I-TASSER results

I-TASSER results for job id Rv3189

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

Input Sequence in FASTA format

>protein (206 residues)
MKLADAIATAPRRTLKGTYWHQGPTRHPVTSCADPARGPGRYHRTGEPGVWYASNKEQGA
WAELFRHFVDDGVDPFEVRRRVGRVAVTLQVLDLTDERTRSHLGVDETDLLSDDYTTTQA
IAAARDANFDAVLAPAAALPGCQTLAVFVHALPNIEPERSEVRQPPPRLANLLPLIRPHE
HMPDSVRRLLATLTRAGAEAIRRRRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MKLADAIATAPRRTLKGTYWHQGPTRHPVTSCADPARGPGRYHRTGEPGVWYASNKEQGAWAELFRHFVDDGVDPFEVRRRVGRVAVTLQVLDLTDERTRSHLGVDETDLLSDDYTTTQAIAAARDANFDAVLAPAAALPGCQTLAVFVHALPNIEPERSEVRQPPPRLANLLPLIRPHEHMPDSVRRLLATLTRAGAEAIRRRRR
Prediction	CCHHHHHHHCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHCCHHHCCCHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHCCCEEEHCCCCCCCCEEEEEEHCCCCCCCCHHHHHCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	96788888757665565899976777765556677777777677888863444678555799999987556777766579987888655445569999998759998774568657789999999989987885554589985899986345667856776558885667776545776668689999999998877899998749
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MKLADAIATAPRRTLKGTYWHQGPTRHPVTSCADPARGPGRYHRTGEPGVWYASNKEQGAWAELFRHFVDDGVDPFEVRRRVGRVAVTLQVLDLTDERTRSHLGVDETDLLSDDYTTTQAIAAARDANFDAVLAPAAALPGCQTLAVFVHALPNIEPERSEVRQPPPRLANLLPLIRPHEHMPDSVRRLLATLTRAGAEAIRRRRR
Prediction	45115212423443243312432465342333355263444234314320121234542110301322254334325233201331333311403435126515042641355415234224203534040002212434503200001231551446335245444302400310323642263034002203423152145458
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHCCHHHCCCHHHHHHHCCCHHHHCCCCHHHHHHHHHHHHHCCCEEEHCCCCCCCCEEEEEEHCCCCCCCCHHHHHCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC
MKLADAIATAPRRTLKGTYWHQGPTRHPVTSCADPARGPGRYHRTGEPGVWYASNKEQGAWAELFRHFVDDGVDPFEVRRRVGRVAVTLQVLDLTDERTRSHLGVDETDLLSDDYTTTQAIAAARDANFDAVLAPAAALPGCQTLAVFVHALPNIEPERSEVRQPPPRLANLLPLIRPHEHMPDSVRRLLATLTRAGAEAIRRRRR

2qs8A

0.17

0.16

0.91

0.72

MUSTER

ISLRDAINS--GKLAGPRIFAAGKT-IATTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGAD-------GIKITVTGGVLSVAK---------SGQNPQFTQEEVDAVVSAAKDYGWVAVHAHGAEGKRAIGVDSIEHGTFDLEADLIENGTPTISAGEFVAEKKIDNFFPEIVRPKAASVGPQISDTFRKAYE

2qs8A2

0.14

0.11

0.82

0.54

dPPAS

----------------------AAGKTATTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGAD-------GIKITVTGGVLSVAK---------SGQNPQFTQEEVDAVVSAAKDYGWVAVHAHGAEGKAGVDSIEHGTFDLEADLIENGTYYVPTAGEFVAEKSKIDNFFPEIVRPKAASVGPQISDTFRKAYE

5ikyA4

0.14

0.13

0.93

0.61

wdPPAS

LHNRFALNADPSGIYSQLIYRLVDKPAKLAYTERQLRINAE---ERLPLLKCFAHSSGIATAQQLDVQACRGLTGDELRALLVSFGSAADIVDVTA-DVRSLAGTTSRHYVQPGEHADVLQHCLVHTQPADYRYDHATGRQGKIVARLTGVFLLDDHARL---DDGHSIRRYLA-------SPLWLRQWIARFHDAGAHAILRELQ

2qs8A

0.17

0.16

0.91

0.73

wMUSTER

ISLRDAINS--GKLAGPRIFAAGKTIA-TTGGHADPTNGKAVDDYDYPVPEQGVVNGPYEVYAAVRQRYKDGAD-------GIKITVTGGVLSVAK---------SGQNPQFTQEEVDAVVSAAKDYGWVAVHAHGAEGKRAIGVDSIEHGTFDLEADLIENGTPTISAGEFVAEKKIDNFFPEIVRPKAASVGPQISDTFRKAYE

