I-TASSER results

I-TASSER results for job id Rv3032A

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

Input Sequence in FASTA format

>protein (129 residues)
MKPQDQGLHFPYRYDLRLAPMWLPFRWPGSQGVTVTEDGRFVARYGPFRVEAPLSSVRDA
HITGPYRWWTAVGPRLSMVDDGLTFGTNAAAGVCIHFEPRIHRVIGLRDHSALTVTVADP
EGLVAALSS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKPQDQGLHFPYRYDLRLAPMWLPFRWPGSQGVTVTEDGRFVARYGPFRVEAPLSSVRDAHITGPYRWWTAVGPRLSMVDDGLTFGTNAAAGVCIHFEPRIHRVIGLRDHSALTVTVADPEGLVAALSS
Prediction	CCCCCCCCEEHCCCCCCCCCCCCCCCCCCCCCEEEEHCCEEEEEHCCEEEEHCCCCCCCCEHCCCCCCEEEHCCCEEEHCCCEEHCCCCCCEEEEEHCCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHC
Conf.Score	998888655555667766754445456787667997578599998677999857655566555784654665345665568857668888658999678887788877788669998799999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MKPQDQGLHFPYRYDLRLAPMWLPFRWPGSQGVTVTEDGRFVARYGPFRVEAPLSSVRDAHITGPYRWWTAVGPRLSMVDDGLTFGTNAAAGVCIHFEPRIHRVIGLRDHSALTVTVADPEGLVAALSS
Prediction	754574545122323340432232132344431303454402042231315233541453434233420321243132344214213444310002144414524423634213131432720352168
	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

CCCCCCCCEEHCCCCCCCCCCCCCCCCCCCCCEEEEHCCEEEEEHCCEEEEHCCCCCCCCEHCCCCCCEEEHCCCEEEHCCCEEHCCCCCCEEEEEHCCCCCCCCCCCCCCCEEEEHCCHHHHHHHHHC
MKPQDQGLHFPYRYDLRLAPMWLPFRWPGSQGVTVTEDGRFVARYGPFRVEAPLSSVRDAHITGPYRWWTAVGPRLSMVDDGLTFGTNAAAGVCIHFEPRIHRVIGLRDHSALTVTVADPEGLVAALSS

3dmeA

0.21

0.99

0.90

MUSTER

IPPEYKGSYFTLAGRAPFSRLIYPVPQHAGLGVHLTLDLGGQAKFGPDTEWIATEDYTLDPYAAVRSYWPALPDALAPGYTGIRPKISGPHEPAADFAPASHGVAGLVESPGLTASLAIAEETLARLA-

5e7tA

0.08

0.07

0.91

0.71

dPPAS

SEYQPDVKVTYYKNSIGTEANGFDTGPVFGGERIYNLASSLSYIRNKINVELPSVYAMAGEVVNNGNELLLINGTEIMR--FVIEGATITKGYVEKVKPPTNLIVSDVTSTSAKISWENG---------

4pk1A2

0.12

0.11

0.88

0.56

wdPPAS

MSPLQFTPTTAWIGNFYSGSVNDFIVDGNR--YLVDQNDALTIDGG-WTQSD----LLHRLLTSP----VLYNGNLVVGDEGYLHWINVEDG--FVAQQKVDS-SGFQTEP--KLLIQAKDGTVYSITR

3dmeA

0.21

0.98

0.95

wMUSTER

IPPE-KGSYFTLAGRAPFSRLIYPVPQHAGLGVHLTLDLGGQAKFGPDTEWIATEDYTLDPYAAVRSYWPALPDALAPGYTGIRPKISGPHEPAADFAPASHGVAGLVESPGLTASLAIAEETLARLA-

3fmwC2

0.21

0.16

0.77

0.57

wPPAS

------------RYATFAPASARPHPWPGRFGLVLRPSGE-PVPAARPLLLDLAGRADLREATRPW------SDRVSVVAGEAT-VEPPAQALLVR---P----DG---YVAWAGSAATADELRASLAR

5fzpA1

0.12

0.94

0.70

dPPAS2

KVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDNTLLATHNDELQRSTDAGCTATLGSGST--WLTAAT------GGRAFAWEKNGGYLARVDRTVTKLSSPSADIGISAIAFNPARMYLGLEE

