I-TASSER results

I-TASSER results for job id Rv0219

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

Input Sequence in FASTA format

>protein (182 residues)
MFDIATRFKNSYGSGPLHLLAMVSGFALLGYIVATARPSALWNQATWWQSIAVWFVAAVV
AHDLLLYPLYALADRILARLVGRRDVSAPRRRPELPVRNYIRIPALAAGLTLLVFLPGII
RQGAPTYLDATGQTQEPFLGRWLLLTAVAFGISAAAYAIRLVVAHVRRRRAGCSRVDAID
EE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MFDIATRFKNSYGSGPLHLLAMVSGFALLGYIVATARPSALWNQATWWQSIAVWFVAAVVAHDLLLYPLYALADRILARLVGRRDVSAPRRRPELPVRNYIRIPALAAGLTLLVFLPGIIRQGAPTYLDATGQTQEPFLGRWLLLTAVAFGISAAAYAIRLVVAHVRRRRAGCSRVDAIDEE
Prediction	CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
Conf.Score	97588999999878866898999999999999997456544578887434678999999999999999999999999987555666677777778755456468999999999999987755787644456899876688999999999999999999999986444556788887776679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MFDIATRFKNSYGSGPLHLLAMVSGFALLGYIVATARPSALWNQATWWQSIAVWFVAAVVAHDLLLYPLYALADRILARLVGRRDVSAPRRRPELPVRNYIRIPALAAGLTLLVFLPGIIRQGAPTYLDATGQTQEPFLGRWLLLTAVAFGISAAAYAIRLVVAHVRRRRAGCSRVDAIDEE
Prediction	65512540352234320100011112011011223243441334433230000010101311101011121101310232244444444554441322210101122122133122110144346424413424563110211120023223200010022022334545545743543578
	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

CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC
MFDIATRFKNSYGSGPLHLLAMVSGFALLGYIVATARPSALWNQATWWQSIAVWFVAAVVAHDLLLYPLYALADRILARLVGRRDVSAPRRRPELPVRNYIRIPALAAGLTLLVFLPGIIRQGAPTYLDATGQTQEPFLGRWLLLTAVAFGISAAAYAIRLVVAHVRRRRAGCSRVDAIDEE

5ezmA

0.12

0.97

0.79

MUSTER

HMWVTVVGYELFGLGEAVALSGLLGIGVSMMAARRWFGARAAAFTG-LLAAPMWSVAAHFNLDMTLAGVMSCVLAFMLMGQHPDASVAARRGWMVACWAAMGVAILTKGLVGIALPGLVLV----VYTLVTRDWGLWRRLHLALGVVVMLVITVPWFYLVSVREFPNFFFIHEHWQRRSGSV

5cowA2

0.11

0.09

0.81

0.60

dPPAS

---------------GLQRSVFKSSVFLGHHIIQIFMGAKKPFQDWSFVG-----LAQDFECPWRRLAIAELLKKFSVSVVEKVFDNPVALIPQHESDNEALIELVTNALRFALWIVEFYETETNEKSIKELAFLDHSSKTLLIESFTKFLVKDQDHLKRIIDALEKS--------------

4xydA2

0.13

0.09

0.70

0.72

wdPPAS

--------------TAITNVLLLGLWGLTLLFLFAFYNPS--NLALWWYVVHLWVEG--------TWELVMASVLAFLMLK-------------LTGVDREIIEKWLYLIVATALFSGILGTGHHYF---IGTPG-----YWQWIGSIFSALEVVPFFGMMAFAFVMVWKGRK---------

5ezmA

0.14

0.13

0.96

0.82

wMUSTER

HMWVTVVGYELFGLGEAVALSGLLGIGVSMMAARRWFGARAAAFTG-LLAAPMWSVAAHFNLDMTLAGVMSCVLAFMLMGQHPDASVAARRGWMVACWAAMGVAILTKGLVGIALPGLVLV----VYTLVTRDWG--LWRRLLALGVVVMLVITVPWFYLVSVRNPFFIHEHWQRRSGSVFY

4xydA2

0.13

0.09

0.66

0.71

wPPAS

--------------TAITNVLLLGLWGLTLLFLFAFYNPS--NLA-WWYVVHLWVEG--------TWELVMASVLAFLMLK----------------LTGVDIEKWLYLIVATALFSGILGTG---F---IGTPG-----YWQWIGSIFSALEVVPFFGMMAFAFVMVWKGRK---------

