I-TASSER results

I-TASSER results for job id Rv0513

[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)
MTPTGDTKPKLLFYEPGASWYWVLTGPLAAVSVLLLEISSGAGVGLITPAIFLVMVSAFV
ALQVKAARIHTSVELTHDALRQGTETIRLAEIVKIYPEADGRETSGEEPAKWQSARTLGE
LVGVPRGRVGIGLKLTGGRTAQAWARRHQQLRAALTPLVQERLGPVDSDVADVNGDDAGP
AR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTPTGDTKPKLLFYEPGASWYWVLTGPLAAVSVLLLEISSGAGVGLITPAIFLVMVSAFVALQVKAARIHTSVELTHDALRQGTETIRLAEIVKIYPEADGRETSGEEPAKWQSARTLGELVGVPRGRVGIGLKLTGGRTAQAWARRHQQLRAALTPLVQERLGPVDSDVADVNGDDAGPAR
Prediction	CCCCCCCCCCCEEHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEHCCCCCEHCEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCEEEEHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Conf.Score	99989988886676689747999999999999999999758987679999999999999998754567899999765544546578868888888488898877777767887777677766788887755578759968998746889999999999997689988888888865455679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 \| \| \| \| \| \| \| \| \| MTPTGDTKPKLLFYEPGASWYWVLTGPLAAVSVLLLEISSGAGVGLITPAIFLVMVSAFVALQVKAARIHTSVELTHDALRQGTETIRLAEIVKIYPEADGRETSGEEPAKWQSARTLGELVGVPRGRVGIGLKLTGGRTAQAWARRHQQLRAALTPLVQERLGPVDSDVADVNGDDAGPAR
Prediction	84566666443010043131210121223022112010134342213211321131233120103123221203134730341344130430250135555563556537527403111323412453561303136443020104437402520351166535566374763565655568
	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

CCCCCCCCCCCEEHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEHCCCCCEHCEEEEEHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCEEEEHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
MTPTGDTKPKLLFYEPGASWYWVLTGPLAAVSVLLLEISSGAGVGLITPAIFLVMVSAFVALQVKAARIHTSVELTHDALRQGTETIRLAEIVKIYPEADGRETSGEEPAKWQSARTLGELVGVPRGRVGIGLKLTGGRTAQAWARRHQQLRAALTPLVQERLGPVDSDVADVNGDDAGPAR

4lg3A

0.15

0.13

0.87

0.67

MUSTER

FAPTKESPYEGI---PGLRYNVRIVLVEQDKQGNYIARRDSSTVSKRQLAATVIAAARYYAQEKRAAVVSITLDSQPGPAFGKT-VLATATYA-----PDGKGVSGSDDWTWNTLQATPRG-------------LTAQKIQCLWGEDERRLKAAIAKKLK--IPAEKVLNPVFPEPPQEWTR

4a99A2

0.07

1.00

0.76

dPPAS

NDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLAPENRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVILANGGMSKVRKFVTDTEVERIFPLEKPWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLVDALILSDNLADGKFNSIEEAVKNYEQQ

3gl5A

0.17

0.15

0.87

0.66

wdPPAS

RAKDDVQPVLTLTAKYGSQAQAGEDNLGAQAAAEGLAYRTRDRDHLLHLAKERGRHEALLDAFYRG-----SVFNDDERLVEG---LDAEEVRAVL---ADPAAYADEVRA-REAAQLG-ATGVP-------FFVLDRAYGVSGAQPAEVFTQALTQAWGERTPLKLIDAEACGPDPG----

3gl5A

0.19

0.16

0.89

0.72

wMUSTER

RAKDDVQPVLTLTAKYGSQAQAGEDNLGAQAAAEGLAYRTRDRDHLLHLAKERGRHEALLDAFYRG-----SVFNDDERLVEG---LDAEEVRAVL---ADPAAYADEVRAEREAAQLG-ATGVP------FFVL-DRAYGVSGAQPAEVFTQALTQAWGER-TPLKLIDAEACGPDGCAVP

4lg3A

0.18

0.15

0.85

0.75

wPPAS

FAPTKESPYEGI---PGLRYNVRIV-LVEQ--GNYIARRDSSTVSKRQLAATVIAAARYYAQEKRAAVVSITLDSQPGPAFGKT-VLATATYA---P--DGKGVSGSDDWTWNTLQA-T-----PRG-------LTA-KIQCLWGRDERRLKAAIAKKLK--IPAEKVLNPVFPEPPQEWTR