2fr0A1

0.22

0.17

0.78

0.81

wPPAS

----DEVSA--RIE-----WRPTGA-------GEPARLDGTW---KYAG---TADETSTAAREALESAVDARCGRDELAERLRSVGEVAGVLSLLAVDEAEP---EAPLALASLADTLSLVQAMVSAE------LGCP------LWTVTESAVATGPFE-----RNAAHGALWGVGRALEN-PELARHLAAVVSGGAGEALRAGVR

5ktkA1

0.16

0.12

0.73

0.64

dPPAS2

------------------------DRAACFSPIGSAVPGTRT-------VAILCCQETADLAAEVSSYFPN------------HLLIDVSRQSDIDWKEFDGL-VDVIGCGWDDEGRLDWIEWVQRLV-------EFGHKEGLRLLCVTKGLESFQNTSVRMAG-----ASRAGLYRQCEYDHRRLAKLIADEFYSDSYCYRDGLR

5ktkA1

0.15

0.12

0.76

0.71

PPAS

---------DRAACFLTKQWSLSP--------IGSAVPGTRT-------VAILCCQETADLAAEVSSYFPN------------HLLIDVSRQSDIDWKEFDGL-VDVIGCGWDDEGRLDWIEWVQRL--------EFGHKEGLRLLCVTKGLESFQNT-----SVRMAGASRAGLYRQCEYDHRRLAKLIADEFYSDSYCYRDGLR

3oi8A

0.19

0.12

0.64

0.68

Env-PPAS

-----------------------------------------------------SNASAEDVLNLLRQAHEQEVFDADTLLRL------EKVLDFSDLEVRDAI-TRSRNVLKENDSIERITAYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYFNPEQF----------HLKSILRPAVFVPEGLTALLKEFREQRNHAI-----

4o95A

0.12

0.97

0.69

MUSTER

SNFSEFTADQER------LISLGSGGGRRFDYVEGFVVAASVLYCLEVTKNYDDETAGSVDQDVDTLLGELNFLPGTVFTTDLPYVDFLDRVHKAELKLRAKGMWEVPHPWLNLFVPASRIADFDRGVFRGVLGGRTAGAGGP-VLIYPMNKHKWDPRSSAVTPDEEVFYLVAFLRSALPGAPESLEALARQNQRILDFCAGTGIG

2m1xA

0.13

0.10

0.75

0.51

dPPAS

-------------------------------------MESSSEQKFYNFVILHARADEHIALRVREKLEALGVPDGATFCEDFQVHGRGE---LSCLQDAIDHSAFIILLLTSNFDCRLSLHQVNQA-----MMSNLTRQGSPDCVIPFLPLESS------PAQLSSDTASLLSGLVRDEHSQIFARKVANTFKPHRLQARKAMWR

(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=-2.05

Estimated TM-score = 0.47±0.15

Estimated RMSD = 10.0±4.6Å

Download Model 2

C-score=-3.82

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.98

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	2qs8A	0.773	2.62	0.143	0.917
2	3be7A	0.750	2.63	0.082	0.893
3	4c5yA	0.740	2.80	0.092	0.898
4	3gnhA	0.736	2.74	0.082	0.888
5	2r8cA	0.732	3.02	0.119	0.898
6	3feqN	0.721	3.12	0.104	0.888
7	2p9bA	0.644	3.05	0.096	0.806
8	4wgxA	0.632	3.89	0.125	0.888
9	4whbE	0.623	4.05	0.122	0.893
10	5dezA	0.573	4.95	0.095	0.864

(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	0.13	7	3be7E	ARG	Rep, Mult	33,90,91,92,133,135,149,168,171,176,190,193,194,197
2	0.10	5	3n2cA	LWY	Rep, Mult	33,84,90,91,93,133,135,149,173
3	0.04	2	2istA	BCT	Rep, Mult	63,66
4	0.04	2	2hn2D	CA	Rep, Mult	109,119
5	0.04	2	3aruA	PNX	Rep, Mult	87,116,117,120,131,132
6	0.02	1	2wl3A	CA	Rep, Mult	75,113
7	0.02	1	3leeD	MG	Rep, Mult	109,113
8	0.02	1	1ay5A	MAE	Rep, Mult	52,187
9	0.02	1	4gkhG	0J9	Rep, Mult	52,75,87,176
10	0.02	1	1y10D	CA	Rep, Mult	77,106
11	0.02	1	2hcbB	MG	Rep, Mult	30,96
12	0.02	1	3pg9A	AZI	Rep, Mult	66,119
13	0.02	1	2v8vD	URP	Rep, Mult	141,171

