I-TASSER results

I-TASSER results for job id Rv3165c

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

Input Sequence in FASTA format

>protein (160 residues)
MKRLIALGIFLIVGIELLALILHDRRLVLAGSGLALALVLLNVRRMLGNRDELTAAPDSD
DLGEGLRRWLSNTETTIRWSESTRADWDRHLRPMLARRFEIATGHRQAKDPVAFAATGRM
LFGDELWEWVNPNNVTHTGDRQPGPGRAALEEILQKLEQV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKRLIALGIFLIVGIELLALILHDRRLVLAGSGLALALVLLNVRRMLGNRDELTAAPDSDDLGEGLRRWLSNTETTIRWSESTRADWDRHLRPMLARRFEIATGHRQAKDPVAFAATGRMLFGDELWEWVNPNNVTHTGDRQPGPGRAALEEILQKLEQV
Prediction	CCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCHHCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
Conf.Score	9634657899999988887654565678763578999999999999857888889987665899999999999999999875566666678899999999997865568999999885544477786457876555567789998599999999999969
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MKRLIALGIFLIVGIELLALILHDRRLVLAGSGLALALVLLNVRRMLGNRDELTAAPDSDDLGEGLRRWLSNTETTIRWSESTRADWDRHLRPMLARRFEIATGHRQAKDPVAFAATGRMLFGDELWEWVNPNNVTHTGDRQPGPGRAALEEILQKLEQV
Prediction	6430101010111113222233443300020333210100110132146545475655465355115413430432043364344413430133014413322444445445324203332225400511337324445665423135104401531576
	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

CCHHHHHHHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCHHCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC
MKRLIALGIFLIVGIELLALILHDRRLVLAGSGLALALVLLNVRRMLGNRDELTAAPDSDDLGEGLRRWLSNTETTIRWSESTRADWDRHLRPMLARRFEIATGHRQAKDPVAFAATGRMLFGDELWEWVNPNNVTHTGDRQPGPGRAALEEILQKLEQV

3e7qB

0.16

0.15

0.92

0.71

MUSTER

GKDALVAEAYLAVTGRVMRLLR---GAIDTAPGGARPRLSAFFEASFSAEL---LDPQLLDAWLAFWGAVGSIEAIGRVHDHSYGEYRALLVGVLRQLAEEGGWADFDAELAAISLSA-LLDGLWLESGLNPATFTPRQ------GVQICEAWVDGLEAG

3bniA

0.15

0.14

0.94

0.63

dPPAS

-RSAERLTRILDACADLLDEVGYDALSTRAVRQMADALAQRNLERYAERVTERLTEAGDGGWRGALDTVLDEYLAMKRTAPGFSLIDFGRVAERLTELLSGYLGRRPDDDLRRVFLVAVETADTLVQLAF---------RVAPDGDEKIIEEARELLRAY

4tt0A

0.17

0.12

0.70

0.53

wdPPAS

QQRAEATERVTAGLREVLAARE--------RRAQLEAEGLANLKTLLKVVAVPATVAKTLDQARSAEEIADQVEILVDQTEKAAVAWLEHAQRTFE----------------------------------HPLSAASGD--GPGL----LTRQGARLQAL

3bniA

0.15

0.14

0.93

0.82

wMUSTER

LTRILDACADLLDEVSTRAVALRPIGSV---RQMADALAQRNLERYAERVTERLTEAGDGGWRGALDTVLDEYLAMKRTAPGFSLIDFGRVAERLTELLSGYLGRRPDDDLRRVFLVAVETADTLVQLAF---------RVAPDGDEKIIEEARELLRAY

3iuvA

0.21

0.18

0.88

0.67

wPPAS

RQRIIDAAIRVVGGLSHRTVAA-PLGSTL------VAALRQANEGFARAAHPALSDPEADLSGELARVLGEWLTGVELEYE-LAALRRPALRPVAAEWAEGVGA-AARTDPTTARALVAVLDGICLQVLLTD---------TPYD-EEYAREVLTRLIPV

