I-TASSER results

I-TASSER results for job id Rv1914c

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

Input Sequence in FASTA format

>protein (135 residues)
MVLSRTSTGRVILVPTQLRFDRWFLPLAVPLGLGPKNSELWVGAGSLHVKMGWAFAADIP
LTSITKAEATNARVYAAGVHFGFGRWLVNGSRKGLVALTIDPPEQAKMWKKSMTVRELWV
SVTDPDALVTACTAK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVLSRTSTGRVILVPTQLRFDRWFLPLAVPLGLGPKNSELWVGAGSLHVKMGWAFAADIPLTSITKAEATNARVYAAGVHFGFGRWLVNGSRKGLVALTIDPPEQAKMWKKSMTVRELWVSVTDPDALVTACTAK
Prediction	CCCCCCCCCCCCCCCCEEEHCHHHHHHHHHHCCCCCCEEEEEHCCEEEEEHCEEEEEHCCCHHHHHHHHHCCCCCEEEEEEHCCCEEEHCCCCCEEEEEHCCCCCEEEHCEEEEEEEEEEEHCCHHHHHHHHHCC
Conf.Score	987666667665787545554455555555368888679999899899997556777555546676788899975665565478578866889589999768975677556677668999867968999998669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVLSRTSTGRVILVPTQLRFDRWFLPLAVPLGLGPKNSELWVGAGSLHVKMGWAFAADIPLTSITKAEATNARVYAAGVHFGFGRWLVNGSRKGLVALTIDPPEQAKMWKKSMTVRELWVSVTDPDALVTACTAK
Prediction	642444433433133550424410320211141325413030465303033123031423333055244375421020112244311122344010203043444040352324233011305414311431468
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCEEEHCHHHHHHHHHHCCCCCCEEEEEHCCEEEEEHCEEEEEHCCCHHHHHHHHHCCCCCEEEEEEHCCCEEEHCCCCCEEEEEHCCCCCEEEHCEEEEEEEEEEEHCCHHHHHHHHHCC
MVLSRTSTGRVILVPTQLRFDRWFLPLAVPLGLGPKNSELWVGAGSLHVKMGWAFAADIPLTSITKAEATNARVYAAGVHFGFGRWLVNGSRKGLVALTIDPPEQAKMWKKSMTVRELWVSVTDPDALVTACTAK

2ebsB

0.13

0.99

0.64

MUSTER

NGPQWGGYGAPHGTPGLTKFGWWMSAVLI-DPFNPEHLMYGTGATIWATDTLSRVEKDWAPSWYLQIDGIEENAILSLRSPKSGAALLSGIGNISGMKHDDLTKPQKMFGAPQNLDSIDAAGNFPNVVVRAGSSG

2iqiF

0.15

0.14

0.97

0.69

dPPAS

PTVRVTPNPAWPQVSWQLLVAK----PSAARIIDSPRINVRPTPGELQVYHGWAQPATDMLEDSVVRAFEDSGKIAAVARIIRSDYKLAIQSLPAATIELNHSSDQRVVASRTFTVARPSSSTDTAAVAAAFEQA

3hx6A1

0.27

0.19

0.68

0.60

wdPPAS

-------------SPATVGKAQYLTYLAQPIEPSGRAPRVYVGDGMLHG--GFAF----PSAVFEKMHQGGGSPVVADAFFGGA-VLIGSLRAGLFALDVTDPANIKLL-WEI----------------------

3rj8A

0.19

0.16

0.86

0.68

wMUSTER

AIEALSAAGVPIDIPGTADYERDVEPFNIRLPYIP-TAIAQTQTTA-HIQ-----------SAVQCAKKLNLKVSAKGGHSYASFGF--GGENGHLMVQLDRMID----VISYNDKTGIAHVARLGHLATVLNDK

