I-TASSER results

I-TASSER results for job id Rv1351

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

Input Sequence in FASTA format

>protein (109 residues)
MTPRSLPRYGNSSRRKSFPMHRPSNVATATRKKSSIGWVLLACSVAGCKGIDTTEFILGR
AGAFELAVRAAQHRHRYLTMVNVGRAPPRRCRTVCMAATDTPRNIRLNG

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MTPRSLPRYGNSSRRKSFPMHRPSNVATATRKKSSIGWVLLACSVAGCKGIDTTEFILGRAGAFELAVRAAQHRHRYLTMVNVGRAPPRRCRTVCMAATDTPRNIRLNG
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHEEEEHCCCCCCCCCCCEEEEHCCCHHHHHHHHHHHHHHEEEEEEHCCCCCCHHHHHHHHCCCCCCEEEHCC
Conf.Score	9865678778877666678888876444344566534455554446886776444676556557889999987763567777678998555444553478986566679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MTPRSLPRYGNSSRRKSFPMHRPSNVATATRKKSSIGWVLLACSVAGCKGIDTTEFILGRAGAFELAVRAAQHRHRYLTMVNVGRAPPRRCRTVCMAATDTPRNIRLNG
Prediction	7545424533566445514444364234334554301100110223414415224202343322411131264443212113235333540331022236335515478
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHEEEEHCCCCCCCCCCCEEEEHCCCHHHHHHHHHHHHHHEEEEEEHCCCCCCHHHHHHHHCCCCCCEEEHCC
MTPRSLPRYGNSSRRKSFPMHRPSNVATATRKKSSIGWVLLACSVAGCKGIDTTEFILGRAGAFELAVRAAQHRHRYLTMVNVGRAPPRRCRTVCMAATDTPRNIRLNG

