I-TASSER results

I-TASSER results for job id Rv1749c

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

Input Sequence in FASTA format

>protein (185 residues)
MLRAVNEIRQHDGTLKLGKGVGMFTIVGVIVALIGAFVQSRRHRHRPAADIHMLWWMVLI
VGVVSIIGAGYHVFDGERTAELIGYTRGDGGFQWENAMGDLAIGVVGLMAYRFRGHFWLA
TIVVLTIQYVGDAAGHIYYWVVENNTNPYNIGVPLWTDILLPIVMWALYAWSWHSNGDAV
PKGQP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLRAVNEIRQHDGTLKLGKGVGMFTIVGVIVALIGAFVQSRRHRHRPAADIHMLWWMVLIVGVVSIIGAGYHVFDGERTAELIGYTRGDGGFQWENAMGDLAIGVVGLMAYRFRGHFWLATIVVLTIQYVGDAAGHIYYWVVENNTNPYNIGVPLWTDILLPIVMWALYAWSWHSNGDAVPKGQP
Prediction	CCHHHHHHHHCCCEEEHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHEHCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Conf.Score	97567888874765675446799999999999999998644556758999999999999999999999999984679999986999999856767889999999999877645697466458999999999999999999998788888744447889999999999999999867888888999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MLRAVNEIRQHDGTLKLGKGVGMFTIVGVIVALIGAFVQSRRHRHRPAADIHMLWWMVLIVGVVSIIGAGYHVFDGERTAELIGYTRGDGGFQWENAMGDLAIGVVGLMAYRFRGHFWLATIVVLTIQYVGDAAGHIYYWVVENNTNPYNIGVPLWTDILLPIVMWALYAWSWHSNGDAVPKGQP
Prediction	73422540474613130442121333333332211000333444544102000112113322321331231111305400521315435421021203333232200100123444110000212332232003000120134452313100121333333133232100012435654446668
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHCCCEEEHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHEHCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
MLRAVNEIRQHDGTLKLGKGVGMFTIVGVIVALIGAFVQSRRHRHRPAADIHMLWWMVLIVGVVSIIGAGYHVFDGERTAELIGYTRGDGGFQWENAMGDLAIGVVGLMAYRFRGHFWLATIVVLTIQYVGDAAGHIYYWVVENNTNPYNIGVPLWTDILLPIVMWALYAWSWHSNGDAVPKGQP

3wdoA2

0.14

0.13

0.92

1.00

wMUSTER

MVGSFSKVLAEPRLLKLNFGIMCLHMLLMSTFVALPGQLADAGFPAAEHWKVYLATMLIAFGSVVPFIIYAEVKRKMKQVFVFCWNAQTQVQLFFVAFNLMEALLPSLISKESPAGYKTAMGVYSTSQFLGVAIGGSLGGWIDGMF---DGQGVFLAGAMLAAVWLAVAS--------KEP---P

5doqB2

0.10

0.09

0.86

0.97

wPPAS

------EVEENAAGVALD-VVLLSVTSVLYISAVFLTYYADAAGDEQARALLRRYALLWSG-PTMLSALLIIYQLRY--NPEH-YD----NVAWMLVISFLFFVITVWLLGRQRRFGWIALLFQYAFAFYAYGISHLYYLTIYDGFTNETVAFIAGLLLLIPSLYLLMRLFLFNK----------

3wdoA2

0.13

0.11

0.83

1.15

dPPAS2

QLADAGPAAEH------WKVYLATMLIAFGSVVPFIIYAEVKRK--------MKQVFVFCVGLIVVAEIVLWNAQTQFWQLVVG------VQLFFVAFNLMEALLPSLISKESPAGYKTAMGVYSTSQFLGVAIGGSLGGWIDGMF---DGQGVFLAGAMLAAVWLAVASTMKEPPY--------

4bwzA2

0.13

0.12

0.95

1.00

PPAS

DILAV--GKE--GGLEIGETLPALFLGTALVVGITARVLQELGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGMAPRGEVGLIVAALGLKAGAVNEELFMVVFTTLFAPFALKPLIAWTERERAAKE-----

3wdoA2

0.16

0.13

0.82

0.96

wPPAS

QLADAGPAAEH-WKV----YLATMLIAFGSVVPFIIYAEVKRK---------MKQVFVFCVGLIVVAEIVLWNAQTQFWQLVVG------VQLFFVAFNLMEALLPSLISKESPAGYKTAMGVYSTSQFLGVAIGGSLGGWIDGMF---DGQGVFLAGAMLAAVWLAVAS--------KEP---P

