I-TASSER results

I-TASSER results for job id Rv1874

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

Input Sequence in FASTA format

>protein (228 residues)
MLMRPEPDDDWCARQRAQVADALLGLGVAGLSINVRDSTVRDSLMTLTTLYPPVAAVVSL
WTQQCYGEQVAAALRLLAQECDELGAYLVTESVPLTFPSLVESGSRTPGLANIALLRRPD
GLDQATWLTRWQRDHTQVAIEAQATFGYTQNWVVRALTPEAPGIAGIVEELFPVAATTDL
KAFFGAADDNDLRNRISRMVASTSAFGANQNIDTVPTSRYVFRTPFKD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MLMRPEPDDDWCARQRAQVADALLGLGVAGLSINVRDSTVRDSLMTLTTLYPPVAAVVSLWTQQCYGEQVAAALRLLAQECDELGAYLVTESVPLTFPSLVESGSRTPGLANIALLRRPDGLDQATWLTRWQRDHTQVAIEAQATFGYTQNWVVRALTPEAPGIAGIVEELFPVAATTDLKAFFGAADDNDLRNRISRMVASTSAFGANQNIDTVPTSRYVFRTPFKD
Prediction	CCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEHCCHHHHCCCCCCCCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCEEEHCCEHCCCCCCCCCCCCCCHHHHEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHCCCHCEEEEEEEEHCCCCCCCCCEEEEHCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEHCCCCC
Conf.Score	988888768999999988999999869985899966767655556777788874457776447777655568999999986544545676447758888888888764564456666589999999999999877788887467454676556665689998754688643664555797887578877899999999999999874678886787666776588889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MLMRPEPDDDWCARQRAQVADALLGLGVAGLSINVRDSTVRDSLMTLTTLYPPVAAVVSLWTQQCYGEQVAAALRLLAQECDELGAYLVTESVPLTFPSLVESGSRTPGLANIALLRRPDGLDQATWLTRWQRDHTQVAIEAQATFGYTQNWVVRALTPEAPGIAGIVEELFPVAATTDLKAFFGAADDNDLRNRISRMVASTSAFGANQNIDTVPTSRYVFRTPFKD
Prediction	743446445400440355035403725054030314355136333525625221100010004324453342025214631540212102433113436426456414001200003336704373036204741141035145123121110133236732301000011135511530321122543650353044015204401527503002124232443168
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEHCCHHHHCCCCCCCCCCCCCCEEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCEEEHCCEHCCCCCCCCCCCCCCHHHHEEEEHCCCCCCHHHHHHHHHHHHHHHHHHHCCCHCEEEEEEEEHCCCCCCCCCEEEEHCCCCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEHCCCCC
MLMRPEPDDDWCARQRAQVADALLGLGVAGLSINVRDSTVRDSLMTLTTLYPPVAAVVSLWTQQCYGEQVAAALRLLAQECDELGAYLVTESVPLTFPSLVESGSRTPGLANIALLRRPDGLDQATWLTRWQRDHTQVAIEAQATFGYTQNWVVRALTPEAPGIAGIVEELFPVAATTDLKAFFGAADDNDLRNRISRMVASTSAFGANQNIDTVPTSRYVFRTPFKD

3hfkB

0.14

0.07

0.46

1.30

wdPPAS

------------------------------------------------------------------------------------------------------PQ-EGRMIRILYLLVKPESMS-HEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDDVGRIDAIGECWFASEE--QYQVYMES-------DIRKAWFEHGKYFIG--QLKPFVTEELV-------

3hfkB

0.14

0.07

0.46

1.19

wPPAS

------------------------------------------------------------------------------------------------------PQ-EGRMIRILYLLVKPESMS-HEQFRKECVVHFQMSAGMPGLHKYEVRLVAGNPTDDVGRIDAIGECWFASEE--QYQVYMES-------DIRKAWFEHGKYFIG--QLKPFVTEELV-------

2ifxA

0.12

0.05

0.43

1.28

wdPPAS

------------------------------------------------------------------------------------------------------------GIR-LLYLLVKPAGSDETFRAECLRHYES--HDVPGLHKYEVRLVAEQPHVDIGHVDAIGECWFKDDA---AYATYASDIRKAWFEHGKTFIGQLKPFRTAPVAG---------------

2ifxA

0.15

0.07

0.43

1.13

wPPAS

------------------------------------------------------------------------------------------------------------GIR-LLYLLVKPAGSDETFRAECLRHYES---DVPGLHKYEVRLVAQPHVPDIGHVDAIGECWFKDDA---AYATYAS-------DIRKAWFEHGKTFIG--QLKPFRTA------PVAG