3egbA

0.23

0.99

0.79

MUSTER

GYRKSLYKRPKANGVKPSTVHVISTPQISCKGQHSISYTLQTVVVEYTHDKDTDMFQVGRSTEFVVTDTITQSTSRFACRIVCDRNEPYTAR-IFAAGFDSSKNIFLGE

5aj3m

0.19

0.18

0.95

0.73

dPPAS

SLRGRLARLGNPRRKPNKPLILANHVGERRREKGEEMSVMMACKQNEFRDEACRKEIQDFFDCASRAEAARKMRSIQENLGELGSLPPKKLNKLLHRFPNKPHV-----

3j39e

0.26

0.22

0.83

0.58

wdPPAS

MTIRPAYR---KKRTKHFIRHKPKGIDNRVRRRFNIGY-----SNKRTRHMLPTKFLV---NVRELEV--LMQNRVYCGEIGVS---SKKRKEIVERAKQ--LSVRLNP

2k9kA

0.20

0.17

0.89

0.68

wMUSTER

FTSATFGDFGSNQQAM--PLYRPVYPSRALKRGVE-GFVTLSFTIDT-TGKAVDINVVDANPMFEREAMQALKKWKYQQIVD-GKAIEQPGQTV-------TVEFKIAK

2k9kA

0.21

0.17

0.83

0.56

wPPAS

FTSATFGDFGSNQQAM--PLYRPVYPSRALKRGVE-GFVTLSFTI---TG--VDINVVDANPKFEREAMQALKKWKY--IVD-GKAIEQPGQTV-------TVEFKIAK

1ffkW

0.35

0.19

0.55

0.62

dPPAS2

PTGRFGPRYGLKIRVREIKHKKKPVCGFPKLKRASTSWVCGHCGIAG--GPETV------AGK---AVMKA--------------------------------------

2k9kA

0.20

0.17

0.89

0.77

PPAS

FTSATFGDFGSNQQAM--PLYRVEPVSRALKRGVE-GFVTLSFTI-DTTGKAVDINVVDANPKFEREAMQALKKWKYQQIVD-GKAIEQPGQTV-------TVEFKIAK

2miqA

0.17

0.13

0.77

0.71

Env-PPAS

MSGGS-PLATGTTANTRGASQKKGGEPPALIVDPLMKYI---CHI--CNGDVEESMLLGCDDSY--------HTFCL----LPPTSIPKLC-PRCVVEEVKPQ------

1pqyA

0.14

0.13

0.92

0.72

MUSTER

TFGDAVPRGGNAG-----GGGQPGWILKCKGWETDPNAYIYFTIQEQCKAIGKPE--WITDPAYSTAHARQPHIFDIFAEIETVTIDKHEAVAYLTQF-DIP-CAPVLS

2mk4A

0.13

0.12

0.94

0.68

dPPAS

VNGQTYLIPDNGSKKRVARSLDSKVPQQTLRRGDVL------MQGAASPELTVSGTLLVEADDASAKALATRHGLNFKQSIALLEAKPGNAIATKLKSEGVNVQIELSG

(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=-2.76

Estimated TM-score = 0.40±0.13

Estimated RMSD = 10.2±4.6Å

Download Model 2

C-score=-4.55

Download Model 3

C-score=-4.73

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	1tolA	0.521	3.66	0.085	0.780
2	2k9kA	0.507	3.75	0.147	0.798
3	4k0eA	0.502	4.61	0.085	0.890
4	2j8sA3	0.500	4.68	0.065	0.881
5	4mt1A2	0.493	4.43	0.047	0.890
6	1lr0A	0.491	3.23	0.074	0.706
7	3k07A2	0.491	4.67	0.067	0.908
8	4g7xB	0.485	3.59	0.042	0.734
9	3iygG	0.479	4.84	0.075	0.908
10	3aqpA2	0.475	4.41	0.046	0.826

(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	8	2kikA	ZN	Rep, Mult	52,72,75
2	0.05	3	4f8hB	LMD	Rep, Mult	66,67,70
3	0.03	2	3u39C	CA	Rep, Mult	8,10
4	0.03	2	1usyF	HIS	Rep, Mult	68,72
5	0.03	2	4j8vH	RU7	Rep, Mult	64,65
6	0.02	1	4a18L	ZN	Rep, Mult	43,48,91,95
7	0.02	1	3v2dF	MG	Rep, Mult	60,61
8	0.02	1	1h7gB	MG	Rep, Mult	12,13
9	0.02	1	1ibk0	III	Rep, Mult	24,25,26
10	0.02	1	1l0l2	III	Rep, Mult	2,3,6,36,104,105
11	0.02	1	1n1gA	BCP	Rep, Mult	95,98,99
12	0.02	1	3gz8A	APR	Rep, Mult	9,18
13	0.02	1	1jwyB	MG	Rep, Mult	16,17
14	0.02	1	3r33A	CA	Rep, Mult	100,101
15	0.02	1	2f7fA	NIO	Rep, Mult	41,42,43,56,58
16	0.02	1	1oxnA	ZN	Rep, Mult	43,48,73,91
17	0.02	1	1dkdD	III	Rep, Mult	4,18,31,71,74,77,78

	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	2plaA	0.425	3.85	0.057	0.697	1.1.1.8	37
2	0.060	2he9A	0.426	4.87	0.085	0.844	5.2.1.8	NA
3	0.060	1n1eA	0.461	4.13	0.052	0.743	1.1.1.8	NA
4	0.060	2z04B	0.429	4.17	0.041	0.725	4.1.1.21	NA
5	0.060	2w22A	0.330	4.36	0.056	0.587	3.1.1.3	NA
6	0.060	1yrlC	0.425	3.90	0.058	0.697	1.1.1.86	78
7	0.060	3g17G	0.429	4.46	0.066	0.761	1.1.1.169	NA
8	0.060	1x0xA	0.425	4.18	0.057	0.725	1.1.1.8	37
9	0.060	2gw2A	0.443	4.43	0.056	0.807	5.2.1.8	8
10	0.060	3h2zA	0.448	4.26	0.050	0.761	1.1.1.17	45,82
11	0.060	3k2cC	0.431	4.80	0.085	0.844	5.2.1.8	NA
12	0.060	1yrlA	0.428	3.84	0.048	0.688	1.1.1.86	65
13	0.060	2nqtA	0.419	4.53	0.044	0.761	1.2.1.38	NA
14	0.060	1txgA	0.448	3.74	0.031	0.697	1.1.1.94	NA
15	0.060	1n4tA	0.349	4.75	0.046	0.651	3.1.4.37	70
16	0.060	2k7nA	0.442	4.59	0.065	0.826	5.2.1.8	8
17	0.060	2e7zA	0.437	4.22	0.038	0.743	4.2.1.71	82
18	0.060	1clhA	0.426	4.78	0.053	0.826	5.2.1.8	18
19	0.060	2wghB	0.429	4.51	0.047	0.780	1.17.4.1	95

