I-TASSER results

I-TASSER results for job id Rv1460

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

Input Sequence in FASTA format

>protein (268 residues)
MTSTTLPHRASLVDRSTEFCHTDVVKIPAVSTTVPAAVSDGHTRRAIVRLLLESGSITAG
EIGDRLGLSAAGVRRHLDALIEAGDAEASAAAPWQQVGRGRPAKRYRLTAAGRAKLDHSY
DDLASAAMRQLREIGGEEAVRTFARRRIDAILADVAPADGPDDAALEAAAERIATALSKA
GYVATTTRVGGPIHGVQICQHHCPVSHVAEEFPELCETEQQAMAEVLGTHVQRLATIVNG
DCACTTHVPLSPAPSPRPPATSTEGASR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MTSTTLPHRASLVDRSTEFCHTDVVKIPAVSTTVPAAVSDGHTRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAGDAEASAAAPWQQVGRGRPAKRYRLTAAGRAKLDHSYDDLASAAMRQLREIGGEEAVRTFARRRIDAILADVAPADGPDDAALEAAAERIATALSKAGYVATTTRVGGPIHGVQICQHHCPVSHVAEEFPELCETEQQAMAEVLGTHVQRLATIVNGDCACTTHVPLSPAPSPRPPATSTEGASR
Prediction	CCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCEEEEHCCHHHHHCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEHCCCCCEEEEEEHCCCCHHHHHHHCHHHHHHHHHHHHHHHCCCCEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCC
Conf.Score	9988888888755556655777755578887666666688769999999999969989999999989999999999999999899699985677678899985789976656776557799999999999999869999999999999999999998765678999999999999999989975899868987589999658847999998857899999999999899746766654799858999966778888888888888889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MTSTTLPHRASLVDRSTEFCHTDVVKIPAVSTTVPAAVSDGHTRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAGDAEASAAAPWQQVGRGRPAKRYRLTAAGRAKLDHSYDDLASAAMRQLREIGGEEAVRTFARRRIDAILADVAPADGPDDAALEAAAERIATALSKAGYVATTTRVGGPIHGVQICQHHCPVSHVAEEFPELCETEQQAMAEVLGTHVQRLATIVNGDCACTTHVPLSPAPSPRPPATSTEGASR
Prediction	7544434554532533641434222434544543444356660143004103743421043007417034500340053037432033344455554321112220332533453125202300220042037324471044005500551155135434567441640242024005634030314537564311100121201230055135005102400441173504332212635410103043544455545566556658
	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                 180                 200                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCCCEEEEHCCHHHHHCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEHCCCCCEEEEEEHCCCCHHHHHHHCHHHHHHHHHHHHHHHCCCCEEEEEHCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCC
MTSTTLPHRASLVDRSTEFCHTDVVKIPAVSTTVPAAVSDGHTRRAIVRLLLESGSITAGEIGDRLGLSAAGVRRHLDALIEAGDAEASAAAPWQQVGRGRPAKRYRLTAAGRAKLDHSYDDLASAAMRQLREIGGEEAVRTFARRRIDAILADVAPADGPDDAALEAAAERIATALSKAGYVATTTRVGGPIHGVQICQHHCPVSHVAEEFPELCETEQQAMAEVLGTHVQRLATIVNGDCACTTHVPLSPAPSPRPPATSTEGASR

3u1dA

0.16

0.09

0.53

1.32

wdPPAS

-----------------ATQDRGERPNGFGDELERRRFVLHETRLDVLHQILAQGVLSVEELLYRPDETEANLRYHVDELVDRGIVEKIPVPRAKSV-DDPPTTFYAVTGEGIAL-LRAVSYEEAAVWRSVYEQERTDRIEAIENLE-TRPDVDYESRGATA----------------------------------------------------------------------------------------------------------

