I-TASSER results

I-TASSER results for job id Rv0185

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

Input Sequence in FASTA format

>protein (169 residues)
MIGADVPRDSQRARVYAAEAFVRTLFDRVTAHGSPTVEFFGTQLTLPPEGRFGSVASVQR
YVDDVLALPAVGQNWPTVSPVRVRARRAATAAHYENHGGTGTIAVPDRHTAGWAMRELVV
LHEVAHHLCQVPPPHGPEFVATVCTLTELVMGPEVGHVFRVVYAQEGVR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MIGADVPRDSQRARVYAAEAFVRTLFDRVTAHGSPTVEFFGTQLTLPPEGRFGSVASVQRYVDDVLALPAVGQNWPTVSPVRVRARRAATAAHYENHGGTGTIAVPDRHTAGWAMRELVVLHEVAHHLCQVPPPHGPEFVATVCTLTELVMGPEVGHVFRVVYAQEGVR
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEHCCEEHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCEEEEHCCCCCCEEEEHCCCCEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCC
Conf.Score	9988888764678999999999999986665788758997657866865445789999999999997778898778888878875457764467747997599976899986688999999999986789999988799999999999986689999999998765789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MIGADVPRDSQRARVYAAEAFVRTLFDRVTAHGSPTVEFFGTQLTLPPEGRFGSVASVQRYVDDVLALPAVGQNWPTVSPVRVRARRAATAAHYENHGGTGTIAVPDRHTAGWAMRELVVLHEVAHHLCQVPPPHGPEFVATVCTLTELVMGPEVGHVFRVVYAQEGVR
Prediction	8666545444433312303410330033246444330312324130315441331630351044015142046415734213034444443231455762120000336624000210000020011137472533350031003003301233002001001254538
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEHCCEEHCCCCCCCCCHHHHHHHHHHHHHCHHHHHHCCCCCCEEEEHCCCCCCEEEEHCCCCEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCCC
MIGADVPRDSQRARVYAAEAFVRTLFDRVTAHGSPTVEFFGTQLTLPPEGRFGSVASVQRYVDDVLALPAVGQNWPTVSPVRVRARRAATAAHYENHGGTGTIAVPDRHTAGWAMRELVVLHEVAHHLCQVPPPHGPEFVATVCTLTELVMGPEVGHVFRVVYAQEGVR

3f1bA

0.13

0.12

0.93

0.74

MUSTER

----RLPRAVREQQLDAAVDVFSDR---FHETSDAIAAKAEISKPL---LYYGSFAACIQREGLRFV-EALAPAGDPGLSPREQLRRALEGGFVGKHRKSWVLYRQAQQAFVVQSSRDRLIELTAHLLESSTKQDFELIAIALVGAGEAVA-VDAAADLLESLAWRGLA

4qhfA

0.09

0.06

0.64

0.69

dPPAS

---------------------------------------------------MKDRKILNEILSNTINELNLNDKKANIK-IKIKPLK-RKIASISLTNKTIYINKNILPYLSDEEIRFILAHELLHL--KYGKYHINEFEEELLFLFPNKEAILINLINKLHQK-----

2x3aA2

0.13

0.11

0.85

0.74

wdPPAS

FSGRCT--NTQKSDLLTALDAASGISNNASSYGQRYRSWFGA----------YSSARWDQAETNFSKIKDAIDN----KPLTFDCSCKQSYFAYVYPDQPYKVYLPVTGSDS---RAGTIVHQLSH-AGTDDLGYGQANARNLAKT------PVKALADNHEYFAENTP

2x3aA2

0.13

0.11

0.84

0.77

wMUSTER

FSGRCT--NTQKSDLLTALDAASGISNNASSYGQRYRSWFGA----------YSSARWDQAETNFSKIKDAIDN----KPLTFDCSKQSYFAYV-YPDQPYKVYLPVTGSDS---RAGTIVHQLSH-AGTDDLGYGQANARNLAKT------PVKALADNHEYFAENTP

