I-TASSER results

I-TASSER results for job id Rv2297

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

Input Sequence in FASTA format

>protein (150 residues)
MAMEMAMMGLLGTVVGASAMGIGGIAKSIAEAYVPGVAAAKDRRQQMNVDLQARRYEAVR
VWRSGLCSASNAYRQWEAGSRDTHAPNVVGDEWFEGLRPHLPTTGEAAKFRTAYEVRCDN
PTLMVLSLEIGRIEKEWMVEASGRTPKHRG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAMEMAMMGLLGTVVGASAMGIGGIAKSIAEAYVPGVAAAKDRRQQMNVDLQARRYEAVRVWRSGLCSASNAYRQWEAGSRDTHAPNVVGDEWFEGLRPHLPTTGEAAKFRTAYEVRCDNPTLMVLSLEIGRIEKEWMVEASGRTPKHRG
Prediction	CCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCEEEEEEEEHCCCEEEEEEEEEEEHCHHHEHCCCCCCCCCCC
Conf.Score	975467776666654444445456778788886555456677777655645565566888888755555678888775677778887665577776467888887544444578888589847999877544434444443688888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MAMEMAMMGLLGTVVGASAMGIGGIAKSIAEAYVPGVAAAKDRRQQMNVDLQARRYEAVRVWRSGLCSASNAYRQWEAGSRDTHAPNVVGDEWFEGLRPHLPTTGEAAKFRTAYEVRCDNPTLMVLSLEIGRIEKEWMVEASGRTPKHRG
Prediction	743431232122223323332123104310532132123255445525252434425114213421141542244154455544234222540164044323443533424322514064220110213244145512251545446668
	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

CCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCEEEEEEEEHCCCEEEEEEEEEEEHCHHHEHCCCCCCCCCCC
MAMEMAMMGLLGTVVGASAMGIGGIAKSIAEAYVPGVAAAKDRRQQMNVDLQARRYEAVRVWRSGLCSASNAYRQWEAGSRDTHAPNVVGDEWFEGLRPHLPTTGEAAKFRTAYEVRCDNPTLMVLSLEIGRIEKEWMVEASGRTPKHRG

4clvA

0.17

0.15

0.89

0.67

MUSTER

RTFRLSVSTLVGALVGVLMAIVGVYVTHSTEEPHTSLHEMLHDAEREILELKEEEFTARRREIESRLRAANGKLAESIAKNPQWSPEVEATREVERAAADL----QRATLVHVFEMR-------GLKPEHRAAYDRVLVDALKR------

4v1fA

0.18

0.10

0.57

0.54

dPPAS

MELDPNALITAGALIGGGIMGGGAIGAGIGDGIAGNALISGIARQ----PEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPGLQ-------------------------------------------------------------

1o54A2

0.17

0.15

0.92

0.52

wdPPAS

SSFIAMMLDV-GDRIGV---GSGAMCAVLARAVGSGKVFAYEKREEF-AKLAESNLTKWGLIERVTIKVRDISEGFDEKD-DVPDPWNYIDKCWEALKG-CPTTNQVQETLKKLQ---ELPFIRIEVWES--LFRPYKPVPERLRPVDRM

1o54A2

0.17

0.15

0.92

0.63

wMUSTER

SSFIAMMLDV-GRITGV---GSGAMCAVLARAVGSSVFAY-EKREEF-AKLAESNLTKWGLIERVTIKVRDISEGFDEKD-DVPDPWNYIDKCWEALKGRFPTTNQVQETLKKLQ---ELPFIRIEVWES--LFRPYKPVPERLRPVDRM

4mkxA1

0.23

0.15

0.68

0.59

wPPAS

MTQK-----IIG-IVGL-----GRLGKIHATNIAQHQAAT-SVVPAE-LDWAKKELGVEEV-----------FEDFDD--QH---ADI--D-------PHLQQIESALN---A-HVFSEKP--IGLDIE----AIEHTQQVIAQHANLKG

2prrK

0.20

0.17

0.85

0.56

dPPAS2

LAHRRAFFAYHDALLKDGGLTKGEREIVVATSAANQVVAHGAILRIYEKKPLVADQVAVNYLKADIPPRQRALDFALK---VCKASHEVNEADFEALREHGFTDEDAW------DI------AAITAFTIGRPNDEFFL---GRVP----

1o54A2

0.16

0.15

0.92

0.60

PPAS

VYDSSFIAMMLDRITGV---GSGAMCAVLARAVGSSVFAY-EKREEF-AKLAESNLTKWGLIERVTIKVRDISEGFDEKDVD-DVPDYI-DKCWEALKGVCPTTNQVQE---TLKKLQELPFIRIEVWES--LFRPYKPVPERLRPVDRM

