I-TASSER results

I-TASSER results for job id Rv0201c

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

Input Sequence in FASTA format

>protein (167 residues)
MTLAAEPHPAPPQQPTVAWSEPDVDRRVEFWPTVAIRSALESGDIATWQRIAAALKRDPY
GRTARQVEEVLEGIPATGIANAFWEVLDRARTHLDANERAEVARQVGLLLDRSGLQRQEF
ASRIGVTAQDLTAYLDGIVSPSASLMIRMRRLSDRFVRAKSVRAADS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTLAAEPHPAPPQQPTVAWSEPDVDRRVEFWPTVAIRSALESGDIATWQRIAAALKRDPYGRTARQVEEVLEGIPATGIANAFWEVLDRARTHLDANERAEVARQVGLLLDRSGLQRQEFASRIGVTAQDLTAYLDGIVSPSASLMIRMRRLSDRFVRAKSVRAADS
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCHCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Conf.Score	98888888899888888778888999865577699999997598999999999998689977899999999757886799999999999999856999999999999999998999999999989998899987657447889999999999999999864677889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MTLAAEPHPAPPQQPTVAWSEPDVDRRVEFWPTVAIRSALESGDIATWQRIAAALKRDPYGRTARQVEEVLEGIPATGIANAFWEVLDRARTHLDANERAEVARQVGLLLDRSGLQRQEFASRIGVTAQDLTAYLDGIVSPSASLMIRMRRLSDRFVRAKSVRAADS
Prediction	75345756644466364663634554314313252023115543143033003204523426315304501732544210300440154036414664244005304411654615354005424143740342153433332311320440153124135544888
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCHCCCHHHHHHHHHHHHHHHHHHHCCCCCC
MTLAAEPHPAPPQQPTVAWSEPDVDRRVEFWPTVAIRSALESGDIATWQRIAAALKRDPYGRTARQVEEVLEGIPATGIANAFWEVLDRARTHLDANERAEVARQVGLLLDRSGLQRQEFASRIGVTAQDLTAYLDGIVSPSASLMIRMRRLSDRFVRAKSVRAADS

3gn5A

0.17

0.13

0.77

0.79

MUSTER

MK---------PVCHQGEMVSGIKDIPYTF-----------RGRKTVLKGIHGLY--VHCE------ESIM----NKEESDAFMAQVKAFRASVNAETVA--PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR----

4uetA

0.11

0.98

0.58

dPPAS

--MGSSHHHHHHSSGHMFKYEDIPADYRDLMP-PEARDFLQNLSDGDKTVLKEVFKAGPYKNTEESIAALKKKSPEGAKVEKLHAMVKSKIAALGPEAKGFAEKSIEIARGIKARYYTTKDDLKASVKEVLKLYKAMSDAGKADFGKQFPFLAKVFESGKAAKFAGE

2kpjA

0.25

0.11

0.43

0.61

wdPPAS

---------------------------------------------------------------------------------------------MVDKQKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPR---MGKVQALADYFNINKSDLIEDK

3gn5A

0.17

0.13

0.76

0.82

wMUSTER

MK---------PVCHQGEMVSGIKDIPYTF-----------RGRKTVLKGIHGLY--VHCE------ESIM----NKEESDAFMAQVKAFRASVNAET----PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR----

3gn5A

0.14

0.10

0.68

0.72

wPPAS

MKMVSGIK----------------DIPYTF-----------RG-----RKTVKGIH-VHCE------ESIM----NKEESDAFMAQVKAFRASVNAET----PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHTIKLLRVLDKPELLNEIR-------

2kpjA

0.25

0.11

0.43

0.85

dPPAS2

--------------------------------------------------------------------------------------------MVKDKQKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPR---MGKVQALADYFNINKSDLIEDK

3kxaA

0.19

0.14

0.71

PPAS

-------------------------IPVTHIKCLRI-----NGQI----KCVKPI--SPNTPAAEHIEHVRKN--------PRRKAADRAAARIAKIALKAGGETFVSLRKK-GFTQSELATAAGLPQPYLSRIENSKQSLQ---DKTVQKLANALGSPLEVRAAFE

3gn5A

0.16

0.13

0.78

1.07

Env-PPAS

MKC--------PVCHQGEMVSGIKDIPYTF-----------RGRKTVLKGIHGLY-CVHCE------ESIM----NKEESDAFMAQVKAFRASVNAET--VAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR----

5cwdA

0.12

0.11

0.95

0.78

MUSTER

---TKEDARSTCEKAARKAAESNDEEVAKQAAKDCLEVAKQAGMRSFCEAAARAAAESNDEEVAKIAAKACLEMPTKEAARSFCEAAARAAAESDEEVAKIAAKACLEVAKQAGMPTKEAARSFCEAAKRAAKESN-----DEEVEKIAKKACKEVAKQAGMPWLE-

