I-TASSER results

I-TASSER results for job id Rv3672c

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

Input Sequence in FASTA format

>protein (273 residues)
MSAGGTPLQAGATPTGSRGTVALRPDAGPSWLRPLVDNVGQIPDAYRRRLPADVLAMVTA
AGAVSAMTSSRRDHREAAVLVLFSGPEAGPGDGGVPDDADLLLTVRASTLRHHAGQAAFP
GGVVDPADDGPVATALREANEETGIDPSRLHPLATMERTFIAPSRFHVVPVLAYSPDPGP
VAVVNEAETAIVARVPVRAFINPANRLMVYRRPHTRRWAGPAFLLNQMLVWGFTGQVISA
VLDVAGWAQPWDTGDIRELDAAMVLIDDESDPR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSAGGTPLQAGATPTGSRGTVALRPDAGPSWLRPLVDNVGQIPDAYRRRLPADVLAMVTAAGAVSAMTSSRRDHREAAVLVLFSGPEAGPGDGGVPDDADLLLTVRASTLRHHAGQAAFPGGVVDPADDGPVATALREANEETGIDPSRLHPLATMERTFIAPSRFHVVPVLAYSPDPGPVAVVNEAETAIVARVPVRAFINPANRLMVYRRPHTRRWAGPAFLLNQMLVWGFTGQVISAVLDVAGWAQPWDTGDIRELDAAMVLIDDESDPR
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCEHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEHCCCCCCCCCCEEEEEEEEEHCCCCCCCCCCHHHHHHHHHHCHHHHHCCCCCEEEEEEHCCEEEEEEEEEHCCEEEEEHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCC
Conf.Score	998888888888888888887788767875666777678875578887666566655556666666677888887657999986578887777778886899998588888889966588887899999999999999999989987765899976886668875589999999789987778995776536764388875977757999997997899778987998997378999999999987889998777777858889875577889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MSAGGTPLQAGATPTGSRGTVALRPDAGPSWLRPLVDNVGQIPDAYRRRLPADVLAMVTAAGAVSAMTSSRRDHREAAVLVLFSGPEAGPGDGGVPDDADLLLTVRASTLRHHAGQAAFPGGVVDPADDGPVATALREANEETGIDPSRLHPLATMERTFIAPSRFHVVPVLAYSPDPGPVAVVNEAETAIVARVPVRAFINPANRLMVYRRPHTRRWAGPAFLLNQMLVWGFTGQVISAVLDVAGWAQPWDTGDIRELDAAMVLIDDESDPR
Prediction	744643435444545446443414364116104313541650464245403463244245364354344666621200000000246524434334740100001006514620010003203213434221200100021014243630200120332213333020000000034452212124412120120104201436423333243444413100021551200000020031005104444115574235144313335656778
	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                 180                 200                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCCCCCCEEEEEEHCCCCCCCCCCEHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEHCCCCCCCCCCEEEEEEEEEHCCCCCCCCCCHHHHHHHHHHCHHHHHCCCCCEEEEEEHCCEEEEEEEEEHCCEEEEEHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCCC
MSAGGTPLQAGATPTGSRGTVALRPDAGPSWLRPLVDNVGQIPDAYRRRLPADVLAMVTAAGAVSAMTSSRRDHREAAVLVLFSGPEAGPGDGGVPDDADLLLTVRASTLRHHAGQAAFPGGVVDPADDGPVATALREANEETGIDPSRLHPLATMERTFIAPSRFHVVPVLAYSPDPGPVAVVNEAETAIVARVPVRAFINPANRLMVYRRPHTRRWAGPAFLLNQMLVWGFTGQVISAVLDVAGWAQPWDTGDIRELDAAMVLIDDESDPR

1nqzA

0.29

0.18

0.63

1.86

MUSTER

--------------------------------------------------PHDPLDDIQADPWALWLS----GYRRAAVLVALTR----------EADPRVLLTVRSK------GQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.63

2.77

dPPAS

--------------------------------------------------PHDPLDDIQADPWALWL----SGYRRAAVLVALTR----------EADPRVLLTVRS------KGQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.63

3.97

wdPPAS

--------------------------------------------------PHDPLDDIQ----ADPWALWLSGYRRAAVLVALTR----------EADPRVLLTVR------SKGQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.62

2.45

wMUSTER

---------------------------------------------------HDPLDDIQADPWALWLS----GYRRAAVLVALTR----------EADPRVLLTVRSK------GQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.63

4.21

wPPAS

--------------------------------------------------PHDPLDDIQ----ADPWALWLSGYRRAAVLVALTR----------EADPRVLLTVR------SKGQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.63