2ftrA

0.09

0.04

0.41

1.20

wdPPAS

-----------------------------------------------------------------------------------------------------------ENVKLIALYEQPED--KQAFDEHYFNTHAPLTRKIPGLRDKVT-----RIVGSPGESKFYLCEYYDD--HESLQQAR-TDEGKASGKDAKFAGKLLTLIGEED------------------

2ftrA

0.09

0.04

0.40

1.07

wPPAS

-----------------------------------------------------------------------------------------------------------ENVKLIALYEQPED--KQAFDEHYFNTHAPLTRKIPGLRDKVT-----RIVGSPGESKFYLCEYYDD--HESLQQART--------DEGKASGKDAKFAGK---LTLIGEED---------

3bf4A

0.11

0.05

0.47

1.06

wdPPAS

------------------------------------------------------------------------------------------------------ENLYFQGIK-VNVYPYTEGAR---FHAYYCDRHPVKARLGSACAYYTVEKGLAGSASGAPPAFVACAFICDS------AENF-----YAAYYHGAEILGDIANYTDIAPV--LQISE--VVVERSD

3bf4A

0.12

0.06

0.46

1.00

wPPAS

------------------------------------------------------------------------------------------------------ENLYFQGIK-VNVYPYTEGAR---FHAYYCDRHPVKARLGSACAYYTVEKGLAGSASGAPPAFVACAFICDS------AENF-----YAAYYHGAEILGDIANYTDIA---VLQISEVVV----SD

3zphA

0.09

0.08

0.93

0.66

MUSTER

DCVSEDYRPKLQRWIYKVHIPDSISQFEPYVTKYA----FYPSFPIPPQGDARMQLTEHHWLVSDLDPRLEAIAETFPMDVLVWQGQIIFAFLPMWWEKDLKGKGRTANYRFNMTIGFPEGVDKAEGEKWLFEKVVPILQAAPECTRVLASAVKKDING--CVMDWVLEIWF-----ENQSGWY-----KVMVDDMKAL-AQQDAFKPYHNVCSAAVADYTPSNNLAN

4n7rC

0.13

0.94

0.58

dPPAS

STHKPFPAEVSRSIMELSSVGTLSTLTHDGWPLGVGDGTPVLCLNRSVSPDKRSALHVQLEQCGLGDDTVLKRLSATWREKFGEEVYVVAVDRVLQMEDFMEDGIWVASSDYKNASPDPLRDIAEDIVNQINANNMEDIFRFCDLDFVVSETKMIWMDRLSPRGVYDVRIPFP-MEVTDEKGAK-----SSFNGMSQLAWEVEKSYCPADFNKVKLLKQVV-------

(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=-2.63

Estimated TM-score = 0.41±0.14

Estimated RMSD = 11.7±4.5Å

Download Model 2

C-score=-4.59

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.05

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	2cb2A	0.639	4.15	0.069	0.890
2	3gn6C	0.621	4.32	0.063	0.868
3	3zphA	0.621	4.47	0.063	0.886
4	5de0A	0.613	4.39	0.052	0.886
5	3qnrA	0.612	4.34	0.077	0.882
6	4gu7A	0.605	4.54	0.047	0.895
7	2hagA	0.599	4.53	0.053	0.873
8	4gt2B	0.594	4.55	0.057	0.877
9	5jxuA	0.594	4.56	0.071	0.882
10	4gs1A	0.594	4.47	0.090	0.873

(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	0.17	12	3q08T	UUU	Rep, Mult	114,116,118,142,143,148,149,150,166,168,170,198
2	0.07	5	3hfkA	4ML	Rep, Mult	114,134,148,170,183,199,200,203,207,212
3	0.06	4	3e8oB	UNL	Rep, Mult	134,148,170,192,214
4	0.04	3	1kqpA	MG	Rep, Mult	37,169
5	0.03	2	3dntA	MG	Rep, Mult	211,228
6	0.01	1	2wl3A	CA	Rep, Mult	52,120
7	0.01	1	2p4sB	PO4	Rep, Mult	180,183
8	0.01	1	2vfsA	XYL	Rep, Mult	112,151,153,168,170
9	0.01	1	3d2hA	UUU	Rep, Mult	130,131,134,199,200
10	0.01	1	3hfkB	4ML	Rep, Mult	114,183,184,196,200,212
11	0.01	1	2dyo1	III	Rep, Mult	7,8,12,14,15,16,18,19,22,23,24,25,26,28,95,96
12	0.01	1	3fgvB	UNL	Rep, Mult	114,168,212
13	0.01	1	3oa0B	HP7	Rep, Mult	166,167
14	0.01	1	3dxpA	CA	Rep, Mult	150,151,179