5fzpA1

0.12

0.96

0.76

PPAS

KVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDNTLLATHNDELQRSTDAGCTWTKV-ATLGS----GSTLTAATGGRAFAWEKNGGYLARVDRTVTKLSSPSADIGISAIAFNPARMYLGLEE

1ywuA

0.16

0.14

0.87

0.66

Env-PPAS

MSQHDERRRFH-RIAFDADSE---ILQGERRWEVLLHDGILVGQPQDWNGD-PQRPFEARLYLGLDVLIRMEI-SLAWARDG---------LLGFECQHDLDSISHLRR--LVELNLGDEELLERELAL

3dmeA1

0.20

0.99

0.72

MUSTER

LEPALHCTYFTLAGRAPFSRLIYPVPQHAGLGVHLTLDLGGQAKFGPDTEWIATEDYTLDPRRADVSYWPALPDALAPGYTGIRPKISGPHEPAADFAPASHGVAGLVESPGLTASLAIAEETLARLA-

5fzpA1

0.15

0.95

0.69

dPPAS

KVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDNTLLATHNDELQRSTDAGCTWTKVAGSGSTWLTAAT------GGRAFAWEKNGGYLARVDGRLSSPSADIGISAIAFNPARPSVMYLGLEE

(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=-3.86

Estimated TM-score = 0.30±0.10

Estimated RMSD = 13.4±4.1Å

Download Model 2

C-score=-4.39

Download Model 3

C-score=-3.42

Download Model 4

C-score=-4.82

Download Model 5

C-score=-4.73

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	3dmeA	0.625	3.59	0.139	0.922
2	1y56B	0.589	3.57	0.106	0.868
3	1x31B	0.581	3.37	0.091	0.853
4	2gb0B	0.580	3.80	0.095	0.891
5	1ddoA	0.571	3.52	0.046	0.845
6	2uzzB	0.570	4.01	0.085	0.891
7	3hzlA	0.569	4.00	0.112	0.891
8	4yshA	0.568	3.62	0.072	0.845
9	4x9mA	0.562	3.80	0.112	0.876
10	1c0lA	0.561	3.72	0.063	0.861

(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	0.07	4	2p7pA	SO4	Rep, Mult	61,63,85,94
2	0.07	4	4yshB	GLY	Rep, Mult	32,34,47,111
3	0.07	4	4f8hB	LMD	Rep, Mult	117,118,121
4	0.04	2	1qiyL	IPH	Rep, Mult	123,126
5	0.02	1	4f8hC	LMD	Rep, Mult	114,117
6	0.02	1	2r4eA	PO4	Rep, Mult	31,32,49,64,66
7	0.02	1	3pcaM	DHB	Rep, Mult	28,42
8	0.02	1	3c2kA	MN	Rep, Mult	5,110
9	0.02	1	1lqkA	MN	Rep, Mult	61,63
10	0.02	1	2wtgA	OXY	Rep, Mult	45,113
11	0.02	1	2buqA	CAQ	Rep, Mult	11,12
12	0.02	1	1vrqB	FMN	Rep, Mult	13,40,42,75,77
13	0.02	1	2olnA	NA	Rep, Mult	52,53,54
14	0.02	1	1jb0M	CLA	Rep, Mult	112,116
15	0.02	1	5ezmA	MPG	Rep, Mult	32,34
16	0.02	1	2g4lA	SO4	Rep, Mult	36,38,39
17	0.02	1	1eliB	PYC	Rep, Mult	2,86,87,88

