I-TASSER results

I-TASSER results for job id Rv3008

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

Input Sequence in FASTA format

>protein (207 residues)
MLTVVAVIGILECGLVLHMPDNDLWYCGPWTLWVMAGRGVASGAGVWRGDRVATPLAVAI
TAAGLVSGARIGPGAAAKRDPQLAQWNEIRSHYQEIAEWIDHDTATAHPAVAATQISAAG
SFGRANMVDYLGLLDSRADETVRRDEFSRWLSAKPDYLVTTEQSVDAATIALPEFRHAYD
RAATIGTLNVYRRNSPDGDEPLPADGN

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLTVVAVIGILECGLVLHMPDNDLWYCGPWTLWVMAGRGVASGAGVWRGDRVATPLAVAITAAGLVSGARIGPGAAAKRDPQLAQWNEIRSHYQEIAEWIDHDTATAHPAVAATQISAAGSFGRANMVDYLGLLDSRADETVRRDEFSRWLSAKPDYLVTTEQSVDAATIALPEFRHAYDRAATIGTLNVYRRNSPDGDEPLPADGN
Prediction	CCHEHHHHHHHHCEEEEHCCCCCCEEHCCEEEEEEHCCCCCCCCCEEHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHEHCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEHCCCCCCHHHHHHHHHHHHHHHHHCEEEEEEEHCCCCCCCCCCCCCCC
Conf.Score	953456666554446887688875676553456654555545665554665554445555555544455557765445566788899999999999999856666666544444443455555546777877655555556678888887647987567645555445544477788776554345677776579988888888999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MLTVVAVIGILECGLVLHMPDNDLWYCGPWTLWVMAGRGVASGAGVWRGDRVATPLAVAITAAGLVSGARIGPGAAAKRDPQLAQWNEIRSHYQEIAEWIDHDTATAHPAVAATQISAAGSFGRANMVDYLGLLDSRADETVRRDEFSRWLSAKPDYLVTTEQSVDAATIALPEFRHAYDRAATIGTLNVYRRNSPDGDEPLPADGN
Prediction	612000011113010001035430110021000011132124322213244103200100202211332412433335444423515503530540151154633333312123414332423333113102103542564144640441153434111324541410202034044125322312203123454563654246778
	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

CCHEHHHHHHHHCEEEEHCCCCCCEEHCCEEEEEEHCCCCCCCCCEEHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHEHCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEHCCCCCCHHHHHHHHHHHHHHHHHCEEEEEEEHCCCCCCCCCCCCCCC
MLTVVAVIGILECGLVLHMPDNDLWYCGPWTLWVMAGRGVASGAGVWRGDRVATPLAVAITAAGLVSGARIGPGAAAKRDPQLAQWNEIRSHYQEIAEWIDHDTATAHPAVAATQISAAGSFGRANMVDYLGLLDSRADETVRRDEFSRWLSAKPDYLVTTEQSVDAATIALPEFRHAYDRAATIGTLNVYRRNSPDGDEPLPADGN

2yjnA1

0.17

0.15

0.89

0.64

MUSTER

VFSSMASKSHLFGLVPLH-----RVVASPALTEDITAAGL---TAVPVGTDVDLVDFMTHAGHDIIDYVR--SLDFSERDPATLTWEHLLGMQTVLTPTFYALMSPDTLIVSFCR--EPLTFAAPIAAAVTGLLWGPDITTRARQNFLGLLPDQPE-----EHREDPLAEWLTWTLEKYDEEVVVGQWTI---PAPAA--RLDTGLK

3vwaA3

0.10

0.09

0.87

0.49

dPPAS

ISQLLATLGFLK-NFVLGTLSKDSVFINIKGEWVLFGLELCSSK----EGLSAFEFASRARSYYNIIGSQLPCEDPNTIDSGLGLLIKSLCLPKDWIVNVNISDGKITIENFRKRLENTETWRSNPLINFYQELRKDPQGKLVVSNLENLYLESREIFRNLTPGIENF--IIPELCEIIKLLTQSISS-------------------

4x8fA1

0.28

0.19

0.69

0.57

wdPPAS

MNKLV-VLGSVNADHVLQVPS-------P-----RPGETLHGGKG-------AN--AVA--AARM--QADVGDDSFGIN---------IRESFKLD---INTAQPNCPTGIAMIQVSDSGE----NSI----CISAEANAKLTAAAIEPDLARDARYLLMQETPLDGILKAA---QEA--KTA--KTNVIL---------PAPA---

2yjnA1

0.18

0.16

0.89

0.60

wMUSTER

MFSSMASKSHLFGLVPLH-----RVVASPALT-DITAAGLTA---VPVGTDVDLVDFMTHAGHDIIDYVR--SLDFSERDPATLTWEHLLGMQTVLTPTFYALMSPIEGMVSFCR--EPLTFAAPIAAAVTGLLWGPDITTRARQNFLGLLPDQPE-----EHREDPLAEWLTWTLEKYDEEVVVGQWTI---PAPAA--RLDTGLK

