 GO:0006707 GO:0006725 GO:0008198 GO:0008202 GO:0008203 GO:0009405 GO:0016042 GO:0016491 GO:0019439 GO:0046872 GO:0047071 GO:0051213 GO:0055114 GO:0070723
4	0.23	0.643	3.24	0.14	0.87	2ehzA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0016702 GO:0019439 GO:0046872 GO:0051213 GO:0055114 GO:1901170
5	0.23	0.643	3.24	0.15	0.87	1eilA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
6	0.16	0.508	2.74	0.14	0.62	4rt5A	GO:0051213 GO:0055114
7	0.15	0.325	2.92	0.23	0.39	1lqkA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
8	0.13	0.541	3.25	0.17	0.74	3rmuA	GO:0004493 GO:0005739 GO:0005759 GO:0016853 GO:0019626 GO:0046491 GO:0046872
9	0.09	0.659	3.17	0.18	0.88	1f1uA	GO:0046872 GO:0051213 GO:0055114
10	0.09	0.646	3.25	0.15	0.87	1kmyA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
11	0.08	0.660	3.13	0.16	0.88	4ghcC	GO:0046872 GO:0051213 GO:0055114
12	0.07	0.627	3.65	0.12	0.87	3vb0A	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
13	0.07	0.514	3.16	0.14	0.68	2rk9B	GO:0051213 GO:0055114
14	0.06	0.376	5.53	0.03	0.72	3e80A	GO:0008201 GO:0015021 GO:0016829 GO:0030211 GO:0042597 GO:0046872 GO:0047488
15	0.06	0.303	3.30	0.14	0.39	3hnqA	GO:0009405
16	0.06	0.385	5.48	0.07	0.74	1gjqA	GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
17	0.06	0.345	5.01	0.07	0.61	1aomB	GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
18	0.06	0.319	2.99	0.15	0.39	1npbA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
19	0.06	0.313	3.39	0.04	0.43	4hc5D	GO:0051213 GO:0055114
20	0.06	0.307	5.62	0.07	0.59	4wghA	GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0008198	GO:0019114
GO-Score	0.69	0.53
Biological Processes	GO:0055114	GO:0019439	GO:0006805	GO:0051704	GO:0016127	GO:0008203	GO:0046164	GO:0036314	GO:0097305	GO:0018931
GO-Score	0.77	0.69	0.57	0.48	0.48	0.48	0.48	0.48	0.48	0.46
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.