I-TASSER results

I-TASSER results for job id Rv0744c

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

Input Sequence in FASTA format

>protein (168 residues)
METLLKTSEAAQILGVSRQHVVNMCDRGEMVCVHVGSHRRVPSSEVERVTSRRLTREEER
SLWLHRALLSPLLTEPDTVVSAARENLRRWSGMHRRDGMAGWYFTKWQRVLNDGLDAVMH
VLTSPSEDAREMRQNSPFAGILPEATRVAVLRSFKDHWDREHERAMTE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| METLLKTSEAAQILGVSRQHVVNMCDRGEMVCVHVGSHRRVPSSEVERVTSRRLTREEERSLWLHRALLSPLLTEPDTVVSAARENLRRWSGMHRRDGMAGWYFTKWQRVLNDGLDAVMHVLTSPSEDAREMRQNSPFAGILPEATRVAVLRSFKDHWDREHERAMTE
Prediction	CCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEHCCCEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
Conf.Score	987789999999989997999999998998856668755444899999999999889999999999999877668689999999999999987555665678999999999877999999998798588999985987766899999999999999999876777669
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| METLLKTSEAAQILGVSRQHVVNMCDRGEMVCVHVGSHRRVPSSEVERVTSRRLTREEERSLWLHRALLSPLLTEPDTVVSAARENLRRWSGMHRRDGMAGWYFTKWQRVLNDGLDAVMHVLTSPSEDAREMRQNSPFAGILPEATRVAVLRSFKDHWDREHERAMTE
Prediction	775424443005316122320240065360325334432333253044135444535543243124422552364255125303631453366445644443115403611653153024102444740441274231323046731340044047415563554358
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEHCCCEHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC
METLLKTSEAAQILGVSRQHVVNMCDRGEMVCVHVGSHRRVPSSEVERVTSRRLTREEERSLWLHRALLSPLLTEPDTVVSAARENLRRWSGMHRRDGMAGWYFTKWQRVLNDGLDAVMHVLTSPSEDAREMRQNSPFAGILPEATRVAVLRSFKDHWDREHERAMTE

4j2nA

0.28

0.09

0.32

1.13

wdPPAS

MPPRASIQQTADYLGVSTKTVRNYIAAGKLKAVRLGRLIRVERDSVEALMRPI-------------------------------------------------------------------------------------------------------------------

5af3A1

0.16

0.14

0.83

1.03

wPPAS

FDVLYTLAEASRYLVVPRATLATWADQPIITALPHGSHARLPFVGIAEAYVLNAFRRA-----------------PMQRIRPSLDWLIKNVGPH--------ALAS-QDLCTDGAEVLWRFAERSGEGSPDDLVVRGLIVPRSGQYKEIVEHYLQQSFADDNLASM--

4j2nA

0.28

0.09

0.32

1.24

wPPAS

MPPRASIQQTADYLGVSTKTVRNYIAAGKLKAVRLGRLIRVERDSVEALMRPI-------------------------------------------------------------------------------------------------------------------

5cwqA2

0.11

0.08

0.70

1.04

dPPAS2

------------------------------------------SEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNKEEAERAYEDARRVEEEARKVKESAEEQGDSEVKRL--------AEEAEQLAREARRHVQECRGGWLEH

4j2nA

0.28

0.09

0.32

1.15

dPPAS2

MPPRASIQQTADYLGVSTKTVRNYIAAGKLKAVRLGRLIRVERDSVEALMRPI-------------------------------------------------------------------------------------------------------------------

5cwmA1

0.13

0.09

0.68

1.04

dPPAS2

----------------------------------------DPEDELKRVEKLVKEAEELLRQAKEKGSEEDLEKALRTAEEAAREAKKVLEQAEKEGDPEVALRAVELVVRVAELLLRIAKESGSEEALERALRV--------AEEAARLAKRVLELAEKQG------