3u1dA

0.17

0.09

0.52

1.39

wPPAS

-----------------ATQDRGERPNGFGDELERRRFVLHETRLDVLHQILAQGVLSVEELLYRPDETEANLRYHVDELVDRGIVEKIPVPRAKSV-DDPPTTFYAVTGEGIAL-LRAVSYEEAAVWRSVYEQERTDRIEAIENLETR----DYESRGATA----------------------------------------------------------------------------------------------------------

1ub9A

0.16

0.06

0.37

1.49

dPPAS2

--------------------------MEELKEIMKSHILGNPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIAD------RPRTVVEITDFGMEE-AKRFLSSLKAVIDGLDL---------------------------------------------------------------------------------------------------------------------------------------

2p4wB

0.16

0.11

0.68

1.26

Env-PPAS

--------------------------MGEELNRLLDVLGN-ETRRRILFLLTKR-PYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE----KIPRGRPRKYYMIKKEMYEAKGVRKSPEYEQAKELIKSQEPINVKMRELAEFLHELNERIREIIEEK-RELEEARILIETYIENT-----MRRLAEENRQ--------IIEEIFRDIEKI--LPPGYARSLKEKFL-------------------------------------

2p4wB

0.16

0.11

0.68

1.14

wdPPAS

---------------------------MGEELNRLLDVLGNETRRRILFLLTKR-PYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVEKIPR----GRPRKYYMIKKEMYEAKGVRKSPEYEQAKELIKSQEPINVKMRELAEFLHELNERIREIIEEKRE-LEEARILIETYIENT-----MRRLAEENRQI--------IEEIFRDIEKI--LPPGYARSLKEKFL-------------------------------------

2p4wB

0.18

0.12

0.68

1.25

wPPAS

MG-----------EELNRL-----------------DVLGNETRRRILFLLTKR-PYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE----KIPRGRPRKYYMIKKEMYEAKGVRKSPEYEQAKELIKSQEPINVKMRELAEFLHELNERIREIIEEK-RELEEARILIETYIENT-----MRRLAEENRQI--------IEEIFRDIEKI--LPPGYARSLKEKFL-------------------------------------

3u1dA

0.15

0.08

0.53

1.36

dPPAS2

-----------------ATQDRGERPNGFGDELERRRFVLHETRLDVLHQILAQGVLSVEELLYRNDETEANLRYHVDELVDRGIVEKIPVPRAKSVD-DPPTTFYAVTGEGIAL-LRAVSYEEAAVWRSVYEQERTDRIEAIENLETRPDVDYESRGATA-----------------------------------------------------------------------------------------------------------

4ijaA1

0.14

0.08

0.57

1.23

Env-PPAS

--------------------------------------PMNDNEKRVLREIYNHHNISRTQISKNLEINKATISSILNKLKYKSLVNEV--------GGGRKPILLKVNHLYGYDLTYSSVEVM------YNYFDGN-----VIKHESYDL----------PDEKVSSILSIIKKHID----IQEKLDTYNGLLGVSVSI-HGVVDNVTYGIS-----IAKKIKEITNVPV-------------------------------------

1ulyA

0.18

0.11

0.63

1.10

wdPPAS

------------------------AKKVKVITDPEVIKVLEDTRRKILKLLRNK--ETISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEKGNLV------KYYGRTDEELRYIARSRLKTKIDIFKRLGQFEENELLNIDRSQKEFDATVRISKYIEEKEDALNEDIIHAIEWLSTA------ELARDEE-----------YLELLKRLGSILK---------------------------------------------------

4g6qA

0.17

0.10

0.62

1.25

wPPAS

-------------------------TTGQPATSSLVDLLHHPLRWRITQLLI-GRSLTTRELAELLPVATTTLYRQVGILVKAGVLVTAEH-----QVRGAVERTYTLNTQAGDADH---DGVDADRLRTFTVFV-AGVGGHLDQYLEREQIDPLADGIAFRQTALDEELAEFLTAFGEF-YVAH--SPAPDRTRRVL--------STI--IPD------------------------------------------------------

