I-TASSER results

I-TASSER results for job id Rv1954c

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

Input Sequence in FASTA format

>protein (173 residues)
MAAGSGGGTVGLVLPRVASLSGLDGAPTVPEGSDKALMHLGDPPRRCDTHPDGTSSAAAA
LVLRRIDVHPLLTGLGRGRQTVSLRNGHLVATANRAILSRRRSRLTRGRSFTSHLITSCP
RLDDHQHRHPTRCRAEHAGCTVATCIPNAHDPAPGHQTPRWGPFRLKPAYTRI

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MAAGSGGGTVGLVLPRVASLSGLDGAPTVPEGSDKALMHLGDPPRRCDTHPDGTSSAAAALVLRRIDVHPLLTGLGRGRQTVSLRNGHLVATANRAILSRRRSRLTRGRSFTSHLITSCPRLDDHQHRHPTRCRAEHAGCTVATCIPNAHDPAPGHQTPRWGPFRLKPAYTRI
Prediction	CCCCCCCCEEEEEEHCHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHCCCCCEEEEHCCCEEEEHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	98888887689875333344688899999887646677758998667899988756788888876545677775467765788557857653667888888776654456788888868677665556976554445787578875788899998889988875567654579
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MAAGSGGGTVGLVLPRVASLSGLDGAPTVPEGSDKALMHLGDPPRRCDTHPDGTSSAAAALVLRRIDVHPLLTGLGRGRQTVSLRNGHLVATANRAILSRRRSRLTRGRSFTSHLITSCPRLDDHQHRHPTRCRAEHAGCTVATCIPNAHDPAPGHQTPRWGPFRLKPAYTRI
Prediction	74435441100000231251442643333463444003313534541544463444210100043141331032234444324145230212044211443454245445123300330442564645334414363241200201342454444463342231414432467
	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

CCCCCCCCEEEEEEHCHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCHHHHHHHCCCCCEEEEHCCCEEEEHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
MAAGSGGGTVGLVLPRVASLSGLDGAPTVPEGSDKALMHLGDPPRRCDTHPDGTSSAAAALVLRRIDVHPLLTGLGRGRQTVSLRNGHLVATANRAILSRRRSRLTRGRSFTSHLITSCPRLDDHQHRHPTRCRAEHAGCTVATCIPNAHDPAPGHQTPRWGPFRLKPAYTRI

4hsrB1

0.22

0.20

0.90

0.69

MUSTER

----TLSPHVGLLRRRLEAL-----GARDDSAAEGLRQML----VAWDGRMDAASEVASAYNAFRRALTRLVTDR-SGLEQAIVSPQGQVWWAVPTLLRDDDAGMLKGWSWDQALSEALSNLTGRSEEH--RPRFTHPLATQAGLLNPASRPIGGGDTVLANGLVPSPQATY-

4hsrB1

0.19

0.17

0.92

0.59

dPPAS

----TLSPHVGLLRRRLEAL-----GARDDSAAEGLRQML----VAWDGRMDAASEVASAYNAFRRALTRLVTDRAISHPFAAVAPGGQVWWAVPTLLRDDDAGMLKGWSWDQALSEALSVASQNLTGRSHRPRFTHPLATQAGLLNPASRPIGGGDTVLANGLVPSAGPQAT

2gr3A1

0.26

0.21

0.82

0.51

wdPPAS

LKA--GAGLASVSFVAELRQAGYQG--LI--------TVVGDEAERPYDRPPLSKDFMAHGDAEKIDCK-WLLGVPQAH-TVALSDGLVLATGNDALARAAGLACDDGIFVDAYGRTTCPDVDVTRQRNPLFERIETWGIAVARHL--VDPTAPGYAE---------------

4hsrB1

0.23

0.20

0.86

0.63

wMUSTER

LSP-----HVGLLRRRLEAL-----GARDDSAAEGLRQML----VAWDGRMDAASEVASAYNAFRRALTRLVTD-RSGLEQAIVSPQGQVWWAVPTLLRDDDAGMLKGWSWDQALSEA--NLTGRSEEH--RPRFTHP---LATQFPNASRPIGGGDTVLANGLV--PSPQTY

1fehA1

0.20

0.12

0.61

0.49

wPPAS

M--------KTIII---------NGVQNTDEDTLKFARDNNDISALCF-LNN--NNDINKTV--EVE--------GTGLVTTLIEDGMIINTNSDAVNEKIKSRISQ------H-----E-FK------GP-C--NRRECEF-------LKLV-KARASK--PFLPK------

3ef6A1

0.24

0.20

0.83

0.59

dPPAS2

----TGNGVGGFTTAQALRAEGFEGEPHLPYDRPSLSKAVGSLERPPILAE------ADWYGEARIDML-TVTALDVQTRTISLDDGAIVIAAEPADQLARQAGLARGVIVDHCGATLAKGVDVASWPLRARRSLETYAAAVAAAI--LGKNVSAPQ----------------