	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	1v03A	0.405	5.90	0.056	0.689	3.2.1.21	NA
2	0.060	3dq0A	0.511	4.90	0.070	0.776	1.5.99.12	NA
3	0.060	3eifA	0.427	5.27	0.046	0.684	3.4.21.110	NA
4	0.060	3i4zA	0.437	5.53	0.062	0.715	2.5.1.34	111
5	0.060	3i99A	0.448	5.14	0.034	0.702	1.1.1.158	NA
6	0.060	1oc5A	0.425	5.20	0.056	0.680	3.2.1.91	NA
7	0.060	3d2jA	0.503	5.06	0.055	0.789	1.21.3.3	44
8	0.060	1dgjA	0.449	5.76	0.033	0.763	1.2.-.-	14
9	0.060	1bgaA	0.364	6.38	0.048	0.675	3.2.1.21	10
10	0.060	2q9fA	0.436	4.91	0.066	0.649	1.14.13.98	172
11	0.060	2je8B	0.429	5.46	0.014	0.711	3.2.1.25	170
12	0.060	1tr1D	0.420	5.65	0.045	0.706	3.2.1.21	NA
13	0.060	1myrA	0.432	5.84	0.082	0.741	3.2.1.147	NA
14	0.060	3nn1A	0.542	4.82	0.087	0.825	1.13.11.49	157,209
15	0.060	3gnoA	0.434	6.10	0.045	0.759	3.2.1.21	NA
16	0.060	1rm6A	0.419	5.69	0.032	0.715	1.3.99.20	NA
17	0.060	3b9jJ	0.280	6.08	0.034	0.474	1.17.1.4,1.17.3.2	174
18	0.060	1e1eB	0.405	5.95	0.074	0.680	3.2.1.21	NA
19	0.060	1i19A	0.508	5.16	0.060	0.794	1.1.3.6	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	0.618	4.50	0.06	0.89	4c9sB	GO:0016853 GO:0045430
1	0.07	0.587	4.61	0.06	0.87	2y4eA	GO:0004601 GO:0006974 GO:0015684 GO:0016491 GO:0016675 GO:0020037 GO:0033212 GO:0042597 GO:0046872 GO:0055114 GO:0098869
2	0.07	0.620	4.48	0.06	0.89	4d06A	GO:0016853 GO:0045430
3	0.07	0.638	4.10	0.08	0.87	3gn6C	GO:0046872
4	0.07	0.603	4.56	0.07	0.89	2gvkA	GO:0004601 GO:0020037 GO:0055114 GO:0098869
5	0.07	0.630	4.31	0.09	0.90	3bxvA	GO:0046872
6	0.07	0.610	4.53	0.05	0.89	2hagA	GO:0004601 GO:0006582 GO:0020037 GO:0046872 GO:0055114 GO:0098869
7	0.07	0.610	4.25	0.06	0.87	5de0B	GO:0004601 GO:0006582 GO:0020037 GO:0055114 GO:0098869
8	0.07	0.634	4.27	0.08	0.90	2cb2A	GO:0005737 GO:0016491 GO:0033755 GO:0046872 GO:0055114
9	0.07	0.605	4.54	0.05	0.89	4gu7A	GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
10	0.07	0.594	4.56	0.09	0.88	5fw4A	GO:0004096 GO:0004601 GO:0005576 GO:0016491 GO:0020037 GO:0046872 GO:0055114 GO:0098869
11	0.07	0.606	4.48	0.07	0.89	3qnsA	GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
12	0.07	0.588	4.55	0.06	0.87	4gt2A	GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
13	0.07	0.577	4.67	0.10	0.88	4grcA	GO:0004601 GO:0005623 GO:0015684 GO:0020037 GO:0033212 GO:0046872 GO:0055114 GO:0098869
14	0.06	0.324	6.42	0.05	0.59	2xe1A	GO:0006810 GO:0006811 GO:0009279 GO:0015288 GO:0016020 GO:0016021 GO:0046930 GO:0055085
15	0.06	0.595	4.49	0.10	0.87	4gs1B	GO:0004601 GO:0020037 GO:0046872 GO:0055114 GO:0098869
16	0.06	0.320	6.10	0.07	0.57	1tuoA	GO:0005975 GO:0016868 GO:0071704
17	0.06	0.383	6.14	0.04	0.68	3ij3A	GO:0004177 GO:0005622 GO:0005737 GO:0006508 GO:0008233 GO:0008235 GO:0016787 GO:0019538 GO:0030145 GO:0046872
18	0.06	0.362	2.72	0.06	0.43	3kg0B	GO:0016491 GO:0016703 GO:0017000 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0045430	GO:0020037	GO:0004601	GO:0046872	GO:0016675
GO-Score	0.13	0.13	0.13	0.13	0.07
Biological Processes	GO:0098869	GO:0055114	GO:0006974	GO:0033212	GO:0015684
GO-Score	0.13	0.13	0.07	0.07	0.07
Cellular Component	GO:0042597
GO-Score	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.