I-TASSER results

I-TASSER results for job id Rv1374c

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

Input Sequence in FASTA format

>protein (152 residues)
MVTSVADENVASRIASWGTGPAPDPRLDYAHAHLKGRRGRSPARPNAPIGARSFAVGRKI
CRVERFTLLEHGFVGHALHRVPCAGLVALVMSACSLAVCREVGNYAQRRVGRFAFFEQTF
VRHALTPRCSRTDSKTSYTQLNRICKFPPHWV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MVTSVADENVASRIASWGTGPAPDPRLDYAHAHLKGRRGRSPARPNAPIGARSFAVGRKICRVERFTLLEHGFVGHALHRVPCAGLVALVMSACSLAVCREVGNYAQRRVGRFAFFEQTFVRHALTPRCSRTDSKTSYTQLNRICKFPPHWV
Prediction	CCCCCHCHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHCCCCEEEEEEEEEEHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCC
Conf.Score	98654445677766546889999976457788875666899999999887543334554555544555444554555434686578999998778888788756787776434455566666555766566777655778777755899889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MVTSVADENVASRIASWGTGPAPDPRLDYAHAHLKGRRGRSPARPNAPIGARSFAVGRKICRVERFTLLEHGFVGHALHRVPCAGLVALVMSACSLAVCREVGNYAQRRVGRFAFFEQTFVRHALTPRCSRTDSKTSYTQLNRICKFPPHWV
Prediction	73442355502530362343434534252131314455455444462323243232044114144122243221231233120110011023202110034125204431231121442114311344154465544244043007235527
	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

CCCCCHCHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHCCCCEEEEEEEEEEHCCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCC
MVTSVADENVASRIASWGTGPAPDPRLDYAHAHLKGRRGRSPARPNAPIGARSFAVGRKICRVERFTLLEHGFVGHALHRVPCAGLVALVMSACSLAVCREVGNYAQRRVGRFAFFEQTFVRHALTPRCSRTDSKTSYTQLNRICKFPPHWV

3w0fA1

0.19

0.15

0.78

0.62

MUSTER

----------------EELDISPKFSFSRAESEVKKQGDR-------MLCDRVLPVGN-IIKNE-FDSGLHPAVVCQLSDKQACHLVKMTRDFSILFYRCCKAGS--------AISKHCKVKRPNCDQCHSKITVCRFGENSRMTYFCPHCQ

3iuvA2

0.16

0.13

0.80

0.55

dPPAS

AALRQANEGFARVVAAHPALSDPEADLSGELARVL---------------GEWLGGDR------TGVELEYELYLAALRRPALRPVAAEWAEGVGALLAARTD--PTTARALVAVLDGICLQVLLTD--TPYDEEYAREVLTRLIPV-----

3cuxA2

0.23

0.17

0.74

0.59

wdPPAS

-IT---EEGLRMNISV----------IQYIASWLSGR-GAAP---YNLMEDAATA---EISRAQVWQWIRHEGGG----RNITLELMEELKEEELAKIEREIG--KEAKKGRFQEATTLFTNLVRNDEF--VPFLTGYEIL-----------

2oap2

0.28

0.22

0.76

0.63

wMUSTER

IVLDQEKLDRVLRLTQ-GKSIA-NPIVD---ATLDGSR--GTE--VTPRGS-SFTI-RKF-TIEPLTLIEKGTVPSGVL----AYLWLAIEHKFSAIVVGETA-------G-----KTTTLNAIFIPPDAKSDTR----EI----KLYENWI

1q3bA2

0.24

0.16

0.69

0.53

wPPAS

-------------------GPDVDPNPEVVKERLLSPRFR-----NRQFAGAFLALG--YLRVE--ILWQVGL--TKAKDLNLDALAHALLEIPRFSYATR-GQV--DENKHHGALFRFKVRD---ERCGEKTTLPFY------C--P-H--

3w0fA1

0.19

0.14

0.78

0.66

dPPAS2

----------------EELDISPKFSFSRAESEVKKQGDR-------MLCDRVLPVGN-IIKNE--ALFDSGLKVCQLSDKQACHLVKMTRDFSILFYRCCKAGS--------AISKHCKVKRPNCDQCHSKITVCRFGENSRMTYFCPHCQ

3w0fA1

0.19

0.14

0.74

0.70

PPAS

----------------EELDISPKFSFSRAESEVKKQGDR-------MLCDRVLPVG--IIKNE-FDSGLHPA-VCQLSDKQACHLVKMTRDFSILFYRCCKAGSA--------ISKHCKVKRPNCDQCHSKITVCRFGENSR-C---PHCQ