4mndA2

0.07

0.06

0.82

0.87

dPPAS2

NRKISTRISAAIKVNPNQMTLISFLVGAFSALASFFSIPLASLKMSKKFVDFLFLAIIALLPKTATVAMFAIFGSVMVSYTSEKYKAEFGESIRVLNYIPGKRDERIFLIMIFCLLSAIS----------------LQWIFWMFLFVAAISLTRVVVTLLAVLVS-----------------

4bwzA2

0.11

0.10

0.94

0.80

PPAS

PFLGGYLYGLEIGFETLPALFLGTALVAVGITARVLQELGVLSRP---YSRIILGAAVIDDVLGLIVLACVNGVAETG------QELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGMAPRGVAALGLKANEEEYAIVLFMVVFTTLFAP--KPLIAWTERERAAKE

3syaA1

0.16

0.11

0.69

0.64

Env-PPAS

VRE-----TYRYLTDIFTTLVDL-----------------------KWRFNLLIFVMVYTVTWLFFGMIWWLIAYIRG------DMDHIEDPSWTPCVTN--LNGFVSAFLFSIETETTIGYG---YRVITD---KCPEGIILLLIQSVLGSIVNAFMVGCMFVKISQ--------------

5ezmA1

0.12

0.98

0.78

MUSTER

HMWVTVVGYELFGLGEWQARLAVALSGLLGIGVSMMAARRWFGARAAAFAPMWSVAAHFNTLDMTLAGVMSCVLAFMLMGQHPDASVAARRGWMVACWAAMGVAILTKGLVGIALPGLVLV----VYTLVTRDWGLWRRLHLALGVVVMLVITVPWFYLVSVREFPNFFFIHEHWQRRSGSV

4bwzA2

0.14

0.13

0.92

0.58

dPPAS

PFLGGYLYGLEIGFETLPALFLGTALVAVGITARVLQELGVLSR-----PYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQGVRSALTVGCGMAPGAVNEEEYAIVLFMVVFTTLFAPFALKPLIAWTERERAAKE----------

(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=-2.51

Estimated TM-score = 0.42±0.14

Estimated RMSD = 10.8±4.6Å

Download Model 2

C-score=-4.67

Download Model 3

C-score=-5.00

Download Model 4

C-score=-5.00

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	5ezmA1	0.794	2.63	0.119	0.967
2	3wajA	0.689	3.86	0.072	0.929
3	3rceA	0.625	3.53	0.105	0.835
4	3perA	0.531	4.92	0.035	0.890
5	5t8vA2	0.528	3.93	0.059	0.725
6	3jacA	0.511	4.89	0.077	0.813
7	3o2qA	0.500	4.41	0.083	0.736
8	1vsy42	0.494	4.27	0.048	0.725
9	3pjzA	0.492	4.86	0.055	0.775
10	2zzgA	0.490	4.36	0.063	0.725

(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	0.14	7	2v6xA	III	Rep, Mult	66,70,73,74,77,80,90,94,97,98,101,102,104,105,108
2	0.10	5	3qi4B	MG	Rep, Mult	62,63
3	0.04	2	2zmyA	CU	Rep, Mult	18,62
4	0.04	2	1fz8D	2BM	Rep, Mult	99,102,103,106
5	0.04	2	1ubwA	MG	Rep, Mult	63,74
6	0.02	1	1xvbD	3BR	Rep, Mult	147,150,151,154
7	0.02	1	3ak1B	EDO	Rep, Mult	77,97
8	0.02	1	5ezmA	PC	Rep, Mult	109,110,169
9	0.02	1	3pm5A	BYC	Rep, Mult	105,109,112,113
10	0.02	1	3u1nA	ZN	Rep, Mult	18,62,63,153
11	0.02	1	1xveC	3BB	Rep, Mult	23,55,61
12	0.02	1	1izlB	CLA	Rep, Mult	106,156