2kknA

0.21

0.16

0.78

0.57

wPPAS

VLISDSHVPVRMALPDEIEYDILLEKFSKEF-HGPFSKVLLVEGVTIGMCHGWGAPWDLK-DRLLKVFNEKPQVILFGTH---GVRFLNGSAEGYAVLELDG--------VRFELKTL-----------------

2iqiF

0.16

0.95

0.81

dPPAS2

PTVRVTPNPAWPQVSWQLLVAK---PSAARIIDSP-RINVRPTPGELQVYHGWA--QPATDDSVVRAFEDSGKIAAVAR-IIRSDYKLAIQSLPAATIELNHSSDQRVVASRTFTVARPSSSTDTAAVAAAFEQA

2mw1A

0.17

0.13

0.80

0.67

PPAS

GCELSDPDGLAD--PMKWSKVP--------SGLKNGELKVEAEGGSSLFACKWISSVKEEGKFK------ENTSY----KEFDGGWYLVKIEDNELKVIINRNETNAS-------RSFTVCVEAGNAFFVQDAAK

1n2aA2

0.16

0.13

0.82

0.68

Env-PPAS

LLAPVNSISR-------YKTIEWLNYIATEL----------------HKGFTPLFRPDTPEEYKPTVRAQLEKKLQVNEALKDEHWIC-GQRFTIADAYLFTVLRAYAVKLNLHIAAFMQRMAERPEVQDALSAK

3twkA

0.08

0.96

0.64

MUSTER

VIIADDNKVIHGISPSDF---QTSILGKTIISARRKNLWLELDSPPFPSFQGAIYIKGVAVTKYKRSAVKDSEEWKFFVELDDGLELSFTDKRRFAKVRLLANPTSVSPIS--ELGPDALLEPTVDEFAESLAKK

1m04A1

0.11

0.09

0.83

0.58

dPPAS

-------DRKAPVRPTPL------------DRVIPAPASVDPGGAPYRITRGTHIRVDDSREARRVGDYLADLL----RPATGYRLPVTAHGHGGIRLRLAGGPYGDGYRLDSGPAGVTITARKAAGLFHGVQTL

(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=-4.16

Estimated TM-score = 0.27±0.08

Estimated RMSD = 14.4±3.8Å

Download Model 2

C-score=-4.34

Download Model 3

C-score=-4.58

Download Model 4

C-score=-4.45

Download Model 5

C-score=-4.76

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	2x0kA1	0.475	3.78	0.029	0.719
2	2iqiF	0.474	4.80	0.119	0.830
3	1u3dA	0.472	4.57	0.054	0.778
4	1wq3A	0.467	4.44	0.089	0.800
5	2vtbA1	0.466	4.59	0.053	0.800
6	1h3eA	0.466	4.69	0.052	0.822
7	3a04A	0.465	3.96	0.053	0.733
8	2g36A	0.465	4.20	0.063	0.733
9	2cyaA	0.464	4.34	0.052	0.756
10	3nd1A	0.464	4.01	0.059	0.719

(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	0.10	5	4u8dB	MG	Rep, Mult	124,126
2	0.06	3	1dbtA	U5P	Rep, Mult	58,59,62
3	0.06	3	3no3A	MG	Rep, Mult	18,21,80
4	0.04	2	2aiyB	IPH	Rep, Mult	128,131
5	0.04	2	1t6xA	ADP	Rep, Mult	35,36,37,38,54,56,59
6	0.02	1	3wmn1	CRT	Rep, Mult	64,68
7	0.02	1	1t6xB	ADP	Rep, Mult	62,63,94,95,96,97
8	0.02	1	1dxoA	DQN	Rep, Mult	53,90
9	0.02	1	2iceA	CA	Rep, Mult	103,121,122,124
10	0.02	1	1t6yA	AMP	Rep, Mult	8,9,12,89,90,92,114,115
11	0.02	1	3bvwA	MPD	Rep, Mult	5,66,67,70
12	0.02	1	1s4mA	LUM	Rep, Mult	19,21,22,24,62,65
13	0.02	1	1xvgD	BRJ	Rep, Mult	55,63
14	0.02	1	1ewjA	BLM	Rep, Mult	81,86,88,95