4x8fA1

0.36

0.23

0.64

0.55

wPPAS

MNKLV-VLGSV--DHVLQFPR------G--TL---HGRG---GKG-------AN--AVA--AARM--QADIA-G----DDS--GIN--IRESFKLD---INTAQPNCPTGIAMIQVSDSGSIE-ANA-----KLTA---AAIEPDL----AIRDARYLLMQETPLDGILKAA---QEA--KTA--KTNVIL---------PAPA---

2yjnA1

0.17

0.15

0.88

0.53

dPPAS2

LFGLVPLAWAFRAG---HEV---RVVASPA----LTEDITAAGLAVPVGTDVDLVDFMTHAGHDIIDYVR--SLDFSERDPATLTWEHLLGMQTVLTPTFYALMS-PDTLIEGMVSFCPLTFAAPIAAAVTGLLWGPDITTRARQNFLGLLPDQPE-----EHREDAEWLTWTLEKYAFDEEVVVGQWTID--PAP----ALDTGLK

3ikhA1

0.22

0.17

0.76

0.54

PPAS

L-RVY-VTGNITVDETWSIPKKG-------SI---HGVKVSQDIG--------KGANQAIILSRC--GIETRLIAATGND---SNGAWIRQQIKN----LLDGHFNQHSDTSIILNSADGD----NAI----ITTTAAADTFSLDEIPHADAVAGDILLQQNFSLDKTRALFQYARSR------TTVFN-----SPDFCHLWPIDI-

3iz5T

0.16

0.13

0.84

0.71

Env-PPAS

SLKLRLASSVLKCGVWLD-PNNEISM----ANSRQNIRKVKDGFIIRKPQKIHSRSRARRAHEAKQKGRHSGYGREARLPTKILWMRRMRVLRRLLRKYREAKKIDKHMYHDMYLKVKGNMFNKRVLMESIHKS---KAEKAREKTLSDQFEAK--------RAKSKASRERKIARREERLAP--GP----ERSC------------

1zd4A1

0.10

0.95

0.60

MUSTER

--TLRAAV--LD-GVLALPAVFGVL-LPRGLLAFQKGGPEGATTRLMKGEITLSQWIPLMEENCRKCSETAKVCLPKNFSEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESCQVGM---VKPEYKFLLDTKASPSEVVF-DIGANLKPARDLG-MVTILVQDTDGIQLLNTPAP

2yjnA1

0.16

0.14

0.91

0.49

dPPAS

LFGLVPLAWAFRAGHEVR------VVASPALTEDITAAGLT---AVPVGTDVDLVDFMTHAGHDIIDYVR--SLDFSERDPATLTWEHLLGMQTVLTPTFYALMSPDTSFCRKWVIWEPLTFAAPIAAAVTGLLWGPDITTRARQNFLGLLPDQPE-----EHREDAEWLTWTLEKYAFDEEVVVGQWTID--PAPAAIR-LDTGLK

(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=-3.90

Estimated TM-score = 0.29±0.09

Estimated RMSD = 14.8±3.6Å

Download Model 2

C-score=-4.08

Download Model 3

C-score=-4.01

Download Model 4

C-score=-3.54

Download Model 5

C-score=-3.59

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	1wyeA	0.514	4.51	0.058	0.768
2	2v78A	0.513	4.55	0.070	0.768
3	1rk2B	0.508	4.42	0.059	0.744
4	2hlzC	0.508	4.51	0.088	0.758
5	2ajrA	0.506	4.75	0.050	0.768
6	1v19A	0.506	4.45	0.083	0.758
7	3uq6A	0.505	4.57	0.056	0.763
8	3looA	0.504	4.63	0.056	0.763
9	1ua4A	0.504	5.01	0.039	0.787
10	4e69A	0.503	4.45	0.101	0.749

(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	0.08	5	2i6aB	5I5	Rep, Mult	12,14,16,58,116,126
2	0.07	4	1kgzA	MN	Rep, Mult	50,199,200
3	0.05	3	1rk2B	ADP	Rep, Mult	8,59,62,66
4	0.05	3	1jb0M	CLA	Rep, Mult	167,171
5	0.03	2	1s2vB	MG	Rep, Mult	80,103
6	0.03	2	3lswA	ZN	Rep, Mult	88,92
7	0.03	2	3b1nA	ADP	Rep, Mult	4,34,58,61
8	0.02	1	2h1iB	CA	Rep, Mult	98,101
9	0.02	1	2e85B	CA	Rep, Mult	85,88
10	0.02	1	2bo6B	MN	Rep, Mult	21,23
11	0.02	1	2z8yM	XE	Rep, Mult	6,142,167,168,171
12	0.02	1	4awyB	MG	Rep, Mult	110,130
13	0.02	1	1t8sA	FMP	Rep, Mult	92,93
14	0.02	1	1un9A	MG	Rep, Mult	180,197,199
15	0.02	1	1uetA	CA	Rep, Mult	141,146
16	0.02	1	5erjA	CPT	Rep, Mult	70,157