(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=-3.66

Estimated TM-score = 0.31±0.10

Estimated RMSD = 14.9±3.6Å

Download Model 2

C-score=-4.13

Download Model 3

C-score=-3.95

Download Model 4

C-score=-4.62

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	2p4wB	0.640	1.72	0.164	0.683
2	4qqxA	0.452	6.18	0.038	0.757
3	4q2cA	0.441	6.24	0.088	0.750
4	3wajA	0.435	6.21	0.049	0.724
5	2yevA	0.434	6.50	0.053	0.780
6	5ezmA	0.433	5.72	0.050	0.705
7	1no3A	0.425	5.20	0.038	0.638
8	5flmA	0.425	5.85	0.044	0.687
9	3rceA	0.425	6.30	0.032	0.728
10	4iggA	0.425	6.53	0.045	0.776

(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	4omyC	NUC	Rep, Mult	41,44,69,71,75,76,90,92,102
2	0.06	3	4omyD	NUC	Rep, Mult	41,44,68,69,71,75,76,79
3	0.06	3	1xrmA	ALA	Rep, Mult	77,80
4	0.04	2	4eotB	NUC	Rep, Mult	141,142,146,149,153
5	0.04	2	3sjqC	PHU	Rep, Mult	170,173
6	0.04	2	1mojA	FE	Rep, Mult	78,82
7	0.02	1	1no3A	4NC	Rep, Mult	173,176,177,205,212
8	0.02	1	4asoB	NUC	Rep, Mult	69,101
9	0.02	1	1y10C	CA	Rep, Mult	240,241
10	0.02	1	2id3B	CA	Rep, Mult	61,65
11	0.02	1	2fiyA	FE	Rep, Mult	203,216,237,244
12	0.02	1	2ha5A	AT3	Rep, Mult	61,76,106
13	0.02	1	2y2vB	P15	Rep, Mult	128,129,143,147
14	0.02	1	3gz6A	NUC	Rep, Mult	71,74,99,100,101,102,103,104
15	0.02	1	3ao1B	BZX	Rep, Mult	100,101,102

	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	3eqoA	0.405	6.47	0.041	0.720	3.2.1.58	85,121
2	0.060	1v8bA	0.411	6.23	0.079	0.709	3.3.1.1	NA
3	0.060	1w36C	0.390	5.69	0.029	0.627	3.1.11.5	166,177
4	0.060	2vdcF	0.399	6.21	0.044	0.683	1.4.1.13	NA
5	0.060	2pmzQ	0.403	6.15	0.056	0.690	2.7.7.6	226,229
6	0.060	1b41A	0.414	6.13	0.058	0.716	3.1.1.7	NA
7	0.060	1dlgA	0.369	5.61	0.060	0.578	2.5.1.7	NA
8	0.060	1f6wA	0.397	6.32	0.079	0.709	3.1.1.13,3.1.1.3	NA
9	0.060	1k4yA	0.398	5.89	0.053	0.668	3.1.1.1	NA
10	0.060	1wz2A	0.386	6.28	0.053	0.679	6.1.1.4	55
11	0.060	2pm8A	0.416	6.11	0.053	0.720	3.1.1.8	NA
12	0.060	1maaD	0.412	6.46	0.055	0.739	3.1.1.7	NA
13	0.060	1llwA	0.395	6.23	0.063	0.687	1.4.7.1	NA
14	0.060	1eveA	0.412	6.19	0.036	0.716	3.1.1.7	NA
15	0.060	1no3A	0.425	5.20	0.038	0.638	1.13.11.12	NA
16	0.060	3d64A	0.360	6.16	0.047	0.619	3.3.1.1	NA
17	0.060	1ea0A	0.398	6.00	0.048	0.668	1.4.1.13	NA
18	0.060	1mioA	0.387	5.88	0.063	0.634	1.18.6.1	NA
19	0.060	2rl2A	0.367	6.49	0.058	0.664	2.5.1.7	31,83