1ys3B

0.19

0.14

0.72

0.65

wPPAS

---------SDHVPV-DITDLLDRAAHDAARIYP------DLDVSLVPSPT-GLPAGLRLAVDNAIA-NAVKHG--GATLVQLSAVSSRAGVEIAIDDNG--SGVPEGE-GLALVAQQAQLHTA--SLENS-PLGGARLV---LRL------PGPS-------------

4jixA

0.11

0.07

0.64

1.05

dPPAS2

-------------------------------------------------GPMAINENKKD-IKDIVN-EILISL-NINESINIEIKPMKQKASFSFKTKTLRLNKYVVENFDEELLHYIILHELIHF-KIKSINHGIKFENELRNYKNECDEIELKIIQKLI-------

3f1bA

0.15

0.14

0.92

0.76

PPAS

----RLPRAVREQQLDAAVDVFSDRFHETSD---AIAAKAEISKPL---LYYGSAACIQREGLRFVEALAPAGD--PGLSPREQLRRALEGGFVGKHRKSWVLYRQQAFVGSVQSSRDRLIELTAHLLESSTKQDFELIAIALVGAGEAVA-VDAAADLLESLAWRGLA

4jiuA

0.19

0.11

0.59

0.97

Env-PPAS

--------------------------------------------------------MVEDLLEHAKDILGY------QRPVKVRIRPLKMSARVSFKYG--TITLPAVLNLEEEEMFYILIHELAHLKAET-SYHSSSFWREVEKV----FPRAKEIEDRIMTKLQRNM

5cwdA

0.11

0.96

0.71

MUSTER

-----TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAARAAAESNDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKES--KIAKKACKEVAKQAGMP

4jixA

0.11

0.07

0.66

0.68

dPPAS

--------------------------------------------------GPMAINENKKDIKDIVNEILISLNINESINIEIKPMK-QKIASFSFKTKTLRLNKYVVENFDEELLHYIILHELIHF-KIKSINHGIKFENELRNYF----SKNECDEIELKIIQKLI-

(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=-2.90

Estimated TM-score = 0.38±0.13

Estimated RMSD = 11.6±4.5Å

Download Model 2

C-score=-3.73

Download Model 3

C-score=-4.37

Download Model 4

C-score=-3.54

Download Model 5

C-score=-4.73

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	3v0aB	0.553	3.93	0.081	0.805
2	1z7hA	0.552	3.98	0.080	0.805
3	3vuoA	0.552	3.94	0.059	0.805
4	3ffzA	0.551	4.12	0.051	0.805
5	3fieA	0.547	4.06	0.073	0.799
6	1zb7A	0.547	4.01	0.058	0.799
7	3btaA1	0.546	4.11	0.080	0.811
8	1f31A1	0.546	4.12	0.072	0.805
9	3dbkA	0.544	4.11	0.090	0.805
10	3c37A	0.543	3.07	0.092	0.698

(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	0.42	25	4qhhA	ZN	Rep, Mult	122,126
2	0.07	5	3mdjA	BES	Rep, Mult	92,93,94,119,122,123,126,136,140,143
3	0.03	2	4xk8l	CLA	Rep, Mult	121,146,150
4	0.01	1	2x3bA	ZN	Rep, Mult	122,126,148
5	0.01	1	5dwkB	78N	Rep, Mult	103,116
6	0.01	1	3sb6A	CU	Rep, Mult	123,127