5l4kR1

0.14

0.13

0.87

0.56

dPPAS

--------------MPLENLEEEGLPKNPDLRIAQLRFLLHRGDAAVRDELMAAVRDNNMAPYYEALCKSLDWQIDVDLLNKMKKANEDELKRLDEELEDAEKNLGESEIRDAMMAKAEYLCRIGDALTAFRKTYDKTVALGHRLDIVFYLLRIGLFYM--------

(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=-3.96

Estimated TM-score = 0.29±0.09

Estimated RMSD = 14.4±3.7Å

Download Model 2

C-score=-4.59

Download Model 3

C-score=-4.60

Download Model 4

C-score=-4.92

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	3gn5A	0.656	2.87	0.130	0.784
2	3ixzA	0.469	4.56	0.027	0.719
3	3kdpA	0.465	4.61	0.054	0.725
4	4ut1A	0.463	4.30	0.109	0.701
5	2d7rA	0.462	5.12	0.046	0.826
6	4zwjA	0.462	4.64	0.054	0.760
7	3c9lA	0.461	4.52	0.039	0.719
8	1xhbA	0.461	5.21	0.028	0.796
9	4f0pA	0.460	5.48	0.075	0.814
10	4owdA	0.459	4.85	0.073	0.754

(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	1perR	NUC	Rep, Mult	110,116,117,128,129,132,136,142
2	0.06	3	3o9xA	QNA	Rep, Mult	36,37,125,126,127,128,129,133,134,139,140
3	0.04	2	2i37A	UUU	Rep, Mult	111,114,115,116,117,118
4	0.04	2	2iulA	FUC	Rep, Mult	81,85
5	0.04	2	1qiyL	IPH	Rep, Mult	87,90
6	0.02	1	3kxaC	ASN	Rep, Mult	37,40,53,54,55,56
7	0.02	1	4dlmA	ZN	Rep, Mult	136,163
8	0.02	1	1gk9B	EDO	Rep, Mult	137,142,143,144
9	0.02	1	4g28B	0W8	Rep, Mult	108,109
10	0.02	1	4y28F	CLA	Rep, Mult	70,83
11	0.02	1	1s0vA	NUC	Rep, Mult	120,123
12	0.02	1	4evbA	ZN	Rep, Mult	85,89
13	0.02	1	1dxeA	MG	Rep, Mult	98,130
14	0.02	1	2ybba	III	Rep, Mult	92,150
15	0.02	1	2c37E	U5P	Rep, Mult	148,155
16	0.02	1	4ej7B	CA	Rep, Mult	25,34
17	0.02	1	3hdlA	UUU	Rep, Mult	97,105
18	0.02	1	3j001	PEV	Rep, Mult	92,100

