I-TASSER results

Input Sequence in FASTA format

>protein (76 residues)
MSVGEVEVLKVENSRVRAEQLAKLYELRSSRDRVRVDAALAELSRAAAARGCAGTSGLGN
NLMAPGPPHSLLGRDR

Predicted Secondary Structure

Sequence	20 40 60 \| \| \| MSVGEVEVLKVENSRVRAEQLAKLYELRSSRDRVRVDAALAELSRAAAARGCAGTSGLGNNLMAPGPPHSLLGRDR
Prediction	CCCCCCCEEEHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCHHHHHCCCCC
Conf.Score	9988765566586999999999999999985899999999999999985898877765565455454566557789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 \| \| \| MSVGEVEVLKVENSRVRAEQLAKLYELRSSRDRVRVDAALAELSRAAAARGCAGTSGLGNNLMAPGPPHSLLGRDR
Prediction	8675514215143661265126305613762467405501630361065576446542431002334645435578
	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

                   |                   |                   |

Sec.Str
Seq

CCCCCCCEEEHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCHHHHHCCCCC
MSVGEVEVLKVENSRVRAEQLAKLYELRSSRDRVRVDAALAELSRAAAARGCAGTSGLGNNLMAPGPPHSLLGRDR

1e1cA

0.34

0.33

0.96

1.33

MUSTER

EHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPD---DKDPDRNLLKLCIDAGRAMATV

1e1cA1

0.37

0.36

0.96

1.42

wMUSTER

EHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPD---DKDPDRNLLKLCRAMATVGRYT

3bicA3

0.25

0.21

0.84

1.44

dPPAS2

LA--------IDNTSVRNRQIEKLKKIKSSRDQALAERCLAALTECAASGDGNILAL----AVDASRARCTVGEHK

1e1cA1

0.37

0.36

0.96

1.24

MUSTER

EHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPD---DKDPDRNLLKLCALEKVFGRYT

4r3uA

0.19

0.17

0.92

1.37

wMUSTER

NEEDKIEIHPYDN-TTAERQISRTRRVRAERDEAKVQAMLDQLVAVAKDESNLMPL-----TIELVKAGATMGTYR

5cwjA1

0.13

0.11

0.83

1.10

dPPAS2

-----------DSEEEQERIRRILKEARKSGTEESLRQAIEDVAQLAKKSQD--SEVLEEAIRVILRIAKESGSEE

4r3uA

0.19

0.17

0.92

1.07

MUSTER

NEEDKIEIHPYDN-TTAERQISRTRRVRAERDEAKVQAMLDQLVAVAKDESNLMPL-----TIELVKAGATMGTYR

4xc6A

0.20

0.18

0.91

1.30

wMUSTER

PNGDPTQTLELAREDEKQSQLHRLTEFHGAHQ-ADAEAMLARLRQAVIDNRNVFAV-----LMDAVRV-CSLGQLF

5cwhA1

0.16

0.13

0.82

1.10

dPPAS2

-----------DSEEVNERVKQLAEKAKEATDKEEVIEIVKELAELAKQSTD---SELVNEIVKQLAEVAKEATDK

4xc6A

0.20

0.18

0.91

1.05

MUSTER

PNGDPTQTLELAREDEKQSQLHRLTEFHGAHQ-ADAEAMLARLRQAVIDNRNVFAV-----LMDAVRV-CSLGALF

(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=-1.32

Estimated TM-score = 0.55±0.15

Estimated RMSD = 6.1±3.8Å

Download Model 2

C-score=-2.74

Download Model 3

C-score=-3.68

Download Model 4

C-score=-2.83

Download Model 5

C-score=-1.76

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	1e1cA	0.712	2.88	0.333	0.961
2	4r3uA	0.696	2.54	0.145	0.908
3	3bicA	0.651	2.91	0.246	0.908
4	4xc6A2	0.633	3.01	0.200	0.908
5	4ci6B	0.560	3.07	0.053	0.842
6	4o5jA1	0.548	3.28	0.056	0.895
7	3ixvM2	0.543	3.52	0.056	0.908
8	5dllA	0.542	3.13	0.086	0.816
9	4hteA	0.542	4.18	0.079	1.000
10	3dxjP1	0.541	3.16	0.074	0.882

(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	0.08	3	4fc5F	ZN	Rep, Mult	20,23
2	0.07	3	3k4sA	0MO	Rep, Mult	36,39,40,43,63
3	0.05	2	2plyA	MG	Rep, Mult	13,17
4	0.05	2	3q72A	CA	Rep, Mult	28,31
5	0.05	2	3sl9B	III	Rep, Mult	16,20,23,24,27,30,32,34,35,42,46,49
6	0.05	2	1xomA	CIO	Rep, Mult	42,43,46,53,64
7	0.05	2	1r5iD	III	Rep, Mult	30,31,32,33,36,38,40
8	0.02	1	3ub8B	ARF	Rep, Mult	17,20
9	0.02	1	2eh3A	MG	Rep, Mult	7,10
10	0.02	1	1revA	MG	Rep, Mult	11,12
11	0.02	1	3pi1A	UUU	Rep, Mult	23,27
12	0.02	1	2a68P	MG	Rep, Mult	19,22