(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	0.25	0.640	1.72	0.16	0.68	2p4wB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
1	0.15	0.286	3.38	0.21	0.34	2oqgA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
2	0.07	0.450	6.24	0.09	0.76	4q2dA	GO:0000166 GO:0005524
3	0.07	0.452	6.09	0.03	0.75	4qqxG	GO:0000166 GO:0005524 GO:0046872
4	0.07	0.452	6.18	0.03	0.76	4qqwA	GO:0000166 GO:0005524 GO:0046872
5	0.06	0.367	6.16	0.08	0.61	2x0lA	GO:0000122 GO:0000784 GO:0000790 GO:0001085 GO:0001701 GO:0002039 GO:0003677 GO:0003682 GO:0003700 GO:0004407 GO:0005634 GO:0005654 GO:0005667 GO:0006351 GO:0006355 GO:0006357 GO:0006482 GO:0007275 GO:0007596 GO:0008134 GO:0008283 GO:0010569 GO:0010725 GO:0016491 GO:0016568 GO:0016575 GO:0019899 GO:0021983 GO:0030374 GO:0030851 GO:0032091 GO:0032451 GO:0032452 GO:0032453 GO:0032454 GO:0033169 GO:0033184 GO:0034644 GO:0034648 GO:0034720 GO:0042162 GO:0043234 GO:0043392 GO:0043426 GO:0043433 GO:0043518 GO:0044212 GO:0045648 GO:0045654 GO:0045892 GO:0045944 GO:0046886 GO:0050660 GO:0050681 GO:0051091 GO:0051572 GO:0051573 GO:0055001 GO:0055114 GO:0061752 GO:0071480 GO:1902166 GO:1903827 GO:1990391 GO:2000179 GO:2000648
6	0.06	0.325	3.81	0.18	0.40	2cweA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0046982
7	0.06	0.280	6.05	0.12	0.47	3sk9A	GO:0000166 GO:0004386 GO:0004518 GO:0004519 GO:0005524 GO:0016787 GO:0046872 GO:0090305
8	0.06	0.261	5.87	0.05	0.43	3i32A	GO:0000166 GO:0003676 GO:0004386 GO:0005524 GO:0016787
9	0.06	0.268	6.23	0.04	0.47	4y8fA	GO:0003824 GO:0004807 GO:0005737 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853
10	0.06	0.274	2.38	0.13	0.31	1ub9A	GO:0003700 GO:0006355
11	0.06	0.265	1.84	0.20	0.28	4ooiB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009405
12	0.06	0.271	3.88	0.11	0.33	2ethA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
13	0.06	0.268	1.65	0.15	0.28	2kkoA	GO:0003677 GO:0003700 GO:0004792 GO:0006351 GO:0006355 GO:0016740
14	0.06	0.275	3.30	0.13	0.32	3f6oA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
15	0.06	0.271	2.19	0.13	0.29	3f72B	GO:0003677 GO:0003700 GO:0005622 GO:0006351 GO:0006355 GO:0046686 GO:0046872
16	0.06	0.295	5.06	0.04	0.42	2qlzB	GO:0003700 GO:0006355
17	0.06	0.264	2.29	0.17	0.29	3cuoA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0045892
18	0.06	0.284	6.21	0.03	0.49	4g6zA	GO:0000049 GO:0000166 GO:0004812 GO:0004818 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006424 GO:0016874 GO:0016876 GO:0043039

Consensus prediction of GO terms

Molecular Function	GO:0032550	GO:0032559	GO:0035639	GO:0003677	GO:0003700
GO-Score	0.37	0.37	0.37	0.36	0.36
Biological Processes	GO:0006355
GO-Score	0.36
Cellular Component
GO-Score

(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.