4crnX1

0.19

0.15

0.76

0.68

Env-PPAS

------VKKLVQSLEKARGNGTSMI--SL---VIPPKGLIPLYQKMLTDEYGTASNIKSRVNRLSVLSAITSTQQKLKLYNTLP-KNVL----YCG---DIITEDGKEKYKNTSLYLCDN----KFHTEV--LSE--LLQA---------

2b5uA3

0.16

0.14

0.88

0.64

MUSTER

-------------PVEAAERNYERARAELNQAN-EDVARNQERQAKA-VQVYNSRKSELDAANKTLADAIAEIKQFNRFAHD---PMAGGMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDKKRSAENNLNDEKN

4clvA

0.17

0.15

0.89

0.52

dPPAS

RTFRLSVSTLVGALVGVLMAIVGVYVTHSTEEPHTSLHEMLHDAEREILELKEEEFTARRREIESRLRAANGKLAESIAKNPQWSPEVEETREVERAAADL----QRATLVHVFEMR------AGLKPEHRAAYDRVLVDALKR------

(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=-3.68

Estimated TM-score = 0.31±0.10

Estimated RMSD = 13.4±4.1Å

Download Model 2

C-score=-4.30

Download Model 3

C-score=-5.00

Download Model 4

C-score=-4.98

Download Model 5

C-score=-5.00

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	3oaaA	0.603	4.06	0.093	0.913
2	3j9tB	0.600	4.14	0.043	0.913
3	1o54A2	0.599	3.44	0.103	0.820
4	3gqbB	0.598	4.05	0.050	0.913
5	1kmhA	0.598	4.09	0.100	0.913
6	2ytzA	0.596	3.85	0.107	0.867
7	5bn3B	0.592	4.22	0.029	0.920
8	3mb5A2	0.590	3.63	0.109	0.833
9	2qe7A	0.590	4.22	0.093	0.920
10	4j1qA2	0.589	4.30	0.070	0.907

(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	0.05	2	4h1zA	MG	Rep, Mult	82,95,106
2	0.05	2	3lhdB	SAH	Rep, Mult	13,25,41,42,100,101,102
3	0.05	2	3lgaA	SAH	Rep, Mult	22,23,24,25,41,42,48,71,72
4	0.05	2	1y9eA	NAD	Rep, Mult	3,7,127,128,129,140
5	0.05	2	3oehK	ANP	Rep, Mult	71,72,79,81
6	0.02	1	2hldB	ANP	Rep, Mult	28,59,63
7	0.02	1	1bmfB	ANP	Rep, Mult	6,29,33
8	0.02	1	3c3yA	CA	Rep, Mult	91,119,120
9	0.02	1	2o78A	TCA	Rep, Mult	114,117
10	0.02	1	3ugvA	MG	Rep, Mult	98,101
11	0.02	1	1i6nA	ZN	Rep, Mult	57,82,84,129
12	0.02	1	3b04D	MG	Rep, Mult	84,87
13	0.02	1	1suiA	CA	Rep, Mult	82,119,120
14	0.02	1	4e5tF	MG	Rep, Mult	95,106
15	0.02	1	3mqtD	MG	Rep, Mult	82,95,106,148