4hsrB1

0.25

0.20

0.82

0.59

PPAS

--------TLGLLRRRLEAL-----GARDDSAAEGLRQML----VAWDGRMDAASEVASAYNAFRRADRSGLEQAAAVAPGVSPQ--GQVWWAVPTLLRDDDAGMLKGWSWDQALSEA--NLTGRSEEH--RPRFTHP---LATQFPPASRPIGGGDTVLANGLV--PSY---

4yk3A

0.15

0.10

0.65

0.59

Env-PPAS

--------TREEIADRMQH------NPLV-QAYQQEVMHWCGNSDVLKEKMQEQKPSEGEDLSRQVAENPTSVHKLAGRNLCGLKTNRRQAEEGFMHLCQALDGYTSAVTQAQENIKHVPQAE--ARRYG-------------------------------------------

4impA2

0.24

0.22

0.91

0.59

MUSTER

QPVRRTRETWLLVVPP----GGIEEALV--ERLTDALNTRGISTLRLDVPPAATSGELATELRAAADGDPVLTALD-ERPHPECKD---VPSGIALLLNLVKALGEADLRIPLWTITRGKAGPADRLLRPMRVAAEHPER-WGGLIPDSLDGDVLTRTNGLAEDQL--AI-R-

1i6wB

0.16

0.13

0.85

0.54

dPPAS

-------EHNPVVM-----VHGIGGASFNFAGIKSYLVSQGWSRDKLYDFWDKTGTNYNNGPVLSRFVQKVLDETGAKK-------VDIVAHSMGGANTLYYIKNLDGGNKVANVVTLGGTGKALPGTDP-------NQKILYTSIYSSADMIVMNYLSRLDGARNVHGVGHI

(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=-3.23

Estimated TM-score = 0.35±0.12

Estimated RMSD = 12.6±4.3Å

Download Model 2

C-score=-5.00

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

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	4hsrB	0.714	3.05	0.153	0.861
2	1cp9B	0.569	3.90	0.110	0.792
3	1e3aB	0.567	3.81	0.098	0.786
4	3k3wB	0.565	3.71	0.094	0.769
5	1oqzB	0.520	3.85	0.108	0.740
6	4yf9C	0.497	4.39	0.064	0.728
7	2wyeB1	0.475	4.44	0.091	0.717
8	1jqkA	0.474	5.10	0.035	0.809
9	2pffB	0.449	5.53	0.056	0.815
10	3ikmD1	0.446	5.14	0.069	0.751

(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	0.06	3	1vf5S	III	Rep, Mult	71,72
2	0.06	3	1u8rD	CO	Rep, Mult	23,38,133,136,137
3	0.04	2	1jqkA	SF4	Rep, Mult	18,19,22,27,34,37
4	0.04	2	3oyxA	MG	Rep, Mult	31,67
5	0.04	2	1qmdA	CA	Rep, Mult	42,43,44,45,48
6	0.04	2	3fefA	MG	Rep, Mult	47,88
7	0.04	2	4z9vA	BCT	Rep, Mult	42,47,57,64
8	0.02	1	4og8A	TBF	Rep, Mult	55,56
9	0.02	1	2yiuC	SMA	Rep, Mult	133,137
10	0.02	1	1y9aC	MG	Rep, Mult	4,52
11	0.02	1	2a69P	MG	Rep, Mult	65,69
12	0.02	1	3s8gA	OLC	Rep, Mult	17,115,116,117
13	0.02	1	1jqkB	SF4	Rep, Mult	8,11,48
14	0.02	1	4rku4	CLA	Rep, Mult	63,66
15	0.02	1	1smyF	MG	Rep, Mult	64,68,115
16	0.02	1	3s8gA	OLC	Rep, Mult	11,15,96,100
17	0.02	1	5d51L	KR	Rep, Mult	16,17,68