	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	2agsA	0.450	4.81	0.057	0.707	3.2.1.18	139
2	0.060	1z11A	0.433	4.48	0.048	0.671	1.14.14.1	NA
3	0.060	3fslA	0.435	4.54	0.068	0.695	2.6.1.57	NA
4	0.060	3ii0C	0.440	4.51	0.071	0.725	2.6.1.1	NA
5	0.060	2okjB	0.430	5.26	0.049	0.737	4.1.1.15	NA
6	0.060	1hn0A	0.428	5.26	0.041	0.737	4.2.2.20	65
7	0.060	1n0hA	0.427	5.07	0.041	0.749	2.2.1.6	106
8	0.060	2okkA	0.388	4.83	0.049	0.665	4.1.1.15	NA
9	0.060	3mebA	0.454	5.14	0.046	0.790	2.6.1.1	NA
10	0.060	2hoxB	0.444	4.46	0.051	0.683	4.4.1.4	NA
11	0.060	3tatC	0.432	4.48	0.098	0.695	2.6.1.57	159
12	0.060	1lk9B	0.377	6.04	0.075	0.743	4.4.1.4	NA
13	0.060	1hskA	0.427	4.92	0.088	0.671	1.1.1.158	NA
14	0.060	1t34A	0.428	4.88	0.071	0.701	4.6.1.2	100,154
15	0.060	1mo7A	0.282	5.70	0.052	0.521	3.6.3.9	147
16	0.060	2d7iA	0.469	5.39	0.058	0.856	2.4.1.41	NA
17	0.060	3czoB	0.453	5.14	0.034	0.766	4.3.1.3	NA
18	0.060	2occN	0.433	5.04	0.026	0.695	1.9.3.1	NA
19	0.060	3ihjA	0.442	5.42	0.051	0.766	2.6.1.2	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	0.20	0.656	2.87	0.13	0.78	3gn5A	GO:0003677 GO:0006351 GO:0006355 GO:0043565 GO:0046872
1	0.07	0.470	4.65	0.04	0.72	3b8eA	GO:0000166 GO:0002028 GO:0005391 GO:0005524 GO:0005886 GO:0005890 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0010107 GO:0010248 GO:0015991 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0030955 GO:0031402 GO:0036376 GO:0042383 GO:0043231 GO:0046872 GO:0051117 GO:0086009 GO:0090662 GO:1990573
2	0.06	0.469	4.56	0.03	0.72	3ixzA	GO:0000166 GO:0000287 GO:0005391 GO:0005524 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0006883 GO:0008900 GO:0010107 GO:0010248 GO:0015991 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030007 GO:0036376 GO:0043231 GO:0046872
3	0.06	0.354	5.72	0.05	0.66	2jg5A	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0008662 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
4	0.06	0.422	5.23	0.07	0.74	1mhsA	GO:0000166 GO:0005524 GO:0005886 GO:0005887 GO:0006754 GO:0006810 GO:0006811 GO:0008553 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0043231 GO:0046872 GO:0051453 GO:1902600
5	0.06	0.338	5.75	0.07	0.63	4bbjA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
6	0.06	0.325	5.19	0.04	0.54	2b8nA	GO:0000166 GO:0000287 GO:0005524 GO:0005737 GO:0006468 GO:0008887 GO:0016301 GO:0016310 GO:0016740 GO:0016773
7	0.06	0.437	4.94	0.07	0.71	3a3yA	GO:0000166 GO:0005391 GO:0005524 GO:0006810 GO:0006811 GO:0006813 GO:0006814 GO:0010248 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0090662
8	0.06	0.339	5.87	0.02	0.65	4cczA	GO:0000096 GO:0005622 GO:0005737 GO:0005829 GO:0007399 GO:0008168 GO:0008270 GO:0008652 GO:0008705 GO:0008898 GO:0009086 GO:0009235 GO:0016740 GO:0031103 GO:0031419 GO:0032259 GO:0042558 GO:0044237 GO:0046872 GO:0048678 GO:0071732
9	0.06	0.319	5.70	0.07	0.62	3skxA	GO:0000166 GO:0004008 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0060003 GO:0098655
10	0.06	0.329	4.74	0.02	0.53	3udcA	GO:0005886 GO:0006810 GO:0006811 GO:0008381 GO:0009992 GO:0016020 GO:0016021 GO:0034220 GO:0055085
11	0.06	0.406	4.60	0.05	0.61	3j09A	GO:0000166 GO:0005507 GO:0005524 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0046872 GO:0098655
12	0.06	0.318	5.22	0.07	0.51	2ayxA	GO:0000155 GO:0000160 GO:0000166 GO:0004673 GO:0004871 GO:0005524 GO:0005622 GO:0005886 GO:0005887 GO:0006355 GO:0007165 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0016772 GO:0018106 GO:0023014 GO:0044010 GO:0046777 GO:0071470
13	0.06	0.334	1.79	0.14	0.37	2ppxA	GO:0003677 GO:0043565
14	0.06	0.330	5.33	0.08	0.59	2yj4B	GO:0000166 GO:0005887 GO:0006812 GO:0008900 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0030001 GO:0035434 GO:0043231 GO:0043682 GO:0046872 GO:0098655 GO:1902600
15	0.06	0.297	5.17	0.04	0.53	4dwoA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872
16	0.06	0.302	5.49	0.10	0.54	2qyhB	GO:0016787
17	0.06	0.385	5.36	0.01	0.66	3w5bA	GO:0000166 GO:0005388 GO:0005509 GO:0005524 GO:0005783 GO:0005789 GO:0005793 GO:0006810 GO:0006811 GO:0006816 GO:0006942 GO:0016020 GO:0016021 GO:0016529 GO:0016787 GO:0031448 GO:0031673 GO:0031674 GO:0033017 GO:0045988 GO:0046872 GO:0048471 GO:0070588
18	0.06	0.260	5.73	0.03	0.50	3r4cA	GO:0005737 GO:0016311 GO:0016787 GO:0016791 GO:0044283 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0035639	GO:0032550	GO:0032559	GO:0003676	GO:0046872
GO-Score	0.48	0.48	0.48	0.40	0.35
Biological Processes	GO:2000112	GO:0010468	GO:1903506	GO:0044765
GO-Score	0.40	0.40	0.40	0.37
Cellular Component	GO:0043227	GO:0071944	GO:0043229
GO-Score	0.37	0.37	0.37

(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.