(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	0.483	3.42	0.11	0.72	1s62A	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0017038 GO:0032153 GO:0043213 GO:0046718 GO:0051301 GO:0071237
1	0.07	0.507	3.75	0.15	0.80	2k9kA	GO:0005886 GO:0006810 GO:0015031 GO:0015343 GO:0015891 GO:0016021 GO:0030288 GO:0031992 GO:0044718
2	0.07	0.521	3.66	0.09	0.78	1tolA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0009405 GO:0015031 GO:0016020 GO:0016021 GO:0016032 GO:0017038 GO:0019012 GO:0019028 GO:0019062 GO:0019076 GO:0032153 GO:0033644 GO:0039666 GO:0043213 GO:0046718 GO:0051301 GO:0071237
3	0.07	0.485	3.59	0.04	0.73	4g7xB	GO:0005215 GO:0006810 GO:0016020 GO:0016021
4	0.07	0.453	4.16	0.10	0.71	2m2kA	GO:0006810
5	0.06	0.420	3.83	0.16	0.67	1u07A	GO:0005886 GO:0006810 GO:0015031 GO:0015343 GO:0015889 GO:0015891 GO:0016020 GO:0016021 GO:0030288 GO:0031233 GO:0031992 GO:0042914 GO:0043213 GO:0044718
6	0.06	0.337	3.64	0.05	0.51	3qvjA	GO:0006807 GO:0036361
7	0.06	0.300	5.18	0.05	0.61	2w1tA	GO:0003677 GO:0006351 GO:0006355 GO:0030435
8	0.06	0.390	4.24	0.07	0.70	2d0jA	GO:0000139 GO:0005794 GO:0005975 GO:0006486 GO:0015018 GO:0016020 GO:0016021 GO:0016740 GO:0030203 GO:0030204 GO:0046872 GO:0050650
9	0.06	0.397	4.55	0.09	0.72	3i6sA	GO:0004252 GO:0005618 GO:0006508 GO:0008233 GO:0008236 GO:0016787
10	0.06	0.477	4.59	0.09	0.88	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
11	0.06	0.500	4.34	0.06	0.84	4dnrA	GO:0005215 GO:0005375 GO:0005507 GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006825 GO:0006878 GO:0008324 GO:0010272 GO:0010273 GO:0015080 GO:0015673 GO:0015679 GO:0016020 GO:0016021 GO:0046688 GO:0060003 GO:1902601
12	0.06	0.370	4.94	0.08	0.72	5en5C	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
13	0.06	0.345	4.96	0.02	0.65	3ge6A	GO:0000166 GO:0016491 GO:0055114
14	0.06	0.313	4.83	0.04	0.58	3qivA
15	0.06	0.406	4.02	0.07	0.68	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
16	0.06	0.456	5.18	0.07	0.89	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
17	0.06	0.305	5.03	0.07	0.59	4i0wD	GO:0004252 GO:0006508 GO:0008233 GO:0008236 GO:0016787
18	0.06	0.324	5.10	0.07	0.64	3jb9Y	GO:0000166 GO:0000387 GO:0000974 GO:0003676 GO:0003723 GO:0005634 GO:0005681 GO:0006397 GO:0007049 GO:0008380 GO:0017070 GO:0036002 GO:0045292 GO:0046872 GO:0071006 GO:0071007

Consensus prediction of GO terms

Molecular Function	GO:0015343	GO:0031992
GO-Score	0.07	0.07
Biological Processes	GO:0045184	GO:1901653	GO:0044763	GO:0044765	GO:0071236	GO:0015833	GO:0030260	GO:0019058	GO:0046678
GO-Score	0.60	0.50	0.50	0.50	0.50	0.50	0.50	0.50	0.50
Cellular Component	GO:0031226	GO:0016021
GO-Score	0.50	0.34

(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.