I-TASSER results

I-TASSER results for job id Rv3122

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

Input Sequence in FASTA format

>protein (156 residues)
MYSGCWINNQNGETRVGEDSLEDLEQRRARLYDQLAATGDFRRGSISENYRRCGKPNCVC
AQEGHPGHGPRYLWTRTVAGRGTKGRQLSVEEVDKVRAELANYHRFAQVSEQIVAVNEAI
CEARPPNPAATAPPAGTTGHKKGGSATRSRRSSPPR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MYSGCWINNQNGETRVGEDSLEDLEQRRARLYDQLAATGDFRRGSISENYRRCGKPNCVCAQEGHPGHGPRYLWTRTVAGRGTKGRQLSVEEVDKVRAELANYHRFAQVSEQIVAVNEAICEARPPNPAATAPPAGTTGHKKGGSATRSRRSSPPR
Prediction	CCCCCCHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCEHCCCCCCCCCCEEEEEEHCCCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	988864557788654578999999999999999999876655443578788878987476578999999857888775986654555677647899998999999999999999999999997998755689999888877888754456788999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MYSGCWINNQNGETRVGEDSLEDLEQRRARLYDQLAATGDFRRGSISENYRRCGKPNCVCAQEGHPGHGPRYLWTRTVAGRGTKGRQLSVEEVDKVRAELANYHRFAQVSEQIVAVNEAICEARPPNPAATAPPAGTTGHKKGGSATRSRRSSPPR
Prediction	734201133752644335631541454355125415424413423234314513454041275445332231223442645434454244651550374154154035015403514451264427344263444444445543544455566468
	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

CCCCCCHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCEHCCCCCCCCCCEEEEEEHCCCCCCEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MYSGCWINNQNGETRVGEDSLEDLEQRRARLYDQLAATGDFRRGSISENYRRCGKPNCVCAQEGHPGHGPRYLWTRTVAGRGTKGRQLSVEEVDKVRAELANYHRFAQVSEQIVAVNEAICEARPPNPAATAPPAGTTGHKKGGSATRSRRSSPPR

4ltyC

0.12

0.96

0.71

MUSTER

IVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHSVATLNESRDIMAFLNTTVV--ASAGHAPQILPRRD-GTPGAVLCPIPFLRPRDIITSQKQQHLLAAITDYYQQHYADACKLRGDQPLPI---LTTVGASKSDAVRDIYIGTLDA

1v95A

0.14

0.11

0.79

0.54

dPPAS

GPVDCSVIVVNKQTKDYAESVGRKVRDLGMVVDLIFLNTEVSLSQALEDVSRGGSPFAIVITQQHQIHR--SCTVNIMFGTPQEHRNMP------------QADAMVLVARNYERYKNECREKEREEIARQASGPSSG------------------

2mf8A

0.26

0.12

0.47

0.57

wdPPAS

-------------------------------------------------LLTCPTPGC----DGS-GH---------ITGNYASHRSLSGCPLAD-------------------KSLRNLMAAHSADLKCPTPGCDGSGHITGNYASHRSLSGCPR

4ltyC

0.17

0.15

0.92

0.72

wMUSTER

IVAGDVFDTGSPPSTLYNRFVVNLQQTGCHL---VVLAGNHSVATLNESRDIMAFLNTTVV--ASAGHAPQILPRRD-GTPGAVLCPIPFLRPRDIITSQKQQHLLAAITDYYQQHYADACKLRGDQPLPI------TGH-VGASKSDAVRDIYIG

3iz5P

0.30

0.25

0.83

0.60

wPPAS

MYK--WRRKQ-------SDVMRFVQRVRCWEYRQQPAI--LTRPTRPDKARRLGKAKYRVRRRG--GRKPV---PKGIVYGKPKHQLKFQRNKRSVAEERAGRKRV--VNEEI------IL--DVAHSAIRNDPRGLTGKKKGTHHARSRRATWKR

5boxA1

0.20

0.13

0.69

0.70

dPPAS2

-----------SKDRMVELLQEHFNLYEARAYVALVAFG---VLTPAELASVSEVPAPRTEKKG---------FAMTQPGKTNKYRPVH-PANVLEKFIQDWQERVKEELEAKKKAKEELLELMAPLIETE-------------------------

2k27A

0.19

0.15

0.81

0.73

PPAS

IRSG----NQNGVVRQRIVDLAHQGVRPCDISRQLR----VSHGCVSKILGRYYETGS-----IRPGVIG--------GSKPKVA-------TPKVVEKIGDYKRQNPTMF-AWEIRDRLLAEGVCDND-TVPSVQQPFNLPMDSGAPGGGSHHHH