	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	0.066	1f38A	0.585	4.04	0.104	0.853	2.1.1.-	NA
2	0.060	1fduC	0.570	4.16	0.088	0.847	1.1.1.62	67
3	0.060	1z45A	0.569	4.14	0.097	0.853	5.1.3.2,5.1.3.3	NA
4	0.060	1xg5C	0.571	4.37	0.086	0.867	1.-.-.-	NA
5	0.060	1yxmA	0.571	4.43	0.076	0.887	1.3.1.38	12,16
6	0.060	2yvlA	0.584	3.50	0.075	0.813	2.1.1.36	NA
7	0.060	3gqbA	0.558	4.64	0.042	0.947	3.6.3.14	NA
8	0.060	1wmaA	0.562	4.16	0.075	0.827	1.1.1.184	64
9	0.060	2pwyA	0.572	3.78	0.117	0.827	2.1.1.36	13
10	0.060	3cbgA	0.569	3.33	0.062	0.787	2.1.1.-	NA
11	0.060	1o54A	0.599	3.44	0.103	0.820	2.1.1.-	37
12	0.060	2r9vA	0.583	4.21	0.094	0.907	3.6.3.14	30
13	0.060	1a27A	0.563	4.24	0.079	0.860	1.1.1.62	48
14	0.060	2gdzA	0.574	4.09	0.050	0.847	1.1.1.141	NA
15	0.060	3b2qA	0.569	4.38	0.064	0.907	3.6.3.14	60
16	0.060	2b9eA	0.570	3.89	0.057	0.833	2.1.1.-	NA
17	0.060	2hrbA	0.560	4.09	0.092	0.820	1.1.1.184	NA
18	0.060	2ixaA	0.572	4.07	0.067	0.860	3.2.1.49	NA
19	0.060	2dpyB	0.588	4.40	0.071	0.933	3.6.3.14	54
20	0.060	2as0A	0.572	3.67	0.080	0.800	2.1.1.-	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	0.07	0.603	4.06	0.09	0.91	3oaaA	GO:0000166 GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016020 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0045261 GO:0046034 GO:0046933 GO:0046961
1	0.07	0.566	4.43	0.05	0.91	3qiaA	GO:0000166 GO:0004518 GO:0004519 GO:0005524 GO:0006314 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016539 GO:0016787 GO:0016820 GO:0033178 GO:0046034 GO:0090305
2	0.07	0.558	4.64	0.04	0.95	3gqbA	GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
3	0.07	0.585	4.04	0.10	0.85	1f38A	GO:0006479 GO:0008168 GO:0008276 GO:0009236 GO:0016740 GO:0032259 GO:0046140
4	0.07	0.590	3.63	0.11	0.83	3mb5A	GO:0008033 GO:0008168 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
5	0.07	0.578	3.68	0.04	0.81	4p7kA	GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
6	0.07	0.590	4.10	0.03	0.91	5bn4B	GO:0005524 GO:0015991 GO:0016820 GO:0033178
7	0.07	0.577	4.25	0.10	0.91	4nphA	GO:0000166 GO:0005524 GO:0005737 GO:0006754 GO:0006810 GO:0006811 GO:0009058 GO:0009405 GO:0015031 GO:0015992 GO:0016787 GO:0016887 GO:0030254 GO:0030257 GO:0030430 GO:0033644 GO:0043621 GO:0044128 GO:0046961 GO:0050714 GO:0051087 GO:1902600
8	0.07	0.585	4.10	0.05	0.91	5bn4A	GO:0000166 GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016787 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
9	0.07	0.583	4.25	0.04	0.91	2rkwB	GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
10	0.07	0.571	3.76	0.12	0.83	5c1iB	GO:0008033 GO:0008168 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
11	0.07	0.574	3.80	0.11	0.83	1i9gA	GO:0005886 GO:0008033 GO:0008168 GO:0008757 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
12	0.07	0.575	3.61	0.09	0.83	5ccxA	GO:0005634 GO:0005654 GO:0006400 GO:0008033 GO:0008168 GO:0016429 GO:0016740 GO:0030488 GO:0031515 GO:0032259
13	0.07	0.555	3.86	0.13	0.82	3busA	GO:0008152 GO:0008168 GO:0016740 GO:0032259
14	0.07	0.562	4.42	0.07	0.93	2oblA	GO:0000166 GO:0005524 GO:0005737 GO:0006754 GO:0009058 GO:0016887 GO:0030254 GO:0030257 GO:0044780 GO:0046872 GO:0046961 GO:1902600
15	0.07	0.552	4.18	0.11	0.84	3oifB	GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0030497 GO:0051289 GO:0055114 GO:0070417
16	0.07	0.577	4.40	0.05	0.91	3tgwA	GO:0005524 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015991 GO:0015992 GO:0016820 GO:0033178 GO:0042777 GO:0046034 GO:0046933
17	0.07	0.570	3.43	0.05	0.80	3duwA	GO:0008168 GO:0008171 GO:0016740 GO:0032259
18	0.07	0.599	3.44	0.10	0.82	1o54A	GO:0016429 GO:0030488 GO:0031515
19	0.07	0.575	3.97	0.11	0.86	4kdcA	GO:0005829 GO:0006744 GO:0008168 GO:0008425 GO:0008689 GO:0008757 GO:0016740 GO:0032259 GO:0043431 GO:0061542 GO:0102004

Consensus prediction of GO terms

Molecular Function	GO:0022804	GO:0016817	GO:0035639	GO:0032550	GO:0032559
GO-Score	0.38	0.38	0.38	0.38	0.38
Biological Processes	GO:0046034	GO:0046129	GO:0015988	GO:0090662	GO:0009168	GO:0009206	GO:0009152
GO-Score	0.38	0.38	0.38	0.38	0.38	0.38	0.38
Cellular Component	GO:0016469
GO-Score	0.38

(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.