	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	1gn8A	0.434	4.48	0.046	0.741	2.7.7.3	NA
2	0.060	2yxnA	0.458	4.71	0.087	0.822	6.1.1.1	91
3	0.060	1kaqA	0.451	4.53	0.056	0.763	2.7.7.18	NA
4	0.060	2c7bA	0.457	3.96	0.096	0.681	3.1.1.1	NA
5	0.060	2cycA	0.459	4.41	0.074	0.770	6.1.1.1	NA
6	0.060	1dozA	0.451	4.18	0.074	0.733	4.99.1.1	NA
7	0.060	2g36A	0.465	4.20	0.063	0.733	6.1.1.2	NA
8	0.060	2cybA	0.451	4.29	0.027	0.741	6.1.1.1	NA
9	0.060	1h3fB	0.423	4.70	0.069	0.741	6.1.1.1	NA
10	0.060	2c8jA	0.451	4.29	0.064	0.741	4.99.1.1	NA
11	0.060	1hrkA	0.446	4.11	0.053	0.719	4.99.1.1	NA
12	0.060	1h3eA	0.466	4.69	0.052	0.822	6.1.1.1	92
13	0.060	2yy5D	0.439	4.60	0.053	0.748	6.1.1.2	NA
14	0.060	2cyaA	0.464	4.34	0.052	0.756	6.1.1.1	66
15	0.060	2ts1A	0.437	5.00	0.088	0.793	6.1.1.1	91
16	0.060	2a4mC	0.458	4.38	0.053	0.756	6.1.1.2	39
17	0.060	1jv3A	0.443	4.75	0.058	0.793	2.7.7.23	NA
18	0.060	3l93A	0.437	4.53	0.056	0.748	2.7.7.3	90,92
19	0.060	2vtbA	0.466	4.59	0.053	0.800	4.1.99.3	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	0.452	4.82	0.04	0.81	1dnpA	GO:0000166 GO:0003677 GO:0003904 GO:0006281 GO:0006974 GO:0016829 GO:0018298
1	0.07	0.471	4.48	0.04	0.77	1u3cA	GO:0000166 GO:0004672 GO:0005524 GO:0005634 GO:0005737 GO:0006952 GO:0007623 GO:0009414 GO:0009416 GO:0009583 GO:0009637 GO:0009638 GO:0009640 GO:0009644 GO:0009646 GO:0009785 GO:0009881 GO:0009882 GO:0010075 GO:0010114 GO:0010117 GO:0010118 GO:0010218 GO:0010244 GO:0010310 GO:0010343 GO:0010617 GO:0016301 GO:0016604 GO:0016605 GO:0018298 GO:0042752 GO:0042802 GO:0046283 GO:0046777 GO:0046872 GO:0050896 GO:0051510 GO:0055114 GO:0060918 GO:0071000 GO:0071949 GO:0072387 GO:0099402 GO:1900426 GO:1901332 GO:1901371 GO:1901529 GO:1901672 GO:1902347 GO:1902448 GO:2000377
2	0.07	0.447	4.82	0.07	0.83	1qnfA	GO:0000166 GO:0003677 GO:0003904 GO:0006281 GO:0006974 GO:0016829 GO:0018298
3	0.07	0.453	4.70	0.08	0.79	4cdnB	GO:0000166 GO:0003904 GO:0006281 GO:0016829
4	0.07	0.475	3.79	0.03	0.72	4uzeA	GO:0000166 GO:0003824 GO:0003919 GO:0005524 GO:0006747 GO:0008152 GO:0008531 GO:0009231 GO:0009398 GO:0016301 GO:0016310 GO:0016740 GO:0016779
5	0.07	0.451	4.70	0.08	0.79	4cdnA	GO:0000166 GO:0003904 GO:0006281 GO:0016829
6	0.07	0.454	4.41	0.06	0.75	1s4mA	GO:0000166 GO:0003919 GO:0005524 GO:0006747 GO:0008531 GO:0009231 GO:0009398 GO:0016301 GO:0016310 GO:0016740 GO:0016779