3gl5A

0.18

0.16

0.92

1.05

dPPAS2

RAKDDVQPVLTLTAKYGSQAQAGEDNLGAQAAAEGLAYRTRDRGSTFDLHRLLHLAKERGRHEALLDAFYRSVFNDDERLVEG---LDAEEVRAVL--ADPAAYADEVRADEREAAQLG-ATGVP-------FFVLDRAYGVSGAQPAEVFTQALTQAWGERTPLKLID-AEACGPDGCAVP

4lg3A

0.13

0.12

0.95

0.77

PPAS

SEAQFFAPTKESPYEPGLRYNVRIVLVEQDKQGNYIARRDSSTVSKRQLAATVIAAARYYAQEKRAAVVSITLDSQPGPAFGKT-VLATAT------APDGKGVSGSDDWTWNTLQATPRGLTAQELKIQCLWGERGKFQVDGST-DERRLKAAIAKKLK--IPAEKVLNPVFPEPPQEWTR

4gn0A

0.18

0.10

0.55

0.70

Env-PPAS

--------------NPA--ENIASEISKSVEGAIQQVKNL-----LTLAADRAEQIVNDLASTT--TST-----ITR----------PIIELSNT-------------------ADKIGNLAEVPHQNRAIG-IL---------AKSIERLRRSLKVAMESL---------------EEALK

2w53A

0.11

0.10

0.92

0.66

MUSTER

GARAGYTRGAVYWHFKNEVLAAIVERVHLPFMQELERTSTDQRDTPVHDLRAVMIHSFIELSEDERLRKTMEIMLRSTEMQQAGFRDALDRMERALRRARDLGQLREGADPKIAARMLHATV------LGVLHGMVEPELMDLKRDGMLALDMTLAAYVKDGVFVPGTVPEPLP--------

3gl5A

0.13

0.95

0.68

dPPAS

RAKDDVQPVLTLTAKYGSQEQAQAGEDNLGAQAAAEGLAYRTRGSTFDLHRLLHLAKERGRHEALLDAFYRGNFADERSVFNDDERLVAEEVRAVL--ADPAAYADEVRADEREAAQLG-ATGVP-------FFVLDRAYGVSGAQPAEVFTQALTQAWGERTPLKLIDAEACGPDGCAVPG

(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=-3.36

Estimated TM-score = 0.34±0.11

Estimated RMSD = 13.0±4.2Å

Download Model 2

C-score=-4.66

Download Model 3

C-score=-5.00

Download Model 4

C-score=-3.22

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	3gl5A	0.643	3.93	0.138	0.890
2	5cnwA	0.585	4.17	0.105	0.852
3	3kzqA	0.497	4.67	0.083	0.786
4	2in3A	0.492	4.44	0.126	0.780
5	2imfA	0.488	4.56	0.045	0.747
6	1yzxA	0.486	4.70	0.089	0.753
7	1r4wA	0.485	4.68	0.088	0.758
8	5hfgA	0.471	4.57	0.114	0.769
9	4zwjA	0.467	5.22	0.053	0.769
10	5a22A	0.464	5.39	0.050	0.824

(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	0.07	4	1xk0A	NO	Rep, Mult	115,119
2	0.07	4	3fz5A	GTT	Rep, Mult	123,124,142,143,144,145
3	0.03	2	1dgjA	FES	Rep, Mult	73,74,79,81,82,83,85,88
4	0.03	2	3kzqE	MG	Rep, Mult	46,51,74
5	0.03	2	2oyqA	N5P	Rep, Mult	48,52,53,128
6	0.03	2	2zyqB	TAR	Rep, Mult	16,17
7	0.03	2	3jcuD	CLA	Rep, Mult	92,112
8	0.03	2	2xloA	NO	Rep, Mult	116,120
9	0.03	2	5bu7A	ZN	Rep, Mult	103,107
10	0.02	1	5ao1A	MG	Rep, Mult	44,129
11	0.02	1	1r4wC	GSH	Rep, Mult	27,127,144,146,147
12	0.02	1	2wvsA	FUF	Rep, Mult	118,119,122,135
13	0.02	1	3p0eC	PO4	Rep, Mult	17,81,83,84
14	0.02	1	1aczA	GLC	Rep, Mult	112,144
15	0.02	1	3womA	ZN	Rep, Mult	91,94
16	0.02	1	2wsc4	CLA	Rep, Mult	138,142