1szqA2

0.15

0.13

0.85

0.78

Env-PPAS

SFPAE---------FHSQTAVEAATLYEQQAAGKTA--ADIEKVTIEACIRIIDKKGPLNNPADRD-HCIQYVAIPLLFGRLT---------AADYEDNVAQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTDGTRFEEVVVE---

5fvmA

0.08

0.99

0.69

MUSTER

PLTVAIKSDSVSRQRAALSIIDKMRMHSPKLVNQAELVSDELIRGLEDASRQFFGEH-KMFATLEPLHEMLKRGPETLREISFQNSFGRDEWVLNYKRDINNLNQAWDIYYNVFRRISRKLPQLQTLDLQHVSPKLSAAKDLELAVPGTYHAGKPI

2r1iA

0.14

0.13

0.91

0.54

dPPAS

--------DDSASVEVPRRATPADAATVAQLHDFNTEFGAPTPGLASRLSHLLAGEDVVVLLAGEPPTGLAVLSFRPNVWYPGPVAILDELYVR------PGRRGHRLGSALLAASCGLVRSRGGALLEINVDGEDTDARRARGFTNTEPNGTEPL

(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=-4.04

Estimated TM-score = 0.28±0.09

Estimated RMSD = 14.4±3.7Å

Download Model 2

C-score=-4.61

Download Model 3

C-score=-4.81

Download Model 4

C-score=-4.99

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	4ltyC	0.654	3.67	0.110	0.929
2	4z0vA2	0.567	4.14	0.060	0.859
3	3ngnA	0.566	4.12	0.038	0.853
4	2z1aA	0.560	4.25	0.051	0.840
5	1oidA	0.557	4.22	0.021	0.846
6	2nxfA	0.556	4.30	0.083	0.853
7	3wcxA	0.551	4.51	0.085	0.891
8	4h1sA	0.551	4.11	0.073	0.827
9	2hs3A3	0.542	4.34	0.074	0.872
10	5ebbA	0.539	4.17	0.051	0.833

(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	0.07	3	3m4oA	C7P	Rep, Mult	119,120,123
2	0.05	2	3rbmD	B73	Rep, Mult	109,113
3	0.05	2	5l8gK	CA	Rep, Mult	112,115
4	0.05	2	1focA	HEM	Rep, Mult	53,58
5	0.02	1	2j78A	CA	Rep, Mult	22,25,56
6	0.02	1	1e1zP	NDG	Rep, Mult	74,116,123
7	0.02	1	2xgxA	AKG	Rep, Mult	114,118
8	0.02	1	1nw5A	CL	Rep, Mult	57,58,127
9	0.02	1	3gjbB	FE2	Rep, Mult	68,140
10	0.02	1	1f4nA	CA	Rep, Mult	123,124,127
11	0.02	1	2hi8X	BR	Rep, Mult	21,30,31
12	0.02	1	1nl1A	CA	Rep, Mult	18,22
13	0.02	1	2gqkA	NI	Rep, Mult	44,53,58,140
14	0.02	1	1p91A	ZN	Rep, Mult	53,58,60,68
15	0.02	1	2hj6L	PS2	Rep, Mult	35,120
16	0.02	1	1n3tO	GTP	Rep, Mult	52,55