	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	1pn0C	0.529	3.97	0.018	0.830	1.14.13.7	49,59
2	0.060	1ftrD	0.462	4.78	0.080	0.814	2.3.1.101	79
3	0.060	1gpeB	0.519	4.28	0.008	0.861	1.1.3.4	117
4	0.060	1galA	0.512	4.18	0.016	0.845	1.1.3.4	50
5	0.060	2gewA	0.489	4.56	0.034	0.853	1.1.3.6	NA
6	0.060	1cf3A	0.508	4.23	0.016	0.845	1.1.3.4	NA
7	0.060	1m5sD	0.456	4.60	0.064	0.791	2.3.1.101	35,79
8	0.060	2uzzB	0.570	4.01	0.085	0.891	1.5.3.-	NA
9	0.060	3fimB	0.497	4.50	0.024	0.861	1.1.3.7	NA
10	0.060	1dodA	0.523	3.69	0.063	0.783	1.14.13.2	NA
11	0.060	1gpeA	0.517	4.20	0.008	0.853	1.1.3.4	NA
12	0.060	2iw5A	0.451	4.65	0.044	0.798	1.-.-.-	NA
13	0.060	2jbvB	0.487	4.43	0.067	0.822	1.1.3.17	NA
14	0.060	1coyA	0.489	4.42	0.032	0.822	1.1.3.6	NA
15	0.060	1y56B	0.589	3.57	0.106	0.868	1.5.99.8	NA
16	0.060	1vrqB	0.580	3.57	0.080	0.868	1.5.3.1	NA
17	0.060	3cgvA	0.498	4.02	0.089	0.791	1.3.1.-	NA
18	0.060	2gmjA	0.493	4.30	0.050	0.822	1.5.5.1	NA
19	0.060	2qcuB	0.546	3.77	0.070	0.845	1.1.5.3	7,82

(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	0.625	3.59	0.14	0.92	3dmeA	GO:0000166 GO:0016491 GO:0055114
1	0.07	0.589	3.57	0.11	0.87	1y56B	GO:0000166 GO:0016491 GO:0055114
2	0.07	0.582	3.78	0.08	0.89	1zovA	GO:0005737 GO:0008115 GO:0016491 GO:0046653 GO:0055114
3	0.07	0.581	3.54	0.08	0.87	3ad7B	GO:0000166 GO:0008115 GO:0016491 GO:0046653 GO:0055114
4	0.07	0.550	3.80	0.11	0.85	3if9A	GO:0005737 GO:0009228 GO:0009229 GO:0009635 GO:0016491 GO:0043799 GO:0050660 GO:0055114
5	0.07	0.568	3.62	0.07	0.84	4yshA	GO:0016491 GO:0050660 GO:0055114
6	0.07	0.562	3.80	0.11	0.88	4x9mA	GO:0016491 GO:0055114
7	0.07	0.570	4.01	0.09	0.89	2uzzB	GO:0005829 GO:0006974 GO:0016491 GO:0016647 GO:0050131 GO:0050660 GO:0055114
8	0.07	0.514	3.80	0.07	0.80	2qa2A	GO:0000166 GO:0016491 GO:0055114 GO:0071949
9	0.07	0.537	4.09	0.08	0.85	2rgoA	GO:0000166 GO:0004368 GO:0004369 GO:0006072 GO:0009331 GO:0016020 GO:0016021 GO:0016491 GO:0055114
10	0.07	0.538	3.70	0.08	0.84	3nycA	GO:0000166 GO:0006525 GO:0006527 GO:0008718 GO:0009405 GO:0016491 GO:0055114
11	0.07	0.545	3.88	0.10	0.85	3axbA	GO:0000166 GO:0016020 GO:0016021 GO:0016491 GO:0055114
12	0.07	0.531	3.79	0.06	0.82	4rslA	GO:0000166 GO:0016491 GO:0055114
13	0.06	0.411	4.89	0.06	0.78	2zxiB	GO:0002098 GO:0005737 GO:0008033 GO:0016491 GO:0050660 GO:0055114
14	0.06	0.457	4.16	0.03	0.75	3kveA	GO:0001716 GO:0005576 GO:0006915 GO:0016491 GO:0019835 GO:0042742 GO:0044179 GO:0046872 GO:0055114
15	0.06	0.369	5.28	0.06	0.69	3he3A	GO:0000166 GO:0008767
16	0.06	0.348	5.54	0.02	0.73	4y4nA	GO:0005975 GO:0016491 GO:0016853 GO:0019693 GO:0043917 GO:0055114
17	0.06	0.452	4.29	0.04	0.77	1o5wC	GO:0005739 GO:0005741 GO:0006584 GO:0008131 GO:0016020 GO:0016021 GO:0016491 GO:0042135 GO:0042424 GO:0042428 GO:0042443 GO:0050660 GO:0051378 GO:0055114
18	0.06	0.333	5.45	0.06	0.70	3uozA	GO:0004497 GO:0004499 GO:0016491 GO:0019383 GO:0050660 GO:0050661 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003824	GO:0036094	GO:1901265
GO-Score	0.41	0.37	0.37
Biological Processes	GO:0044710
GO-Score	0.58
Cellular Component	GO:0005737
GO-Score	0.13

(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.