3bniA

0.16

0.15

0.94

0.86

dPPAS2

-RSAERLTRILDACADLLDEVGYDARAVALRRQMADALAQRNLERYAERVTERLTEAGDGGWRGALDTVLDEYLAMKRTAPGFSLIDFGRVAERLTELLSGYLGRRPDDDLRRVFLVAVETADTLVQLAF---------RVAPDGDEKIIEEARELLRAY

3bniA

0.15

0.14

0.92

0.80

PPAS

LTRILDACADLLDEV-TRAVALRPIGSV---RQMADALAQRNLERYAERVTERLTEAGDGGWRGALDTVLDEYLAMKRTAPGFSLIDFGRVAERLTELLSGYLGRRPDDDLRRVFLVAVETADTLVQLAF---------RVAPDGDEKIIEEARELLRAY

1p3y1

0.13

0.12

0.93

0.78

Env-PPAS

IKKLLIGSISSVGISSYLLYFKSFKEIRVVMTKTAEDLIAHTVSYFCDHVYSEHGENGKRHSHVEIGRWAATANILGQTANGV-AM-NLVATTVLAHPFFPNMNDLMWNKTVVSRNIEQRKDG---HIVIEPVEIM-RGLITPDKALLAIEKGFK-----

5cwoA

0.08

0.97

0.67

MUSTER

VEWVARAAKVAAEVIKVAIQAEKEGNRDLFRAALELVRAVIEAIEEAVKQGNP---ELVEWVARAAKVAAEVIKVAIQAEKEGNRDLFRAALELVRAVIEAIEEAVKQGNPELVERVARLA--KKAAELIKIRAEKEGNRDERREALERVREVIERIEEL

2dg8B

0.15

0.14

0.94

0.58

dPPAS

IARVSHRRIAQRAGVPLGSMTYHFTQLLREAFGRFTDHIVAVFDEHLGAAADRDEAREAVADLVHELSEDSQRDLVLTQELYTLAARQPAYRELTHEWMRRSRVHEKHFDPGTARQLDALIEGLTLHRALAREPHG----------RALTLEAIARITTT

(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=-2.05

Estimated TM-score = 0.47±0.15

Estimated RMSD = 9.4±4.6Å

Download Model 2

C-score=-4.42

Download Model 3

C-score=-2.81

Download Model 4

C-score=-4.89

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	3bniA	0.721	3.02	0.132	0.944
2	2hxoA	0.706	3.64	0.091	0.944
3	3mnlA	0.693	3.04	0.110	0.906
4	2hytA	0.691	3.26	0.120	0.931
5	2f07A	0.691	3.31	0.107	0.925
6	2y2zA	0.690	3.74	0.086	0.944
7	3lwjA	0.687	3.24	0.088	0.912
8	2hkuA	0.686	3.43	0.100	0.931
9	3nxcA	0.682	3.49	0.094	0.931
10	2gfnB	0.681	3.30	0.099	0.925

(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	0.08	4	1jt0C	QNA	Rep, Mult	38,82,83,84,86,89,90
2	0.06	3	3btiA	BER	Rep, Mult	42,45,46,49,69,92,95
3	0.05	2	1bjyB	CTC	Rep, Mult	150,154,157
4	0.04	2	5f08A	5TG	Rep, Mult	47,65,66,70,73,92,95,98,119,122,126,157
5	0.04	2	1qpiA	QNA	Rep, Mult	125,152,153,156
6	0.02	1	2oigD	523	Rep, Mult	125,129
7	0.02	1	2j8rB	AZI	Rep, Mult	130,146
8	0.02	1	2whkA	CA	Rep, Mult	81,123
9	0.02	1	3btjB	DEQ	Rep, Mult	74,77,126,127
10	0.02	1	1jumA	BER	Rep, Mult	42,43,46,92,95,122
11	0.02	1	1jusA	RHQ	Rep, Mult	39,43,46,49,74,80,83,95,126,127
12	0.02	1	2zozA	ET	Rep, Mult	130,131
13	0.02	1	1y10C	CA	Rep, Mult	139,140
14	0.02	1	3aqtA	RCO	Rep, Mult	50,66,69,70,73,98,99,103
15	0.02	1	3pg9A	AZI	Rep, Mult	97,152
16	0.02	1	1xrrA	PRO	Rep, Mult	95,99,127,132,133