4j2nA

0.28

0.09

0.32

1.23

Env-PPAS

MPPRASIQQTADYLGVSTKTVRNYIAAGKLKAVRLGRLIRVERDSVEALMRPI-------------------------------------------------------------------------------------------------------------------

4tqlA1

0.09

0.08

0.87

1.05

dPPAS2

------YKQMVQELEKARDRMEKLYKE--------------MVELIQKAIELMRKIFQEVKQEVEKAIEEKLLEKLKQIMQEAKQKMEKLLKQLKE--EMKKMKEKMEKLLKEMKQRMEEVKKKMDDELLEKIKKNIDDLKKIAEDLIKKAEENIKEAKKIAEQLVKR

5c8dE

0.16

0.15

0.95

0.81

MUSTER

-SGVYTIAEVEAMTGLSAEVLRQWERRYGFKPRRTGGHRLYSAEDVEALKTIKRWLEEGATPKAAIRRYLAQEVRPEDLGTGLLEALLRG-----DLAGAEALFRRGLRFWG-PEGVLEHLLLPVLREVGEAWHRGEI-GVAEEHLASTFLRARLQELLDLAGFPPGP

4tqlA1

0.09

0.08

0.87

0.71

dPPAS

------YKQMVQELEKARDRMEKLYKE--------------MVELIQKAIELMRKIFQEVKQEVEKAIEEKLLEKLKQIMQEAKQKMEKLLKQLKE--EMKKMKEKMEKLLKEMKQRMEEVKKKMDDELLEKIKKNIDDLKKIAEDLIKKAEENIKEAKKIAEQLVKR

(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=-3.67

Estimated TM-score = 0.31±0.10

Estimated RMSD = 13.6±4.0Å

Download Model 2

C-score=-3.97

Download Model 3

C-score=-4.22

Download Model 4

C-score=-3.87

Download Model 5

C-score=-3.81

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	5cwqA	0.637	3.80	0.092	0.821
2	3eb7A	0.601	3.68	0.073	0.816
3	1dlcA	0.595	3.68	0.063	0.804
4	1ji6A	0.595	3.89	0.090	0.839
5	2c9kA	0.589	4.50	0.068	0.875
6	5cwmA	0.585	3.44	0.084	0.750
7	3x0uA1	0.581	4.24	0.060	0.851
8	3fnbA	0.581	3.78	0.090	0.786
9	1w99A	0.581	3.80	0.057	0.768
10	1ciyA	0.580	3.87	0.089	0.816

(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	0.06	3	4niqB	III	Rep, Mult	51,54,55,58,62,65,68,69,80,92,93,94,98,99,101,102,105,106,109,112,113,116
2	0.06	3	2yf3A	MN	Rep, Mult	80,83,113,116
3	0.04	2	3q73B	3CX	Rep, Mult	9,10,42,43,44,45
4	0.04	2	2ze7A	ZN	Rep, Mult	113,161,162
5	0.04	2	3mpsA	FEO	Rep, Mult	53,86
6	0.04	2	3sfyB	3FX	Rep, Mult	2,3,9,10,11,12,13
7	0.04	2	4fhvA	MG	Rep, Mult	36,37,47
8	0.02	1	3a5cE	ADP	Rep, Mult	17,18
9	0.02	1	4ev6E	MG	Rep, Mult	64,119
10	0.02	1	3rkoL	LFA	Rep, Mult	20,23,24
11	0.02	1	3bnxD	POP	Rep, Mult	7,11,15
12	0.02	1	1bf5A	QNA	Rep, Mult	10,11,25
13	0.02	1	3o2nB	MZX	Rep, Mult	114,119,141
14	0.02	1	3f1f2	MG	Rep, Mult	5,9
15	0.02	1	3b6aD	ZCT	Rep, Mult	115,116
16	0.02	1	4mhlA	ARF	Rep, Mult	105,109
17	0.02	1	2yxhA	MG	Rep, Mult	87,113