	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	3hj6A	0.486	4.46	0.088	0.715	2.7.1.4	129,188
2	0.060	3b3lA	0.504	4.32	0.055	0.725	2.7.1.3	NA
3	0.060	2qcvA	0.496	4.53	0.085	0.749	2.7.1.92	57
4	0.060	3ie7A	0.477	4.98	0.064	0.768	2.7.1.-	NA
5	0.060	2nxfA	0.447	5.37	0.089	0.730	3.6.1.16,3.6.1.53,3.6.1.13	NA
6	0.060	1ua4A	0.504	5.01	0.039	0.787	2.7.1.147	154
7	0.060	1sqfA	0.461	5.43	0.088	0.763	2.1.1.-	NA
8	0.060	3ktnA	0.496	4.65	0.043	0.754	2.7.1.45	NA
9	0.060	1l2lA	0.483	4.96	0.045	0.763	2.7.1.147	62
10	0.060	2frxA	0.464	5.56	0.044	0.778	2.1.1.-	NA
11	0.060	3drwA	0.476	4.95	0.058	0.749	2.7.1.146	115,188,190
12	0.060	2hlzC	0.508	4.51	0.088	0.758	2.7.1.3	NA
13	0.060	1z45A	0.442	4.69	0.058	0.652	5.1.3.2,5.1.3.3	NA
14	0.060	3k9eB	0.483	4.63	0.071	0.744	2.7.1.-	NA
15	0.060	1vm7A	0.475	4.56	0.074	0.710	2.7.1.15	NA
16	0.060	2c49A	0.499	4.17	0.049	0.710	2.7.1.-	NA
17	0.060	1rpnC	0.454	4.49	0.102	0.652	4.2.1.47	NA
18	0.060	2v78A	0.513	4.55	0.070	0.768	2.7.1.4	59
19	0.060	3e2dA	0.442	5.18	0.061	0.730	3.1.3.1	124

(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	0.18	0.503	4.60	0.04	0.76	3ktnA	GO:0016301 GO:0016310 GO:0016740
1	0.13	0.507	4.42	0.06	0.74	1gqtB	GO:0000166 GO:0004747 GO:0005524 GO:0005737 GO:0005829 GO:0005975 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835 GO:0046872
2	0.10	0.490	4.76	0.08	0.77	3in1A	GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
3	0.07	0.495	4.69	0.10	0.75	4k8pA	GO:0000166 GO:0016301 GO:0016310 GO:0016740 GO:0016773
4	0.07	0.484	4.79	0.10	0.77	3pl2A	GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0046835
5	0.07	0.505	4.64	0.08	0.77	2afbA	GO:0008673 GO:0016301 GO:0016310 GO:0016740 GO:0046835 GO:0046872
6	0.07	0.506	4.45	0.08	0.76	1v19A	GO:0000166 GO:0004747 GO:0005524 GO:0005975 GO:0006014 GO:0008673 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
7	0.07	0.479	4.42	0.07	0.71	2nwhA	GO:0016301 GO:0016310 GO:0016740 GO:0016773
8	0.07	0.498	4.62	0.12	0.75	3uboA	GO:0000166 GO:0008865 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
9	0.07	0.487	4.78	0.04	0.75	2jg5A	GO:0000166 GO:0005524 GO:0005975 GO:0005988 GO:0008662 GO:0009024 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
10	0.07	0.503	4.50	0.11	0.75	4e69B	GO:0000166 GO:0016301 GO:0016310 GO:0016740 GO:0016773
11	0.07	0.492	4.73	0.08	0.74	3lhxA	GO:0016301 GO:0016310 GO:0016740 GO:0016773
12	0.07	0.499	4.62	0.09	0.77	2qcvA	GO:0000166 GO:0005524 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019310 GO:0047590
13	0.07	0.490	4.76	0.06	0.76	4n09A	GO:0000166 GO:0004001 GO:0006166 GO:0006167 GO:0009152 GO:0016301 GO:0016310 GO:0016740
14	0.07	0.488	4.49	0.04	0.72	3b1nB	GO:0000166 GO:0016301 GO:0016310 GO:0016740 GO:0016773
15	0.07	0.492	4.80	0.07	0.77	4gm6C	GO:0016301 GO:0016310 GO:0016740
16	0.07	0.487	4.90	0.07	0.79	3k9eB	GO:0016301 GO:0016310 GO:0016740
17	0.07	0.476	4.71	0.10	0.73	2rbcA	GO:0016301 GO:0016310 GO:0016740
18	0.07	0.475	4.56	0.07	0.71	1vm7A	GO:0004747 GO:0005524 GO:0005737 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0019303 GO:0046835

Consensus prediction of GO terms

Molecular Function	GO:0019200	GO:1901265	GO:0036094
GO-Score	0.44	0.37	0.37
Biological Processes	GO:0044262	GO:0016310	GO:0019321
GO-Score	0.54	0.44	0.44
Cellular Component	GO:0005829
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.