I-TASSER results

Input Sequence in FASTA format

>protein (109 residues)
MVSGSDSRSEPSQLSDRDLVESVLRDLSEAADKWEALVTQAETVTYSVDLGDVRAVANSD
GRLLELTLHPGVMTGYAHGELADRVNLAITALRDEVEAENRARYGGRLQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MVSGSDSRSEPSQLSDRDLVESVLRDLSEAADKWEALVTQAETVTYSVDLGDVRAVANSDGRLLELTLHPGVMTGYAHGELADRVNLAITALRDEVEAENRARYGGRLQ
Prediction	CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEHCCCEEEEHCCCCCEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Conf.Score	9988998877656885899999999999999999999998774567776675788876899689999766545787657888999999999999999887655588999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MVSGSDSRSEPSQLSDRDLVESVLRDLSEAADKWEALVTQAETVTYSVDLGDVRAVANSDGRLLELTLHPGVMTGYAHGELADRVNLAITALRDEVEAENRARYGGRLQ
Prediction	7363566545445144441043015404611641441144054232413243032235563321403133131343334402531431032136526464445455648
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEHCCCEEEEHCCCCCEEEEEHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
MVSGSDSRSEPSQLSDRDLVESVLRDLSEAADKWEALVTQAETVTYSVDLGDVRAVANSDGRLLELTLHPGVMTGYAHGELADRVNLAITALRDEVEAENRARYGGRLQ

4k6nA

0.09

0.97

0.66

MUSTER

IRIALSYFKIDFSTSLNDLLKLLVENLINCKEGNSEYHEKIQKMINERQCYKMRVLVSKTGD-IRIEAIP--MPMEPILKLTTDYDSVSTYFIKTMLNGFLIDSTINWD

3f42A

0.14

0.11

0.79

0.77

dPPAS

------------------HDFSQLGGLLDGKKEFSQLEEKNKDTIHTSKSGGVSVSFNGLGELVDLQIDDSLLEDKEAQIYLSALNDGYKAVEENRKNLAFNLG-----

1pugA

0.14

0.11

0.76

0.70

wdPPAS

-----------------------MKQAQQMQEKMQKMQEEIAQLEVTGE-GLVKVTINGAHNCRRVEIDPSLLED-DKEMLEDLVAAAFNDAARRIEETQKEK-GMQLP

4k6nA

0.10

0.09

0.89

0.67

wMUSTER

I---------DFSTSLNDLLKLLVENLINCKEGNSEYHEKIQKMINERQCYKMRVLVSKTGD-IRIEAIP--MPMEPILKLTTDYDSVSTYFIKTMLNGFLIDSTINWD

1pugA

0.13

0.10

0.78

0.59

wPPAS

-----------------------MKQAQQMQEKMQKMQEEIAQLEVTGESGAVKVTINGAHNCRRVEIDPSLLED-DKEMLEDLVAAAFNDAARRIEETQKEKMASGMQ

1pugA

0.14

0.11

0.78

dPPAS2

-----------------------MKQAQQMQEKMQKMQEEIAQLEVTGESGAVKVTINGAHNCRRVEIDPSLLED-DKEMLEDLVAAAFNDAARRIEETQKEKMGMQLP

1pugA

0.13

0.10

0.78

0.74

PPAS

-----------------------MKQAQQMQEKMQKMQEEIAQLEVTGESGAVKVTINGAHNCRRVEIDPSLLED-DKEMLEDLVAAAFNDAARRIEETQKEKMASGMQ

3f42A

0.16

0.13

0.79

0.84

Env-PPAS

----------------HD--FSQLGGLLDGKKEFSQLEEKNKDTIHTSKSGGVSVSFNGLGELVDLQIDDSLLEDKEAQIYLSALNDGYKAVEENRKNLAFNL-G----

1w36E

0.10

1.00

0.64

MUSTER

FESGMLFEQQLIEDESLLRYQACADFWRRHCYPLPREIAQVVFETWKGPLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELDALIESSGID

1ybxB

0.17

0.14

0.81

0.74

dPPAS

-----------------NINNLVKQAQKQRDERVQEELKEKT-VEASAGGGAVTVVATGRKDIKEITIKPEVVDP-DDVELQDLILAAVNEALRKADEVTAEI--SKIT

(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=-3.12

Estimated TM-score = 0.36±0.12

Estimated RMSD = 11.1±4.6Å

Download Model 2

C-score=-3.72

Download Model 3

C-score=-3.22

Download Model 4

C-score=-3.05

Download Model 5

C-score=-4.69

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	1pugA	0.678	1.98	0.118	0.780
2	3f42A	0.635	2.24	0.151	0.789
3	3ixzA4	0.589	3.82	0.111	0.890
4	4uhwA	0.577	4.14	0.067	0.927
5	1ybxB	0.575	2.65	0.186	0.734
6	3vuoA	0.574	3.64	0.031	0.862
7	1wygA	0.565	4.23	0.056	0.973
8	3snhA2	0.554	3.10	0.083	0.789
9	2w6dA2	0.552	3.55	0.104	0.872
10	3g61A	0.549	3.98	0.041	0.807