4o6yA

0.10

0.09

0.95

1.12

dPPAS2

VLTWTVHYRSSDNKDHIFNVHPVMMVIGLILFNGEAMLAYKSVQGTKNLKKLVHLTLQLTAFILSLIGVWAALKFHIDKGIE-NFYSLHSWLGLACLFLFAFQWAAGFVTYWYPGGSRISIYALALVTATTGILEKVTFLQVNQVITRYSTEAMLVNTMGVLILILGGFVILGVVT---------

4zowA2

0.11

0.09

0.81

1.11

dPPAS2

GE----------Q---LSSYEYGLLQVPIFGALIAGNLLLARLTSRRTVRSLIIMGGWPIMIGLLVAAAATVISSHAYLWMTA-------GLSIYAFGIGLANAGLVRLTLFASDMSKVSAAMGMLQMLIFTVGIEISKHAWLN----GGNGLFNLFNLVNGILWLSLMVIFLK-----------

5ctgA

0.07

0.06

0.87

1.08

dPPAS2

PVTTFKRILKAKST---ERFDGLPYLFSLLNCLICLWYGLPWVADG---RLLVATVNGIGAVFQLAYICLFIFYADSRKTRMK-------IIGLLVLVVCGFALVSHASVFFFDQPFVGAVSMASLISMFASPLAVMGVVIRSESVEFMP----FYLSLSTFLMSASFALYGLLL-------RDF

4pgrA

0.14

0.12

0.87

1.06

dPPAS2

IGQFVP-------------VALMLPLSILEVAMIILAFWMRRRKAVG-YAFVYTFAFVSGITLFPIVSHYASIAGAYVVLEAFGMKKDLSFLWSFLLVAVLALAVVGIFNIFSPLNSAAMAYSVIGTIVFSLYILYDLNQIKHRHITEDLIPVSLYLDFINLFINLLRFFGILSS----------

5an8A

0.12

0.11

0.96

0.83

MUSTER

VVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRL---FIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEW----YLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIVILRDLLRFLLVYLVFLFGFAVALVSLSREPP

(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=-2.95

Estimated TM-score = 0.38±0.13

Estimated RMSD = 12.0±4.4Å

Download Model 2

C-score=-3.15

Download Model 3

C-score=-3.29

Download Model 4

C-score=-4.55

Download Model 5

C-score=-4.52

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	4o6yA	0.742	2.87	0.081	0.930
2	4akkA	0.642	3.63	0.040	0.881
3	4a01A	0.628	4.38	0.059	0.957
4	5doqB	0.625	4.10	0.079	0.903
5	4av3A	0.621	4.34	0.044	0.930
6	1sj8A	0.591	4.26	0.054	0.838
7	1zrtC1	0.585	3.59	0.050	0.757
8	2ibzC	0.584	3.85	0.050	0.768
9	3h1jC	0.577	3.83	0.045	0.757
10	5iwkA2	0.576	3.94	0.058	0.795

(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	0.10	5	2yiuD	HEM	Rep, Mult	29,30,33,34,37,58,59,62,65,100,104,105,107,108,122,125
2	0.08	4	4xefA	III	Rep, Mult	9,19,23,27,31,34,126,129,133,136
3	0.06	3	4ogqA	2WM	Rep, Mult	31,34,38,133
4	0.06	3	3i0oA	MG	Rep, Mult	150,158
5	0.04	2	3n0gA	MG	Rep, Mult	95,102
6	0.04	2	3mz8A	ZN	Rep, Mult	45,136
7	0.02	1	3d9sB	PS6	Rep, Mult	101,183
8	0.02	1	2iubA	MG	Rep, Mult	132,136
9	0.02	1	3c2mA	MN	Rep, Mult	86,89
10	0.02	1	2dyrC	CDL	Rep, Mult	14,19,22,31,133,136,137
11	0.02	1	2avkA	FEA	Rep, Mult	22,25,68,69,72,89,93,128,129,132,133,136
12	0.02	1	4o6yA	HEC	Rep, Mult	37,40,41,51,54,55,58,103,106,107,110,111,115,116,117,174