	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	1jqoA	0.473	5.50	0.058	0.830	4.1.1.31	NA
2	0.060	3hxxA	0.468	4.59	0.052	0.714	6.1.1.7	102
3	0.060	2eabA	0.480	5.12	0.098	0.797	3.2.1.63	NA
4	0.060	1fziA	0.468	5.46	0.069	0.824	1.14.13.25	NA
5	0.060	1ygbA	0.464	4.58	0.052	0.731	6.1.1.7	151
6	0.060	2ztgA	0.462	4.26	0.041	0.692	6.1.1.7	62
7	0.060	3ee4A	0.466	4.96	0.056	0.786	1.17.4.1	NA
8	0.060	1gw6A	0.463	5.28	0.049	0.786	3.3.2.6	NA
9	0.060	1gowA	0.484	5.27	0.064	0.819	3.2.1.23	NA
10	0.060	1w6sC	0.439	5.40	0.045	0.769	1.1.99.8	NA
11	0.060	2pulA	0.462	5.25	0.053	0.775	2.7.1.100	NA
12	0.060	1mhyB	0.479	4.97	0.054	0.775	1.14.13.25	66,70
13	0.060	2cqsA	0.446	5.57	0.096	0.786	2.4.1.20	NA
14	0.060	2e9lA	0.459	5.02	0.042	0.742	3.2.1.21	NA
15	0.060	1xjjA	0.474	5.34	0.061	0.802	1.17.4.1	69
16	0.060	2x1cA	0.463	5.23	0.072	0.813	2.3.1.164	101
17	0.060	2vuxB	0.421	5.14	0.025	0.725	1.17.4.1	NA
18	0.060	2zzgA	0.490	4.36	0.063	0.725	6.1.1.7	24
19	0.060	1edqA	0.444	5.39	0.051	0.764	3.2.1.14	74

(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	0.16	0.794	2.82	0.12	0.98	5f15A	GO:0016020 GO:0016021 GO:0016740
1	0.11	0.695	3.85	0.08	0.93	3wakA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
2	0.11	0.689	3.86	0.07	0.93	3wajA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0046872
3	0.07	0.625	3.53	0.10	0.84	3rceA	GO:0000287 GO:0004576 GO:0005886 GO:0006486 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0018279 GO:0046872
4	0.06	0.401	4.89	0.04	0.64	2lgzA	GO:0004576 GO:0004579 GO:0005783 GO:0005789 GO:0006486 GO:0006487 GO:0008250 GO:0016020 GO:0016021 GO:0016740 GO:0016757 GO:0018279 GO:0043687
5	0.06	0.378	5.89	0.04	0.70	4xmpG	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
6	0.06	0.316	5.42	0.07	0.55	2amxA	GO:0009168 GO:0019239
7	0.06	0.435	4.49	0.07	0.64	1lshA	GO:0005319 GO:0006869 GO:0045735
8	0.06	0.341	5.17	0.07	0.57	5azaA	GO:0004576 GO:0005215 GO:0005363 GO:0006486 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0016020 GO:0016021 GO:0016740 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
9	0.06	0.331	5.08	0.01	0.54	2anuA	GO:0003677 GO:0003824 GO:0003887 GO:0006260 GO:0046872 GO:0071897
10	0.06	0.336	5.65	0.07	0.59	3c8uA	GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0046835
11	0.06	0.327	5.59	0.08	0.59	3vgpA	GO:0004576 GO:0006486 GO:0016020 GO:0016021 GO:0016740
12	0.06	0.336	6.45	0.05	0.69	1r5aA	GO:0016740 GO:0046872
13	0.06	0.373	5.74	0.04	0.68	4j6rG	GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
14	0.06	0.355	4.86	0.03	0.54	4gklA	GO:0003824 GO:0005975
15	0.06	0.337	5.52	0.04	0.61	3oenA	GO:0004872 GO:0004970 GO:0004972 GO:0005216 GO:0005234 GO:0005261 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0016020 GO:0016021 GO:0016595 GO:0017146 GO:0022843 GO:0030054 GO:0034220 GO:0034765 GO:0035235 GO:0035249 GO:0042165 GO:0045202 GO:0045211 GO:0098655
16	0.06	0.340	5.55	0.06	0.62	3oekA	GO:0004872 GO:0004970 GO:0004972 GO:0005216 GO:0005234 GO:0005261 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0016020 GO:0016021 GO:0016595 GO:0017146 GO:0022843 GO:0030054 GO:0034220 GO:0034765 GO:0035235 GO:0035249 GO:0042165 GO:0045202 GO:0045211 GO:0098655
17	0.06	0.316	5.82	0.04	0.59	3vu0B	GO:0004576 GO:0006486 GO:0016020 GO:0016021
18	0.06	0.321	5.90	0.04	0.60	3waiA	GO:0004576 GO:0005215 GO:0005363 GO:0006486 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0016020 GO:0016021 GO:0016740 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0046872 GO:0055052 GO:0060326 GO:1901982 GO:1990060

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0004576
GO-Score	0.52	0.31
Biological Processes	GO:0006486
GO-Score	0.31
Cellular Component	GO:0016021
GO-Score	0.42

(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.