7	0.07	0.452	4.83	0.08	0.80	2e0iB	GO:0000166 GO:0003904 GO:0016829 GO:0018298
8	0.07	0.444	5.01	0.08	0.81	4k03B	GO:0000060 GO:0000166 GO:0003913 GO:0005634 GO:0005641 GO:0005737 GO:0006351 GO:0006355 GO:0007602 GO:0007623 GO:0008020 GO:0009416 GO:0009584 GO:0009588 GO:0009637 GO:0009649 GO:0009785 GO:0009881 GO:0009882 GO:0018298 GO:0042332 GO:0042752 GO:0043153 GO:0043234 GO:0045187 GO:0045475 GO:0045892 GO:0048471 GO:0048511 GO:0050660 GO:0050896 GO:0050958 GO:0050980 GO:0071000 GO:0071949
9	0.07	0.462	4.56	0.05	0.78	3cvvA	GO:0000166 GO:0003914
10	0.07	0.466	4.59	0.05	0.80	2vtbA	GO:0000166 GO:0003677 GO:0003913 GO:0005524 GO:0005739 GO:0006281 GO:0007165 GO:0009507 GO:0009536 GO:0009881 GO:0018298 GO:0050896
11	0.07	0.445	4.75	0.10	0.79	3op1B	GO:0000166 GO:0003919 GO:0005524 GO:0006747 GO:0008531 GO:0009231 GO:0009398 GO:0016301 GO:0016310 GO:0016740 GO:0016779
12	0.07	0.430	4.87	0.12	0.79	4u63A	GO:0000719 GO:0003677 GO:0003904 GO:0006281 GO:0006974 GO:0016829 GO:0018298 GO:0071949
13	0.06	0.445	4.50	0.07	0.73	3fy4A	GO:0000166 GO:0003677 GO:0003914 GO:0006281 GO:0006974 GO:0009411 GO:0016829
14	0.06	0.452	4.73	0.08	0.81	1np7A	GO:0003677 GO:0003913 GO:0006281 GO:0006351 GO:0006355 GO:0018298
15	0.06	0.429	5.13	0.06	0.80	4i6jA	GO:0000122 GO:0000166 GO:0000976 GO:0000989 GO:0003677 GO:0003684 GO:0003697 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0006351 GO:0006355 GO:0006606 GO:0007165 GO:0007623 GO:0009881 GO:0018298 GO:0019900 GO:0019901 GO:0019902 GO:0019915 GO:0032515 GO:0032868 GO:0032922 GO:0035257 GO:0042593 GO:0042752 GO:0042754 GO:0043130 GO:0043153 GO:0045892 GO:0048511 GO:0050896 GO:0071949 GO:2000323 GO:2000850
16	0.06	0.408	4.25	0.03	0.67	1cozA	GO:0003824 GO:0005737 GO:0009058 GO:0016740 GO:0016779 GO:0019350 GO:0046872 GO:0047348 GO:0071555
17	0.06	0.370	4.75	0.04	0.60	3im9A	GO:0003824 GO:0004314 GO:0006629 GO:0006631 GO:0006633 GO:0008152 GO:0016740 GO:0016746
18	0.06	0.441	4.90	0.08	0.80	2j07A	GO:0000166 GO:0003677 GO:0003904 GO:0006281 GO:0006974 GO:0016829 GO:0018298

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0003913
GO-Score	0.57	0.57	0.37
Biological Processes	GO:0006974	GO:0006259	GO:0006464
GO-Score	0.37	0.37	0.37
Cellular Component	GO:0016605	GO:0005737
GO-Score	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.