	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	1e1cA	0.712	2.88	0.333	0.961	5.4.99.2	NA
2	0.060	3cirM	0.500	3.40	0.054	0.842	1.3.99.1	NA
3	0.060	3i39X	0.523	3.55	0.060	0.855	1.2.99.2	NA
4	0.060	1og5B	0.496	3.56	0.087	0.855	1.14.13.48,1.14.13.49,1.14.13.80	22
5	0.060	2gtqA	0.503	3.57	0.096	0.829	3.4.11.2	NA
6	0.060	3hxxA	0.501	4.08	0.122	0.908	6.1.1.7	NA
7	0.060	3afhA	0.498	3.28	0.029	0.803	6.1.1.17	NA
8	0.060	1w07B	0.528	3.40	0.058	0.908	1.3.3.6	NA
9	0.060	3cirA	0.499	3.49	0.053	0.842	1.3.99.1	NA
10	0.060	2h7fX	0.523	4.21	0.096	0.947	5.99.1.2	NA
11	0.060	2qubA	0.532	3.29	0.047	0.842	3.1.1.3	35
12	0.060	1sojL	0.515	3.63	0.125	0.921	3.1.4.17	NA
13	0.060	2fonB	0.535	3.23	0.072	0.908	1.3.3.6	NA
14	0.060	2qymA	0.533	3.30	0.062	0.855	3.1.4.17	NA
15	0.060	3bicA	0.651	2.91	0.246	0.908	5.4.99.2	NA
16	0.060	3cf4A	0.503	4.02	0.097	0.882	1.2.99.2	NA
17	0.060	2ouyA	0.501	3.69	0.027	0.868	3.1.4.17	38
18	0.060	2hroA	0.434	3.12	0.082	0.618	2.7.3.9	NA
19	0.060	1kfyA	0.508	3.25	0.055	0.816	1.3.99.1	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	0.14	0.712	2.88	0.33	0.96	1e1cA	GO:0003824 GO:0004494 GO:0008152 GO:0016853 GO:0016866 GO:0031419 GO:0046872
1	0.12	0.696	2.54	0.14	0.91	4r3uA	GO:0003824 GO:0004494 GO:0008152 GO:0016853 GO:0016866 GO:0031419
2	0.08	0.651	2.91	0.25	0.91	3bicA	GO:0003824 GO:0004494 GO:0005739 GO:0005759 GO:0008152 GO:0009235 GO:0009791 GO:0016853 GO:0016866 GO:0019626 GO:0031419 GO:0046872 GO:0050667 GO:0072341
3	0.07	0.633	3.01	0.20	0.91	4xc6A	GO:0000166 GO:0000287 GO:0003824 GO:0003924 GO:0004494 GO:0005525 GO:0006637 GO:0008152 GO:0016787 GO:0016853 GO:0016866 GO:0031419 GO:0034784 GO:0046872 GO:0047727
4	0.07	0.489	3.61	0.09	0.86	3shoA	GO:0003677 GO:0003700 GO:0005975 GO:0006355 GO:0030246
5	0.06	0.399	4.04	0.07	0.71	4xg1B	GO:0003824 GO:0008652 GO:0008836 GO:0009085 GO:0009089 GO:0016829 GO:0016831 GO:0030170
6	0.06	0.357	3.54	0.02	0.54	4jgiB	GO:0031419 GO:0046872
7	0.06	0.381	3.50	0.06	0.57	5csaA	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295
8	0.06	0.378	3.39	0.04	0.50	5cm2M	GO:0005634 GO:0005829 GO:0018364 GO:0030488 GO:0070476
9	0.06	0.355	4.35	0.04	0.74	3o8oB	GO:0000166 GO:0003729 GO:0003824 GO:0003872 GO:0005524 GO:0005737 GO:0005739 GO:0005741 GO:0005945 GO:0006002 GO:0006096 GO:0008152 GO:0015992 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0046872 GO:0046961 GO:0061615 GO:1902600
10	0.06	0.419	3.85	0.12	0.75	3bulA	GO:0005622 GO:0005737 GO:0005829 GO:0006479 GO:0008168 GO:0008270 GO:0008276 GO:0008652 GO:0008705 GO:0008898 GO:0009086 GO:0016740 GO:0031419 GO:0032259 GO:0035999 GO:0042558 GO:0044237 GO:0046872 GO:0050667
11	0.06	0.415	4.19	0.11	0.83	7reqB	GO:0003824 GO:0004494 GO:0008152 GO:0016853 GO:0016866 GO:0019652 GO:0031419 GO:0046872
12	0.06	0.450	4.22	0.03	0.75	1dl2A	GO:0004571 GO:0005509 GO:0005783 GO:0005789 GO:0006486 GO:0006491 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0030433 GO:0035977 GO:0046872 GO:0097466
13	0.06	0.411	3.63	0.12	0.61	5ietA	GO:0000502 GO:0005618 GO:0005886 GO:0022624 GO:0051260 GO:0061136 GO:0070628 GO:1901800
14	0.06	0.344	4.06	0.03	0.55	4jroA	GO:0000166 GO:0004316 GO:0006633 GO:0016491 GO:0051287 GO:0055114
15	0.06	0.318	3.95	0.03	0.55	4qj1D	GO:0003824 GO:0003938 GO:0005737 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
16	0.06	0.327	3.47	0.03	0.51	1y80A	GO:0008168 GO:0008705 GO:0009086 GO:0015948 GO:0016740 GO:0031419 GO:0032259 GO:0046872 GO:0050897
17	0.06	0.369	3.35	0.06	0.53	5cs4B	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295
18	0.06	0.413	3.91	0.06	0.83	5i6eA	GO:0000166 GO:0003824 GO:0003989 GO:0004075 GO:0005524 GO:0005737 GO:0005783 GO:0005789 GO:0006606 GO:0006629 GO:0006631 GO:0006633 GO:0006998 GO:0008152 GO:0016020 GO:0016874 GO:0042759 GO:0046872 GO:2001295

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0031419	GO:0004494
GO-Score	0.53	0.35	0.35
Biological Processes	GO:0008152
GO-Score	0.35
Cellular Component	GO:0005759
GO-Score	0.08

(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.

I-TASSER results for job id Rv1489A

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

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