(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	0.22	18	1n1qA	FEO	Rep, Mult	95,99
2	0.05	4	2w6dB	CPL	Rep, Mult	46,47,48,49,50,91,92,95
3	0.04	3	2h9dD	CA	Rep, Mult	80,83
4	0.03	2	2qtsC	MAL	Rep, Mult	97,100,101,104
5	0.03	2	3prqX	CLA	Rep, Mult	85,92
6	0.02	2	2ckjA	FES	Rep, Mult	49,50,51,53,86,87,88,89
7	0.02	2	2w6dA	GDP	Rep, Mult	44,45,46,47,94
8	0.01	1	3au2A	CA	Rep, Mult	16,18
9	0.01	1	3i0oA	MG	Rep, Mult	58,65
10	0.01	1	4ehtA	ACT	Rep, Mult	31,61,62,63
11	0.01	1	4n6hA	OLA	Rep, Mult	88,91,92,95
12	0.01	1	2ckjB	FES	Rep, Mult	48,56,57,58,61,63,89,95
13	0.01	1	1pug0	III	Rep, Mult	61,63,66,67,68,70,73,78,81,82,85,86,89,90
14	0.01	1	2nsfA	ZN	Rep, Mult	65,69
15	0.01	1	1smyF	MG	Rep, Mult	51,52
16	0.01	1	3fqnA	MG	Rep, Mult	42,93

	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	1fo4A	0.573	3.71	0.050	0.890	1.17.1.4	NA
2	0.060	1t9kD	0.490	4.26	0.079	0.817	5.3.1.23	NA
3	0.060	1flcD	0.530	3.25	0.067	0.761	3.1.1.53	44
4	0.060	1b65A	0.488	3.49	0.065	0.688	3.4.11.9	46,58
5	0.060	2np0A	0.512	4.11	0.096	0.807	3.4.24.69	103
6	0.060	3b9jC	0.376	5.07	0.010	0.771	1.17.3.2,1.17.1.4	NA
7	0.060	2pflA	0.498	3.92	0.028	0.826	2.3.1.54	47,90
8	0.060	2ckjA	0.438	4.96	0.071	0.817	1.17.1.4,1.17.3.2	NA
9	0.060	1q8iA	0.523	3.97	0.061	0.817	2.7.7.7	95
10	0.060	3ikmC	0.499	3.42	0.058	0.780	2.7.7.7	NA
11	0.060	3g61A	0.549	3.98	0.041	0.807	3.6.3.44	41
12	0.060	1g5iD	0.524	3.80	0.067	0.835	2.7.7.7	44
13	0.060	2e1qA	0.508	3.92	0.108	0.826	1.17.3.2,1.17.1.4	NA
14	0.060	1iv8A	0.487	4.20	0.047	0.817	5.4.99.15	NA
15	0.060	3b8eC	0.543	4.03	0.020	0.862	3.6.3.9	NA
16	0.060	1clqA	0.539	4.04	0.083	0.862	2.7.7.7	92
17	0.060	3ikmB	0.389	4.86	0.048	0.761	2.7.7.7	NA
18	0.060	1up8A	0.472	3.98	0.056	0.743	1.11.1.18	NA
19	0.060	3b9jJ	0.351	4.74	0.065	0.679	1.17.1.4,1.17.3.2	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	0.24	0.678	1.98	0.12	0.78	1pugA	GO:0003677 GO:0005737 GO:0005829 GO:0009295 GO:0043590
1	0.21	0.635	2.18	0.11	0.77	1j8bA	GO:0003677 GO:0005737 GO:0009295 GO:0043590
2	0.20	0.669	2.22	0.14	0.83	3f42A	GO:0003677 GO:0005737 GO:0009295 GO:0043590
3	0.16	0.595	2.63	0.17	0.75	1ybxB	GO:0003677 GO:0005737 GO:0009295 GO:0043590
4	0.07	0.480	4.47	0.05	0.87	4uhxA	GO:0003824 GO:0004031 GO:0004854 GO:0005506 GO:0005737 GO:0005829 GO:0006954 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0042816 GO:0043546 GO:0046872 GO:0050660 GO:0051287 GO:0051536 GO:0051537 GO:0055114 GO:0070062 GO:0072593
5	0.07	0.438	4.96	0.07	0.82	2ckjA	GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
6	0.07	0.472	4.55	0.06	0.85	3a3yA	GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
7	0.07	0.466	4.33	0.08	0.82	3w5bA	GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
8	0.07	0.485	4.41	0.08	0.86	3b8eA	GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
9	0.07	0.493	3.55	0.02	0.76	1mhsA	GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
10	0.07	0.476	3.77	0.06	0.74	4bbjA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
11	0.07	0.494	4.56	0.03	0.87	3ixzA	GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
12	0.07	0.505	3.67	0.07	0.75	3j09A	GO:0000166 GO:0005507 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
13	0.07	0.465	2.79	0.04	0.63	1ffuB	GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
14	0.07	0.468	2.83	0.06	0.62	1t3qB	GO:0016491 GO:0055114
15	0.07	0.445	4.28	0.07	0.78	3b8cA	GO:0000166 GO:0000287 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0046872 GO:0051453
16	0.06	0.411	2.56	0.11	0.51	1n63B	GO:0005507 GO:0016491 GO:0018492 GO:0030151 GO:0046872 GO:0055114
17	0.06	0.436	3.39	0.06	0.62	3fahA	GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
18	0.06	0.319	4.93	0.08	0.61	1t3qC	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.59
Biological Processes	GO:0009115	GO:0072593	GO:0006954	GO:0055114	GO:0042816
GO-Score	0.07	0.07	0.07	0.07	0.07
Cellular Component	GO:0043590	GO:0044444
GO-Score	0.59	0.57

(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 Rv0030

[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]