	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	0.127	3g4xA	0.487	2.71	0.035	0.595	1.15.1.1	24,119
2	0.083	1q0mD	0.483	2.77	0.052	0.595	1.15.1.1	NA
3	0.060	3gtdA	0.533	4.09	0.033	0.773	4.2.1.2	NA
4	0.060	1k7wD	0.522	4.29	0.049	0.773	4.3.2.1	80
5	0.060	3czoB	0.548	4.82	0.045	0.870	4.3.1.3	NA
6	0.060	2z4yB	0.501	5.08	0.036	0.832	2.5.1.29	NA
7	0.060	1qleA	0.520	4.38	0.078	0.773	1.9.3.1	NA
8	0.060	2epoB	0.550	4.69	0.049	0.838	3.2.1.52	NA
9	0.060	1jswB	0.554	4.01	0.077	0.773	4.3.1.1	NA
10	0.060	1j3uA	0.537	3.88	0.045	0.757	4.3.1.1	79
11	0.060	2o6yA	0.545	4.08	0.073	0.773	4.3.1.-	NA
12	0.060	1m56A	0.523	4.39	0.073	0.773	1.9.3.1	NA
13	0.060	3gm1B	0.528	3.13	0.106	0.670	2.7.10.2	62,91,93,100,102,132
14	0.060	2ohyB	0.534	4.83	0.062	0.854	5.4.3.6	117
15	0.060	3cxhN	0.583	3.76	0.045	0.762	1.10.2.2	30,33
16	0.060	2occN	0.525	4.40	0.078	0.778	1.9.3.1	NA
17	0.060	1occA	0.526	4.36	0.079	0.773	1.9.3.1	NA
18	0.060	1i0aA	0.536	4.30	0.064	0.773	4.3.2.1	NA
19	0.060	3e04D	0.537	4.46	0.065	0.795	4.2.1.2	102
20	0.060	1qleC	0.540	3.22	0.058	0.676	1.9.3.1	120
21	0.060	1jtnA	0.339	5.12	0.034	0.535	3.2.1.17	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	0.20	0.748	2.83	0.07	0.94	4o7gB	GO:0005794 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
1	0.15	0.447	5.84	0.07	0.82	2jk6A	GO:0000166 GO:0005623 GO:0015036 GO:0015042 GO:0016491 GO:0016668 GO:0045454 GO:0050660 GO:0055114
2	0.09	0.331	5.74	0.03	0.58	1jlrA	GO:0000166 GO:0003824 GO:0004845 GO:0005525 GO:0008152 GO:0016740 GO:0016757 GO:0044206
3	0.09	0.432	5.84	0.03	0.80	1feaA	GO:0005737 GO:0015036 GO:0015042 GO:0016491 GO:0016668 GO:0045454 GO:0050660 GO:0055114
4	0.08	0.625	4.10	0.08	0.90	5doqB	GO:0016020 GO:0016021 GO:0055114
5	0.08	0.628	4.38	0.06	0.96	4a01A	GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
6	0.07	0.642	3.63	0.04	0.88	4akkA	GO:0003723 GO:0006351 GO:0006355 GO:0031564
7	0.07	0.591	4.26	0.05	0.84	1sj8A	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
8	0.07	0.601	4.59	0.09	0.94	4av6A	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
9	0.07	0.484	4.74	0.05	0.76	4av3B	GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
10	0.06	0.428	3.85	0.04	0.58	1u89A	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
11	0.06	0.433	5.02	0.04	0.71	2jswA	GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
12	0.06	0.340	5.87	0.04	0.64	3l0mA	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
13	0.06	0.423	4.23	0.04	0.63	3l0iC	GO:0000166 GO:0003824 GO:0005085 GO:0005524 GO:0005576 GO:0005622 GO:0006612 GO:0008152 GO:0008289 GO:0009405 GO:0016020 GO:0016740 GO:0016779 GO:0017137 GO:0018117 GO:0018260 GO:0033644 GO:0043087 GO:0043547 GO:0044161 GO:0044162 GO:0044600 GO:0070273 GO:0070733
14	0.06	0.318	6.01	0.02	0.61	3k5pA	GO:0004617 GO:0006564 GO:0008152 GO:0016491 GO:0016597 GO:0016616 GO:0051287 GO:0055114
15	0.06	0.271	6.09	0.02	0.54	4n8jA	GO:0003824 GO:0005829 GO:0006084 GO:0008410 GO:0016740
16	0.06	0.300	4.62	0.03	0.44	2ipaB	GO:0004725 GO:0016491 GO:0016787 GO:0030612 GO:0035335 GO:0046685 GO:0055114
17	0.06	0.274	4.99	0.05	0.43	2wlkA	GO:0005242 GO:0005244 GO:0006810 GO:0006811 GO:0006813 GO:0016020 GO:0016021 GO:0034765 GO:0071805
18	0.06	0.279	5.44	0.03	0.46	1s8nA	GO:0000160 GO:0003723 GO:0005618 GO:0005622 GO:0005886 GO:0006351 GO:0006355 GO:0031564 GO:0040007

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:1901265	GO:0016667	GO:0016651	GO:0050662	GO:0043169
GO-Score	0.45	0.45	0.44	0.44	0.44	0.40
Biological Processes	GO:0019725	GO:0050794	GO:0055114
GO-Score	0.44	0.44	0.43
Cellular Component	GO:0031224	GO:0044444	GO:0012505	GO:0043231
GO-Score	0.42	0.40	0.40	0.40

(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.