	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	3giqA	0.525	4.73	0.091	0.777	3.5.1.82	124,132
2	0.060	1m53A	0.529	5.23	0.055	0.845	5.4.99.12	NA
3	0.060	1itxA	0.533	4.46	0.048	0.757	3.2.1.14	NA
4	0.060	1bwkA	0.522	4.66	0.047	0.772	1.6.99.1	NA
5	0.060	2vncB	0.493	4.97	0.047	0.786	3.2.1.-	NA
6	0.060	2g3fA	0.522	3.65	0.089	0.709	3.5.2.7	NA
7	0.060	3b9eA	0.561	4.62	0.026	0.820	3.2.1.14	NA
8	0.060	1s46A	0.529	4.90	0.037	0.820	2.4.1.4	54
9	0.060	1ydnA	0.525	3.89	0.098	0.743	4.1.3.4	NA
10	0.060	2ftwA	0.532	4.16	0.062	0.767	3.5.2.2	96
11	0.060	1fa2A	0.532	4.53	0.023	0.777	3.2.1.2	NA
12	0.060	1tz9A	0.544	4.58	0.033	0.816	4.2.1.8	NA
13	0.060	1veoA	0.537	4.96	0.112	0.820	3.2.1.2	90,136
14	0.060	1hp4A	0.543	4.64	0.052	0.820	3.2.1.52	NA
15	0.060	1kc7A	0.539	4.86	0.084	0.820	2.7.9.1	91
16	0.060	3gbdA	0.528	5.20	0.050	0.850	5.4.99.11	131,148
17	0.060	2gokA	0.524	3.65	0.103	0.704	3.5.2.7	NA
18	0.060	1djnA	0.529	4.57	0.054	0.777	1.5.8.2,1.5.99.7	NA
19	0.060	1zjaA	0.529	5.19	0.065	0.845	5.4.99.11	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	0.15	0.779	2.52	0.13	0.92	2qs8A	GO:0016787 GO:0016810 GO:0046872
1	0.13	0.741	2.73	0.08	0.89	3mtwA	GO:0016787 GO:0016810 GO:0046872
2	0.13	0.720	3.20	0.08	0.90	4c60A	GO:0006508 GO:0016787 GO:0016805 GO:0016810 GO:0046872 GO:0102009 GO:1900817
3	0.13	0.750	2.63	0.08	0.89	3be7A
4	0.12	0.731	3.03	0.12	0.90	3mkvA	GO:0016787 GO:0016810 GO:0046872
5	0.12	0.734	2.88	0.12	0.89	3n2cA
6	0.09	0.661	3.04	0.09	0.83	2p9bA	GO:0016787 GO:0016810
7	0.09	0.632	3.89	0.12	0.89	4ub9A	GO:0016787 GO:0016810
8	0.07	0.622	3.89	0.11	0.88	4whbA	GO:0016787 GO:0016810
9	0.07	0.507	4.76	0.04	0.77	3ighX	GO:0006259 GO:0016810 GO:0016888
10	0.07	0.443	5.75	0.05	0.78	3hm7B	GO:0000256 GO:0004038 GO:0006144 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0046872 GO:0050897
11	0.07	0.508	4.81	0.05	0.77	3griB	GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
12	0.07	0.442	5.32	0.06	0.72	4gz7A	GO:0005737 GO:0016787 GO:0016810 GO:0046872
13	0.07	0.518	4.51	0.09	0.77	1nfgA	GO:0005737 GO:0016787 GO:0016810 GO:0046872
14	0.07	0.494	4.96	0.07	0.77	3icjA	GO:0006259 GO:0016810 GO:0016888 GO:0046872
15	0.07	0.522	4.42	0.11	0.75	4l9xB	GO:0004040 GO:0016787 GO:0016810 GO:0046872
16	0.07	0.511	4.35	0.03	0.75	4bjhA	GO:0004151 GO:0006221 GO:0008270 GO:0016787 GO:0016810 GO:0016812 GO:0044205 GO:0046872
17	0.07	0.494	3.87	0.10	0.68	4dykA	GO:0004000 GO:0016787 GO:0016810 GO:0019700 GO:0046872 GO:0050270
18	0.07	0.520	4.91	0.07	0.79	1m7jA	GO:0016787 GO:0016810 GO:0016811 GO:0046872 GO:0047420

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0016810
GO-Score	0.43	0.43
Biological Processes	GO:0006508	GO:1900817
GO-Score	0.13	0.13
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.