7.59

dPPAS2

--------------------------------------------------PHDPLDDIQADPWALWL----SGYRRAAVLVALTR----------EADPRVLLTVRS------KGQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.63

3.14

PPAS

--------------------------------------------------PHDPLDDIQADPWALWL----SGYRRAAVLVALTR----------EADPRVLLTVRS------KGQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

1nqzA

0.29

0.18

0.63

3.86

Env-PPAS

--------------------------------------------------PHDPLDDIQADPWALWL----SGYRRAAVLVALT----------READPRVLLTVRS------KGQIAFPGGSLDAGE-TPTQAALREAQEEVALDPAAVTLLGELDD-VFTPVGFHVTPVLGRIAPEALDTLRVTPEVAQIITPTLAELRAVPLVRERRTLPDGTEVPLYRYPWRGLDIWGMTARVLHDLLE------------------------------

4zb3A

0.12

0.10

0.84

0.88

MUSTER

---QIPLLEGETDNYD-TMVEPMDSEVFTESLRASLSHWRE--PLGLANLVEAAVSEVSWISETPDTIPANASHVVGAGALVIN-----------KNTKEVLVVQERSGFFKDKNVWKLPTGVINEGE-DIWTGVAREVEEETGIIADFVEVLAFRQSHKAILKKKTDMFFLCVLSPRSYDITEQKSEILQAKWMPIQEYVDQP------WNKKNEMFK-------------FMANICQKKCEFAIVPTTTSSGKESFI------CNADHA--

1su2A

0.19

0.11

0.58

1.05

dPPAS

---------------------------------------------------------------MEHDERTHVPVELRAAGVVLLNERGD-----------ILLVQEKGIPPEKAGLWHIPSGAVEDG-ENPQDAAVREACEETGLRVRPVKFLGAYLGRFPDGVLILRHVWLAEPEPGQTLAPAFTDEIAEASFVSREDFAQLYAAGQIRMY--------------------QTKLFYADALREKGFPALPV---------------------

(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=-2.33

Estimated TM-score = 0.44±0.14

Estimated RMSD = 11.4±4.5Å

Download Model 2

C-score=-2.81

Download Model 3

C-score=-3.01

Download Model 4

C-score=-3.43

Download Model 5

C-score=-2.93

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	1nqzA	0.586	1.74	0.292	0.626
2	2pnyA	0.489	4.00	0.101	0.626
3	2fmlA	0.487	4.31	0.129	0.637
4	3dupA	0.486	4.41	0.070	0.641
5	2qkmB	0.486	3.53	0.096	0.604
6	2i6kA	0.484	3.94	0.092	0.615
7	4zb3A	0.478	4.71	0.083	0.667
8	3fjyB	0.463	3.90	0.142	0.579
9	1viqA	0.462	3.22	0.097	0.549
10	1mqwA	0.461	4.03	0.131	0.590

(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	0.47	26	2a8sA	MN	Rep, Mult	121,138,141,142,188
2	0.20	13	2a8sA	GTP	Rep, Mult	79,106,119,121,122,123,138,141,142,168,188,233,234,237
3	0.02	2	1q33A	BGC	Rep, Mult	77,79,121,122,160,166,237
4	0.01	1	2qjtB	MN	Rep, Mult	123,125,137,138
5	0.01	1	2yvpA	RBY	Rep, Mult	78,121,122,123,138,142,166,168