3e7nD

0.23

0.19

0.84

0.70

Env-PPAS

AKGTVLNSEISSVISRLGHT---D-TLVVCDAGLPIPNS--TARIDATQGVPSFQVVDVVTRVEAAILAT---EIKQQN----PQLHETLLTHLEQLQQHQGNTIKISYTTHEQFKKLTADSQAVI----RSGECSPYA--NVICAF-----

3iuvA2

0.19

0.15

0.78

0.57

MUSTER

AALRQANEGFARVVAAHPALSDPEADLSGELARVL---------------GEWLGGDR------TGVELEYELYLAALRR-P---ALRPVAAEWAEGVGALLAARTDPTTARVAVLDGICLQVLLTPY-DEEYAREVLTRLIPV--------

2k3mA

0.21

0.16

0.80

0.55

dPPAS

-MSDFDTERVSRAVAAALVGPGG---VALVVKVCAGLPGHTPAR-------RGFFRCNP----ERIQIGDWRYEVAHDGRLLAAHMVNGIVIAEDALIAEAVGPHLARALGQIVCRYIPNINAAIEVLGTGTDYRF----------------

(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=-3.19

Estimated TM-score = 0.36±0.12

Estimated RMSD = 12.1±4.4Å

Download Model 2

C-score=-3.77

Download Model 3

C-score=-4.89

Download Model 4

C-score=-4.83

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	3gpyA	0.614	4.05	0.154	0.882
2	3w0fA	0.613	3.66	0.113	0.855
3	1ee8A	0.605	4.20	0.116	0.895
4	4mb7A	0.602	4.10	0.113	0.908
5	1pjjA	0.602	4.15	0.104	0.868
6	1k82A	0.584	4.12	0.105	0.855
7	1q3bA	0.576	3.74	0.116	0.816
8	3a46A	0.565	4.35	0.089	0.855
9	3twkA	0.558	3.79	0.105	0.809
10	1tdhA	0.555	4.49	0.108	0.888

(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	2	4q54z	CLA	Rep, Mult	98,106
2	0.06	2	3wmnQ	BCL	Rep, Mult	87,98,102
3	0.06	2	3a0bX	CLA	Rep, Mult	89,92,93,96
4	0.06	2	4pj0X	CLA	Rep, Mult	88,89,93
5	0.06	2	3wmoS	BCL	Rep, Mult	87,98
6	0.06	2	1kfvA	QNA	Rep, Mult	14,57,58,59,60
7	0.03	1	1rpsA	NO	Rep, Mult	34,86,90
8	0.03	1	3tmdA	FE	Rep, Mult	28,31,83
9	0.03	1	4pdiA	2ON	Rep, Mult	66,67,69,128,151
10	0.03	1	1q39A	CA	Rep, Mult	76,150

	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	1iduA	0.461	5.17	0.087	0.763	1.11.1.10	NA
2	0.060	1xrtA	0.421	4.20	0.027	0.651	3.5.2.3	NA
3	0.060	1ygeA	0.369	5.94	0.072	0.730	1.13.11.12	NA
4	0.060	1mx9D	0.453	5.46	0.067	0.809	3.1.1.1	NA
5	0.060	2iukB	0.381	5.12	0.034	0.691	1.13.11.12	87
6	0.060	1pm5A	0.600	4.03	0.110	0.862	3.2.2.23	NA
7	0.060	1qo9A	0.457	5.27	0.067	0.809	3.1.1.7	NA
8	0.060	1aqfE	0.453	4.65	0.114	0.750	2.7.1.40	NA
9	0.060	1ee8A	0.605	4.20	0.116	0.895	3.2.2.23	NA
10	0.060	3gpyA	0.614	4.05	0.154	0.882	3.2.2.23	52
11	0.060	3a45A	0.564	4.56	0.081	0.875	3.2.2.23	NA
12	0.060	3juvA	0.462	4.38	0.065	0.678	1.14.13.70	6,34,64
13	0.060	2ve3A	0.463	4.09	0.040	0.658	1.14.-.-	64
14	0.060	1k4yA	0.351	5.34	0.022	0.638	3.1.1.1	NA
15	0.060	2zf5Y	0.472	5.08	0.048	0.836	2.7.1.30	10
16	0.060	2vr2A	0.460	4.53	0.023	0.730	3.5.2.2	NA
17	0.060	1pjjA	0.602	4.15	0.104	0.868	3.2.2.23	62,64
18	0.060	1ak0A	0.460	5.19	0.053	0.816	3.1.30.1	38
19	0.060	3i3kA	0.395	4.82	0.073	0.671	1.14.13.70	16