	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	2wybB	0.493	4.57	0.088	0.751	3.5.1.97	NA
2	0.060	1p1jA	0.431	5.26	0.060	0.746	5.5.1.4	4
3	0.060	2eabA	0.430	5.24	0.047	0.728	3.2.1.63	NA
4	0.060	1ca1A	0.435	5.08	0.071	0.740	3.1.4.3	NA
5	0.060	1khoA	0.434	5.02	0.071	0.734	3.1.4.3	NA
6	0.060	3gvhA	0.442	5.46	0.045	0.751	1.1.1.37	NA
7	0.060	2d4aD	0.433	5.48	0.033	0.746	1.1.1.37	16
8	0.060	1e3aB	0.567	3.81	0.098	0.786	3.5.1.11	NA
9	0.060	1cp9B	0.569	3.90	0.110	0.792	3.5.1.11	NA
10	0.060	3d0oB	0.420	5.56	0.039	0.746	1.1.1.27	50
11	0.060	2a92C	0.431	5.44	0.013	0.728	1.1.1.27	NA
12	0.060	1xmeA	0.441	4.94	0.063	0.705	1.9.3.1	137
13	0.060	2e37C	0.414	5.43	0.056	0.734	1.1.1.27	NA
14	0.060	2v7pA	0.430	5.40	0.054	0.728	1.1.1.27	NA
15	0.060	1ldxA	0.408	5.45	0.061	0.728	1.1.1.27	33,118
16	0.060	1uxiA	0.437	5.42	0.040	0.740	1.1.1.37	97
17	0.060	1ojsA	0.418	5.67	0.046	0.763	1.1.1.37	67
18	0.060	2ewdA	0.435	5.32	0.019	0.734	1.1.1.27	17
19	0.060	1i10A	0.427	5.21	0.034	0.746	1.1.1.27	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	0.569	3.90	0.11	0.79	1cp9B	GO:0016787 GO:0016811 GO:0017000 GO:0046872
1	0.07	0.565	3.71	0.09	0.77	3k3wB	GO:0008953 GO:0016787 GO:0016811 GO:0017000 GO:0046872
2	0.07	0.569	3.81	0.10	0.79	4pemD	GO:0016787 GO:0016811 GO:0017000
3	0.07	0.567	3.81	0.10	0.79	1e3aB	GO:0008953 GO:0016787 GO:0016811 GO:0017000 GO:0042597 GO:0046677 GO:0046872
4	0.06	0.519	3.86	0.11	0.74	3s8rB	GO:0016787 GO:0016811 GO:0017000 GO:0033968 GO:0042597 GO:0046677
5	0.06	0.488	4.56	0.10	0.75	4m1jC	GO:0009372 GO:0009392 GO:0016787 GO:0016811 GO:0017000 GO:0042597
6	0.06	0.497	4.39	0.06	0.73	4yf9C	GO:0016787 GO:0016811 GO:0017000
7	0.06	0.338	5.03	0.08	0.57	5it0A	GO:0000287 GO:0004647 GO:0006564 GO:0008152 GO:0008652 GO:0016311 GO:0016597 GO:0016787 GO:0016791 GO:0046872
8	0.06	0.315	5.34	0.05	0.57	2p73A	GO:0000166 GO:0016021 GO:0016740 GO:0016757 GO:0046872
9	0.06	0.266	5.30	0.07	0.47	3g5kA	GO:0005506 GO:0005739 GO:0006412 GO:0008284 GO:0016787 GO:0018206 GO:0031365 GO:0042586 GO:0046872
10	0.06	0.291	5.45	0.04	0.51	2e6lA	GO:0003676 GO:0005524 GO:0006139 GO:0006310 GO:0008026 GO:0008408 GO:0046872 GO:0090305
11	0.06	0.327	5.12	0.06	0.54	3cq5B	GO:0000105 GO:0003824 GO:0004400 GO:0008483 GO:0008652 GO:0009058 GO:0016740 GO:0030170 GO:0080130
12	0.06	0.333	5.76	0.08	0.62	1u1wB	GO:0002047 GO:0003824 GO:0009058 GO:0009405 GO:0016853 GO:0017000
13	0.06	0.256	5.05	0.04	0.40	4ctiD	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004721 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0005887 GO:0006470 GO:0007165 GO:0009898 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0046777 GO:0047484
14	0.06	0.269	5.16	0.07	0.46	5e16A	GO:0000166 GO:0004672 GO:0004674 GO:0004692 GO:0005524 GO:0005737 GO:0005783 GO:0006468 GO:0016301 GO:0016310 GO:0016740 GO:0019898
15	0.06	0.254	5.20	0.02	0.44	4aggA	GO:0030246
16	0.06	0.254	5.19	0.04	0.44	2vldA	GO:0000014 GO:0003677 GO:0004518 GO:0004519 GO:0005737 GO:0006259 GO:0016787 GO:0042802 GO:0090305
17	0.06	0.238	3.94	0.04	0.33	4xalA	GO:0016032 GO:0019012 GO:0019033 GO:0030430 GO:0042025 GO:0044177
18	0.06	0.196	5.55	0.06	0.36	3f7qA	GO:0001664 GO:0004872 GO:0005634 GO:0005886 GO:0006914 GO:0007154 GO:0007155 GO:0007160 GO:0007229 GO:0008305 GO:0009611 GO:0009986 GO:0016020 GO:0016021 GO:0030054 GO:0030056 GO:0030198 GO:0031252 GO:0031581 GO:0031994 GO:0035878 GO:0038132 GO:0043235 GO:0043588 GO:0048333 GO:0048565 GO:0048870 GO:0070062 GO:0072001 GO:0097186

Consensus prediction of GO terms

Molecular Function	GO:0016810	GO:0043169
GO-Score	0.58	0.37
Biological Processes	GO:0044249	GO:0016999
GO-Score	0.58	0.58
Cellular Component	GO:0042597
GO-Score	0.13

(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.