	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	1k62B	0.491	4.78	0.070	0.768	4.3.2.1	NA
2	0.060	2v8tA	0.508	4.60	0.023	0.756	1.11.1.6	NA
3	0.060	1m56A	0.493	5.30	0.039	0.804	1.9.3.1	NA
4	0.060	1jk0A	0.484	4.12	0.107	0.696	1.17.4.1	NA
5	0.060	1tazA	0.494	4.66	0.051	0.792	3.1.4.17	NA
6	0.060	2jbwD	0.577	3.91	0.092	0.768	3.7.1.-	NA
7	0.060	1qd1B	0.365	5.40	0.040	0.673	2.1.2.5,4.3.1.4	NA
8	0.060	1gaiA	0.481	4.87	0.039	0.768	3.2.1.3	58
9	0.060	2ozoA	0.487	4.66	0.067	0.768	2.7.10.2	NA
10	0.060	2occN	0.483	5.34	0.038	0.809	1.9.3.1	91
11	0.060	1j0mA	0.491	5.09	0.046	0.827	4.2.2.12	NA
12	0.060	2oa6D	0.500	4.26	0.056	0.732	4.2.3.9	NA
13	0.060	2pfdB	0.493	3.61	0.083	0.667	2.1.2.5,4.3.1.4	50
14	0.060	2cqsA	0.508	4.79	0.073	0.780	2.4.1.20	NA
15	0.060	1ihgA	0.502	3.56	0.075	0.655	5.2.1.8	NA
16	0.060	3ckeD	0.487	4.20	0.050	0.714	4.2.3.9	NA
17	0.060	1ojnA	0.484	4.25	0.068	0.720	4.2.2.1	52
18	0.060	3evhA	0.489	5.06	0.084	0.780	4.2.2.3	NA
19	0.060	1ug9A	0.493	4.47	0.042	0.732	3.2.1.70	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	0.580	3.87	0.09	0.82	1ciyA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
1	0.07	0.595	3.89	0.09	0.84	1ji6A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
2	0.07	0.580	4.08	0.06	0.84	3x0uA	GO:0009405
3	0.07	0.563	4.17	0.08	0.78	4d8mA	GO:0009405 GO:0030435
4	0.07	0.578	3.79	0.07	0.80	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
5	0.07	0.613	4.02	0.06	0.86	4moaA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
6	0.07	0.589	4.50	0.07	0.88	2c9kA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
7	0.07	0.601	3.68	0.07	0.82	3eb7A	GO:0005102 GO:0006952 GO:0009405 GO:0030435
8	0.07	0.595	3.68	0.06	0.80	1dlcA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
9	0.07	0.559	4.18	0.07	0.82	1i5pA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
10	0.06	0.402	5.00	0.06	0.67	4p4oA	GO:0003677 GO:0003887 GO:0005634 GO:0006281 GO:0034061 GO:0071897
11	0.06	0.460	4.28	0.09	0.67	3ck6E	GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
12	0.06	0.387	3.74	0.04	0.52	1yo7A	GO:0006351 GO:0006355
13	0.06	0.360	5.96	0.07	0.70	3o38A	GO:0004316 GO:0016491 GO:0055114 GO:0102132
14	0.06	0.323	5.15	0.05	0.54	4k3vB	GO:0006810 GO:0007155 GO:0030001 GO:0046872
15	0.06	0.375	5.02	0.04	0.66	4bvkB	GO:0016787
16	0.06	0.387	5.16	0.04	0.65	3odpA	GO:0005975 GO:0016853 GO:0030246
17	0.06	0.329	4.05	0.10	0.49	3nrwA	GO:0003677 GO:0006310 GO:0015074
18	0.06	0.309	4.46	0.01	0.48	1g6oA	GO:0000166 GO:0005524 GO:0005737 GO:0006810 GO:0009405

Consensus prediction of GO terms

Molecular Function	GO:0005515
GO-Score	0.37
Biological Processes	GO:0051704	GO:0048646	GO:0030154	GO:0043934	GO:0006950
GO-Score	0.58	0.48	0.48	0.48	0.37
Cellular Component
GO-Score

(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.