	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	1j0mA	0.422	5.54	0.061	0.758	4.2.2.12	NA
2	0.060	1de5A	0.412	5.62	0.051	0.731	5.3.1.14	NA
3	0.060	2vdcA	0.414	5.86	0.062	0.758	1.4.1.13	NA
4	0.060	1od2A	0.373	5.69	0.030	0.670	6.3.4.14,6.4.1.2	NA
5	0.060	1llwA	0.425	5.78	0.046	0.780	1.4.7.1	NA
6	0.060	1bxcD	0.419	5.50	0.056	0.753	5.3.1.5	NA
7	0.060	1a0cA	0.454	5.15	0.041	0.769	5.3.1.5	NA
8	0.060	1r4wC	0.485	4.66	0.082	0.758	2.5.1.18	NA
9	0.060	1s0kA	0.385	5.85	0.058	0.725	3.2.1.18	NA
10	0.060	1ofdA	0.426	5.97	0.063	0.797	1.4.7.1	NA
11	0.060	3cmmC	0.438	5.73	0.057	0.797	6.3.2.19	51,95
12	0.060	1a0eA	0.424	5.10	0.047	0.709	5.3.1.5	NA
13	0.060	3iayA	0.428	5.18	0.056	0.725	2.7.7.7	NA
14	0.060	1h19A	0.414	5.88	0.071	0.797	3.3.2.6	4,52,73,76
15	0.060	1yzxB	0.485	4.72	0.089	0.753	2.5.1.18	113
16	0.060	2jerD	0.412	5.36	0.011	0.703	3.5.3.12	114
17	0.060	1k3iA	0.412	5.90	0.058	0.791	1.1.3.9	NA
18	0.060	2zueA	0.423	5.79	0.044	0.797	6.1.1.19	NA
19	0.060	1ea0A	0.414	5.86	0.062	0.758	1.4.1.13	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	0.07	0.642	3.98	0.12	0.90	3gl5A	GO:0015035 GO:0055114
1	0.07	0.492	4.44	0.13	0.78	2in3A	GO:0015035 GO:0055114
2	0.07	0.485	4.68	0.09	0.76	1r4wA	GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869
3	0.07	0.497	4.67	0.08	0.79	3kzqA
4	0.07	0.487	4.73	0.08	0.75	3rpnA	GO:0004364 GO:0004602 GO:0005102 GO:0005622 GO:0005739 GO:0005743 GO:0005759 GO:0005777 GO:0006749 GO:0015035 GO:0016020 GO:0016740 GO:0030855 GO:0043231 GO:0055114 GO:0070062 GO:0098869 GO:1901687
5	0.07	0.489	4.55	0.04	0.75	2imdA	GO:0015035 GO:0016853 GO:0018845 GO:0019439 GO:0055114 GO:1901170
6	0.07	0.456	4.86	0.06	0.73	3fz5C	GO:0015035 GO:0016853 GO:0046872 GO:0055114
7	0.06	0.392	4.62	0.06	0.62	4p3yB	GO:0015035 GO:0016853 GO:0042597 GO:0055114
8	0.06	0.278	6.17	0.04	0.54	1r30B	GO:0003824 GO:0004076 GO:0005506 GO:0009102 GO:0016740 GO:0046872 GO:0051536 GO:0051537 GO:0051539
9	0.06	0.368	4.86	0.06	0.60	3gykA
10	0.06	0.322	5.42	0.05	0.55	1vcnA	GO:0000166 GO:0003883 GO:0005524 GO:0006221 GO:0006541 GO:0016874 GO:0044210
11	0.06	0.340	5.02	0.09	0.54	4wkwA	GO:0015035 GO:0055114
12	0.06	0.301	4.95	0.04	0.48	4o7uB	GO:0004799 GO:0005737 GO:0006231 GO:0006235 GO:0008168 GO:0009165 GO:0016740 GO:0032259
13	0.06	0.357	5.26	0.03	0.62	3gmfA	GO:0016020 GO:0016021 GO:0016853
14	0.06	0.346	5.98	0.03	0.64	1q2lA	GO:0003824 GO:0004222 GO:0005737 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016485 GO:0016787 GO:0030288 GO:0042597 GO:0046872
15	0.06	0.278	6.12	0.03	0.52	4n83A	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
16	0.06	0.289	6.27	0.05	0.60	1dusA	GO:0008168 GO:0016740 GO:0032259
17	0.06	0.299	6.39	0.03	0.59	1flcA	GO:0001681 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0016788 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0020002 GO:0033644 GO:0039654 GO:0039663 GO:0046718 GO:0046789 GO:0055036
18	0.06	0.277	5.13	0.07	0.45	1jzdA	GO:0003756 GO:0015035 GO:0030288 GO:0042597 GO:0045454 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0015036
GO-Score	0.48
Biological Processes	GO:0044710
GO-Score	0.48
Cellular Component	GO:0005743	GO:0070062	GO:0005777	GO:0005759
GO-Score	0.13	0.13	0.13	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.