	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	2r0nA	0.526	4.39	0.066	0.806	1.3.99.7	70
2	0.060	1kwgA	0.502	4.33	0.043	0.762	3.2.1.23	NA
3	0.060	3gpbA	0.519	3.94	0.092	0.769	2.4.1.1	68
4	0.060	2ix6E	0.503	4.59	0.050	0.806	1.3.3.6	NA
5	0.060	3ii9C	0.516	4.40	0.079	0.800	1.3.99.7	125
6	0.060	1e1yA	0.528	4.11	0.092	0.775	2.4.1.1	NA
7	0.060	2ix6A	0.504	4.66	0.043	0.812	1.3.3.6	151
8	0.060	1t9gC	0.490	4.50	0.057	0.800	1.3.99.3	117,158
9	0.060	1hbmA	0.498	4.23	0.049	0.738	2.8.4.1	NA
10	0.060	3djlA	0.542	4.27	0.057	0.812	1.3.99.-	NA
11	0.060	2p8uA	0.501	4.56	0.067	0.800	2.3.3.10	88
12	0.060	2azdB	0.546	3.81	0.080	0.800	2.4.1.1	85
13	0.060	1bxnE	0.327	5.98	0.032	0.662	4.1.1.39	38
14	0.060	2nvrA	0.447	5.13	0.059	0.806	3.5.1.98	158
15	0.060	1siqA	0.527	4.23	0.067	0.794	1.3.99.7	NA
16	0.060	2v4wD	0.506	4.71	0.059	0.819	2.3.3.10	NA
17	0.060	1rboB	0.500	3.70	0.080	0.706	4.1.1.39	NA
18	0.060	2c4mC	0.545	3.83	0.077	0.781	2.4.1.1	NA
19	0.060	1rblA	0.500	3.75	0.088	0.713	4.1.1.39	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	0.23	0.721	3.02	0.13	0.94	3bniA	GO:0003677 GO:0006351 GO:0006355
1	0.22	0.700	3.29	0.09	0.93	3whcA	GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
2	0.21	0.649	3.86	0.07	0.94	2id6A	GO:0003677 GO:0006351 GO:0006355
3	0.21	0.628	3.99	0.09	0.96	3bhqA	GO:0003677 GO:0006351 GO:0006355
4	0.20	0.675	3.25	0.09	0.92	2qibA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
5	0.19	0.681	3.65	0.14	0.96	3bqyA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
6	0.19	0.671	3.77	0.13	0.95	4auxA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
7	0.18	0.670	3.70	0.09	0.93	3b6aA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677
8	0.18	0.639	3.65	0.13	0.89	3htaA	GO:0003677 GO:0006351 GO:0006355
9	0.18	0.651	3.73	0.12	0.92	3lhqA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
10	0.14	0.705	3.13	0.14	0.92	3bjbB	GO:0003677 GO:0006351 GO:0006355
11	0.14	0.693	3.04	0.11	0.91	3mnlA	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0042803
12	0.13	0.712	3.64	0.09	0.95	2hxoA	GO:0003677 GO:0006351 GO:0006355 GO:0045892
13	0.13	0.681	3.54	0.11	0.94	3c07A	GO:0003677 GO:0006351 GO:0006355
14	0.11	0.669	3.82	0.12	0.96	2vprA	GO:0003677 GO:0006351 GO:0006355 GO:0045892 GO:0046677 GO:0046872
15	0.10	0.629	3.82	0.11	0.91	3p9tA	GO:0003677 GO:0006351 GO:0006355
16	0.10	0.648	3.58	0.11	0.91	2genA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
17	0.09	0.632	3.50	0.10	0.90	5d1wD	GO:0003677 GO:0006351 GO:0006355
18	0.09	0.649	3.81	0.07	0.92	2hyjA	GO:0003677 GO:0003700 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677	GO:0001071
GO-Score	0.70	0.40
Biological Processes	GO:0006355	GO:0044255	GO:0044712	GO:0032787	GO:1901575
GO-Score	0.70	0.44	0.44	0.44	0.44
Cellular Component	GO:0044424
GO-Score	0.44

(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.