	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	1zkxB	0.550	4.07	0.066	0.799	3.4.24.69	NA
2	0.060	1jkyA	0.483	4.53	0.049	0.746	3.4.24.83	NA
3	0.060	2np0A	0.514	4.04	0.094	0.746	3.4.24.69	NA
4	0.060	1z1wA	0.521	3.98	0.103	0.740	3.4.11.-	NA
5	0.060	2imcB	0.546	3.95	0.088	0.793	3.4.24.69	NA
6	0.060	1zb7A	0.547	4.01	0.058	0.799	3.4.24.69	123
7	0.060	1bqbA	0.523	4.14	0.101	0.781	3.4.21.19,3.4.24.29	123
8	0.060	1ezmA	0.536	4.27	0.110	0.805	3.4.24.26	123
9	0.060	8tlnE	0.528	4.09	0.072	0.775	3.4.24.27	38
10	0.060	1espA	0.529	4.23	0.070	0.793	3.4.24.28	NA
11	0.060	2r7oA	0.504	4.91	0.065	0.840	2.7.7.48	125
12	0.060	3ciaA	0.508	4.18	0.079	0.746	3.4.11.-	NA
13	0.060	1h19A	0.538	3.77	0.110	0.746	3.3.2.6	105
14	0.060	1fj3A	0.532	4.05	0.070	0.781	3.4.24.27	NA
15	0.060	2gtqA	0.511	4.03	0.112	0.734	3.4.11.2	NA
16	0.060	1zn3A	0.549	3.99	0.058	0.799	3.4.24.69	19
17	0.060	1e1hC	0.452	3.49	0.062	0.627	3.4.24.69	19
18	0.060	3debA	0.516	3.98	0.054	0.746	3.4.24.69	NA
19	0.060	3cskA	0.494	4.46	0.049	0.746	3.4.14.4	19

(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	0.29	0.516	3.98	0.05	0.75	3debA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
1	0.28	0.555	3.94	0.08	0.80	1yvgA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
2	0.25	0.514	4.04	0.09	0.75	2np0A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
3	0.25	0.547	4.06	0.07	0.80	3fieA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
4	0.24	0.547	4.01	0.06	0.80	1zb7A	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0046872 GO:0050827 GO:0051609 GO:0071806
5	0.17	0.452	3.11	0.13	0.59	4jiuA	GO:0046872
6	0.07	0.553	3.93	0.08	0.80	3v0aB	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
7	0.07	0.552	3.94	0.06	0.80	3vuoA	GO:0004222 GO:0005576 GO:0006508 GO:0009405 GO:0050827 GO:0051609
8	0.07	0.508	4.19	0.02	0.76	5bqnA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
9	0.07	0.552	3.98	0.08	0.80	1z7hA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
10	0.07	0.554	3.97	0.08	0.81	1xtfA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
11	0.07	0.546	3.95	0.09	0.79	2imcB	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
12	0.06	0.359	5.52	0.04	0.66	3obrA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
13	0.06	0.547	4.13	0.08	0.81	3v0aA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806
14	0.06	0.355	5.90	0.05	0.71	3azvA	GO:0004222 GO:0005576 GO:0006508 GO:0008270 GO:0009405 GO:0050827 GO:0051609
15	0.06	0.367	5.75	0.07	0.69	3r4sA	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033619 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0045955 GO:0046872 GO:0050827 GO:0051609
16	0.06	0.307	5.59	0.07	0.56	1a8dA	GO:0004222 GO:0005576 GO:0005829 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0030666 GO:0030669 GO:0046872 GO:0046929 GO:0050827 GO:0051609 GO:0071806
17	0.06	0.324	5.55	0.06	0.60	3mppG	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016787 GO:0046872 GO:0050827 GO:0051609 GO:0071806
18	0.06	0.359	5.92	0.07	0.70	3rsjA	GO:0004222 GO:0005576 GO:0006508 GO:0008270 GO:0009405 GO:0050827 GO:0051609
19	0.06	0.550	4.07	0.07	0.80	1zkxB	GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0008320 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0020002 GO:0030430 GO:0033644 GO:0044156 GO:0044164 GO:0044221 GO:0044231 GO:0046872 GO:0050827 GO:0051609 GO:0071806

Consensus prediction of GO terms

Molecular Function	GO:0008270	GO:0004222	GO:0050827	GO:0008320
GO-Score	0.78	0.78	0.78	0.69
Biological Processes	GO:0006508	GO:0009405	GO:0051609	GO:0071806	GO:0017158	GO:1903306	GO:0046928	GO:0050805
GO-Score	0.78	0.78	0.78	0.69	0.58	0.58	0.55	0.55
Cellular Component	GO:0005576	GO:0016021	GO:0044156	GO:0044231	GO:0044164	GO:0030666	GO:0030665	GO:0071944	GO:0045334
GO-Score	0.78	0.60	0.60	0.60	0.60	0.55	0.55	0.55	0.55

(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.