	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	1nqkA	0.491	4.87	0.056	0.859	1.14.14.5	4
2	0.060	1warA	0.493	4.44	0.091	0.782	3.1.3.2	63
3	0.060	3cuxA	0.501	4.84	0.049	0.859	2.3.3.9	33
4	0.060	3g0sA	0.490	4.59	0.043	0.808	4.2.1.52	NA
5	0.060	1fsuA	0.520	4.75	0.122	0.853	3.1.6.12	NA
6	0.060	1qoxM	0.501	5.39	0.053	0.910	3.2.1.21	35
7	0.060	1oidA	0.557	4.22	0.021	0.846	3.6.1.45,3.1.3.5	NA
8	0.060	2ddtA	0.525	4.50	0.103	0.859	3.1.4.12	NA
9	0.060	1p4kA	0.493	4.45	0.046	0.788	3.5.1.26	NA
10	0.060	2gq3A	0.503	5.18	0.084	0.891	2.3.3.9	NA
11	0.060	2z1aA	0.560	4.25	0.051	0.840	3.1.3.5	76
12	0.060	1ayyD	0.375	4.78	0.083	0.603	3.5.1.26	67
13	0.060	2jc5A	0.499	4.55	0.053	0.827	3.1.11.2	NA
14	0.060	1ho5A	0.554	4.14	0.036	0.833	3.1.3.5,3.6.1.45	52
15	0.060	2c8nA	0.494	5.06	0.035	0.859	3.2.1.55	NA
16	0.060	2voaA	0.498	4.42	0.068	0.814	4.2.99.18	NA
17	0.060	2a3zB	0.503	4.49	0.039	0.814	3.1.21.1	NA
18	0.060	1qoxA	0.501	5.42	0.060	0.917	3.2.1.21	NA
19	0.060	1pz2A	0.495	5.07	0.049	0.859	3.2.1.55	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	0.09	0.659	3.49	0.11	0.92	4ltyA	GO:0004518 GO:0004519 GO:0004527 GO:0006259 GO:0006260 GO:0006310 GO:0008408 GO:0016787 GO:0046872 GO:0090305
1	0.07	0.569	4.03	0.03	0.85	3ngoA	GO:0000288 GO:0000289 GO:0004518 GO:0004527 GO:0004535 GO:0005634 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0006397 GO:0006417 GO:0006977 GO:0008284 GO:0010606 GO:0016787 GO:0030014 GO:0031047 GO:0046872 GO:0061157 GO:0090503
2	0.07	0.561	4.14	0.10	0.83	3qg5D	GO:0003677 GO:0004518 GO:0004519 GO:0004527 GO:0006259 GO:0006260 GO:0006310 GO:0008408 GO:0016787 GO:0046872 GO:0090305
3	0.07	0.560	4.25	0.05	0.84	2z1aA	GO:0000166 GO:0009166 GO:0016787 GO:0016788 GO:0046872
4	0.07	0.517	4.59	0.06	0.85	4zkfA	GO:0004518 GO:0004527 GO:0004535 GO:0005739 GO:0005759 GO:0006397 GO:0016787 GO:0046872 GO:0090305 GO:0090503
5	0.07	0.554	4.14	0.04	0.83	1ho5A	GO:0000166 GO:0008253 GO:0008768 GO:0009166 GO:0016311 GO:0016787 GO:0016788 GO:0030288 GO:0042597 GO:0046872
6	0.07	0.530	4.15	0.07	0.82	3mprA	GO:0004519 GO:0004527 GO:0090305
7	0.07	0.549	4.09	0.07	0.83	4h1yP	GO:0000166 GO:0005737 GO:0005886 GO:0006164 GO:0006195 GO:0006196 GO:0006259 GO:0007159 GO:0007420 GO:0008198 GO:0008253 GO:0009166 GO:0009986 GO:0010044 GO:0016020 GO:0016311 GO:0016787 GO:0016788 GO:0031225 GO:0046085 GO:0046086 GO:0046135 GO:0046872 GO:0046889 GO:0050728 GO:0070062 GO:0097060
8	0.07	0.532	4.37	0.06	0.83	3c9fB	GO:0009166 GO:0016787 GO:0046872
9	0.07	0.545	4.19	0.04	0.82	3ivdA	GO:0000166 GO:0009166 GO:0016787 GO:0016788 GO:0046872
10	0.07	0.536	4.17	0.07	0.83	4uwqA	GO:0000166 GO:0009166 GO:0016787 GO:0046872
11	0.07	0.533	3.85	0.05	0.76	3jyfA	GO:0000166 GO:0008663 GO:0009117 GO:0009166 GO:0016787 GO:0016788 GO:0046872
12	0.07	0.515	4.65	0.09	0.83	3ztvA	GO:0000166 GO:0008253 GO:0009166 GO:0016311 GO:0016787 GO:0016788 GO:0042597 GO:0046872
13	0.07	0.540	4.16	0.06	0.81	3g6sA	GO:0004519 GO:0004527 GO:0090305
14	0.07	0.512	3.97	0.08	0.77	3dscA	GO:0004518 GO:0004519 GO:0004527 GO:0006281 GO:0006302 GO:0006974 GO:0016787 GO:0030145 GO:0042802 GO:0046872 GO:0090305
15	0.07	0.526	4.27	0.05	0.83	4q7fA	GO:0000166 GO:0009166 GO:0016787 GO:0016788 GO:0046872
16	0.07	0.492	4.51	0.05	0.79	3d03A	GO:0000166 GO:0004115 GO:0016787 GO:0046872
17	0.07	0.515	4.64	0.09	0.83	3zu0B	GO:0000166 GO:0008253 GO:0009166 GO:0016311 GO:0016787 GO:0016788 GO:0042597 GO:0046872
18	0.07	0.502	4.52	0.05	0.82	4ykeB	GO:0004518 GO:0004519 GO:0004527 GO:0005634 GO:0006281 GO:0006302 GO:0006974 GO:0008408 GO:0016787 GO:0030145 GO:0030870 GO:0046872 GO:0051321 GO:0090305

Consensus prediction of GO terms

Molecular Function	GO:0016788	GO:0046872
GO-Score	0.52	0.31
Biological Processes	GO:0090304
GO-Score	0.41
Cellular Component	GO:0030014	GO:0005634	GO:0005829	GO:0005759
GO-Score	0.07	0.07	0.07	0.07

(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.