(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	0.16	0.605	4.20	0.12	0.89	1ee8A	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
1	0.14	0.584	4.12	0.10	0.86	1k82A	GO:0000703 GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0004519 GO:0006281 GO:0006284 GO:0006285 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104 GO:0046872 GO:0090305
2	0.13	0.576	3.74	0.12	0.82	1q3bA	GO:0000703 GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0004519 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872 GO:0090305
3	0.09	0.564	4.56	0.08	0.88	3a45A	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829
4	0.08	0.613	3.66	0.11	0.86	3w0fA	GO:0000405 GO:0003676 GO:0003677 GO:0003684 GO:0003690 GO:0003697 GO:0003824 GO:0003906 GO:0005634 GO:0005654 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104 GO:0046872
5	0.08	0.617	4.01	0.15	0.88	2f5qA	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
6	0.07	0.601	4.07	0.10	0.87	4pd2A	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
7	0.07	0.602	4.10	0.11	0.91	4mb7A	GO:0003676 GO:0003684 GO:0003906 GO:0006284 GO:0006289 GO:0008270 GO:0016799 GO:0046872
8	0.07	0.559	3.97	0.15	0.79	4g4nA	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0046872
9	0.07	0.564	4.00	0.09	0.82	3twkA	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0005634 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0006979 GO:0008152 GO:0008270 GO:0008534 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104
10	0.06	0.428	4.77	0.04	0.70	1ffyA	GO:0000166 GO:0002161 GO:0004812 GO:0004822 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006428 GO:0006450 GO:0008270 GO:0016874 GO:0046872
11	0.06	0.326	5.29	0.03	0.61	3a3tA	GO:0005623 GO:0045454
12	0.06	0.364	5.61	0.02	0.69	3cogD	GO:0000098 GO:0003824 GO:0003962 GO:0004123 GO:0005516 GO:0005634 GO:0005737 GO:0005829 GO:0006534 GO:0008652 GO:0016829 GO:0016846 GO:0018272 GO:0019343 GO:0019344 GO:0019346 GO:0030170 GO:0030968 GO:0043066 GO:0043123 GO:0044524 GO:0044540 GO:0047982 GO:0051092 GO:0051289 GO:0070062 GO:0070814 GO:0071266 GO:0080146 GO:1904831 GO:2001234
13	0.06	0.382	5.04	0.04	0.66	3p09A	GO:0008800 GO:0016787 GO:0030655 GO:0046677
14	0.06	0.555	4.49	0.11	0.89	1tdhA	GO:0003676 GO:0003677 GO:0003684 GO:0003824 GO:0003906 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005815 GO:0005856 GO:0006281 GO:0006284 GO:0006289 GO:0006974 GO:0006979 GO:0008022 GO:0008152 GO:0008270 GO:0016787 GO:0016798 GO:0016799 GO:0016829 GO:0019104 GO:0032074 GO:0045008
15	0.06	0.294	4.34	0.06	0.45	4aqyM	GO:0000049 GO:0003676 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006412 GO:0019843 GO:0030529
16	0.06	0.304	4.32	0.06	0.45	4g7nA	GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005737 GO:0005814 GO:0005856 GO:0006468 GO:0007052 GO:0007099 GO:0007140 GO:0007288 GO:0016301 GO:0016310 GO:0016740 GO:0031647 GO:0035186 GO:0045732 GO:0046599 GO:0046777 GO:0051297 GO:0051298
17	0.06	0.190	1.91	0.07	0.20	4dhxA	GO:0000166 GO:0002376 GO:0003677 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006260 GO:0006606 GO:0006810 GO:0015031 GO:0016740 GO:0016746 GO:0031965 GO:0051028
18	0.06	0.208	4.70	0.04	0.36	2l7yA	GO:0005576 GO:0005618 GO:0005737 GO:0016020 GO:0033925

Consensus prediction of GO terms

Molecular Function	GO:0003684	GO:0008270	GO:0008534
GO-Score	0.48	0.48	0.35
Biological Processes	GO:0006284	GO:0006289
GO-Score	0.48	0.48
Cellular Component	GO:0005654
GO-Score	0.08

(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.