	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	1viuB	0.421	3.55	0.124	0.516	3.6.1.-	NA
2	0.060	2a6tA	0.441	3.51	0.097	0.538	3.6.1.30	125,132,138,141
3	0.060	1itwB	0.303	6.23	0.019	0.516	1.1.1.42	121
4	0.060	1xsbA	0.451	3.05	0.163	0.527	3.6.1.17	136,142
5	0.060	2r5wB	0.438	3.77	0.120	0.546	2.7.7.1	121
6	0.060	2c4mC	0.368	6.40	0.057	0.656	2.4.1.1	NA
7	0.060	2w00B	0.392	5.83	0.035	0.648	3.1.21.3	236,239
8	0.060	1mqwA	0.461	4.03	0.131	0.590	3.6.1.13	NA
9	0.060	1b0pA	0.374	6.25	0.050	0.634	1.2.7.1	NA
10	0.060	2pnyA	0.489	4.00	0.101	0.626	5.3.3.2	144
11	0.060	2yvmA	0.448	3.40	0.136	0.546	3.6.1.-	106,188
12	0.060	1vlbA	0.370	6.59	0.033	0.663	1.2.99.7	NA
13	0.060	2w4eA	0.422	2.98	0.148	0.494	3.6.1.13	NA
14	0.060	1v8mA	0.415	3.77	0.162	0.513	3.6.1.13	NA
15	0.060	2ar0A	0.369	5.90	0.047	0.601	2.1.1.72	NA
16	0.060	1bxrA	0.382	6.60	0.047	0.692	6.3.5.5	NA
17	0.060	1f1sA	0.342	6.90	0.023	0.641	4.2.2.1	NA
18	0.060	3l4uA	0.367	6.63	0.037	0.670	3.2.1.20,3.2.1.3	135
19	0.060	2pdaA	0.374	6.10	0.067	0.623	1.2.7.1	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	0.39	0.586	1.74	0.29	0.63	1nqzA	GO:0016787
1	0.29	0.421	2.77	0.15	0.49	2o1cA	GO:0000287 GO:0008828 GO:0016787 GO:0019177 GO:0046654 GO:0046656 GO:0046872
2	0.25	0.428	2.65	0.20	0.49	1ktgA	GO:0000166 GO:0004081 GO:0005524 GO:0006167 GO:0006172 GO:0006754 GO:0006915 GO:0008796 GO:0015967 GO:0016787 GO:0019693 GO:0043135
3	0.21	0.461	4.03	0.13	0.59	1mqwA	GO:0016787 GO:0030145 GO:0046872
4	0.16	0.433	3.11	0.14	0.51	2kdvA	GO:0005737 GO:0006402 GO:0016787 GO:0016818 GO:0034353 GO:0046872 GO:0050779
5	0.16	0.405	2.93	0.18	0.48	3hhjB	GO:0006281 GO:0008413 GO:0016787
6	0.16	0.425	3.43	0.15	0.53	4jzsA	GO:0016787 GO:0046872
7	0.16	0.491	4.27	0.13	0.64	2fmlA	GO:0016787
8	0.16	0.412	3.43	0.13	0.50	2a6tB	GO:0000166 GO:0000287 GO:0000290 GO:0000340 GO:0000932 GO:0003723 GO:0003727 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005845 GO:0006397 GO:0010494 GO:0016787 GO:0030145 GO:0031087 GO:0046872 GO:0050072 GO:0098745
9	0.14	0.440	4.21	0.17	0.57	3q4iA	GO:0016787
10	0.11	0.406	3.15	0.18	0.49	3gg6A	GO:0000287 GO:0005829 GO:0009117 GO:0016787 GO:0034656 GO:0044715 GO:0044716 GO:0044717 GO:0046057 GO:0046067 GO:0046712 GO:0046872
11	0.11	0.438	2.96	0.18	0.52	1su2A	GO:0000166 GO:0005524 GO:0016787
12	0.10	0.416	2.78	0.14	0.48	2rrkA	GO:0006281 GO:0016787
13	0.10	0.423	3.49	0.13	0.52	5bonA	GO:0005829 GO:0006203 GO:0008413 GO:0016787 GO:0017110 GO:0034656 GO:0035539 GO:0046872
14	0.10	0.416	3.32	0.10	0.51	4hfqA	GO:0016787
15	0.07	0.486	3.53	0.10	0.60	2qkmB	GO:0000166 GO:0000287 GO:0000290 GO:0000340 GO:0000932 GO:0003723 GO:0003727 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0005845 GO:0006397 GO:0010494 GO:0016787 GO:0030145 GO:0031087 GO:0046872 GO:0050072 GO:0098745
16	0.07	0.445	3.22	0.17	0.53	1xsaA	GO:0000166 GO:0000302 GO:0004081 GO:0005525 GO:0005739 GO:0005759 GO:0006139 GO:0006915 GO:0008796 GO:0008803 GO:0016787
17	0.06	0.438	2.80	0.19	0.51	1f3yA	GO:0000166 GO:0004081 GO:0005524 GO:0016787
18	0.06	0.433	3.59	0.15	0.52	1vhzA	GO:0000287 GO:0005829 GO:0016787 GO:0019144 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0047429	GO:0032550	GO:0032559	GO:0035639	GO:0008796	GO:0046914
GO-Score	0.57	0.49	0.49	0.49	0.49	0.42
Biological Processes	GO:0042364	GO:0043604	GO:0009396	GO:0046655	GO:0046653	GO:0016053	GO:0046034	GO:0009180	GO:0015961	GO:0046129	GO:0046031	GO:0012501	GO:0046033	GO:0009152	GO:0009168	GO:0015965	GO:0009206	GO:0043487	GO:0006401	GO:0016071
GO-Score	0.57	0.57	0.57	0.57	0.57	0.57	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.49	0.33	0.33	0.33
Cellular Component	GO:0044424
GO-Score	0.33

(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.