I-TASSER results

I-TASSER results for job id Rv0057

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

Input Sequence in FASTA format

>protein (173 residues)
MPVVTAVGRRRGFAMPWVSTARSGAVMLANYSAGVCGRVSSPGLNVRKMCLKANTPGAVT
WLDTPKRFLSTQTASRCMAVNSSDVVTGRIDPQVLHTPLNTDVDGYAHAMHSSINSGPLE
YLPATFSVFPALGDVGDLGGGVGAATYALDRLSNMRSGACVGGGESPWRSLMT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPVVTAVGRRRGFAMPWVSTARSGAVMLANYSAGVCGRVSSPGLNVRKMCLKANTPGAVTWLDTPKRFLSTQTASRCMAVNSSDVVTGRIDPQVLHTPLNTDVDGYAHAMHSSINSGPLEYLPATFSVFPALGDVGDLGGGVGAATYALDRLSNMRSGACVGGGESPWRSLMT
Prediction	CCCEEHCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCCCCCCEEEHHHCCCCCCEEEHCCCHHHHHHHHHHHEEHCCCCCEEEHCCCCCEHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCC
Conf.Score	97544434555655654444567657776555665555578987534445546899765664686455545555433444677656655885445577888887556666545777875557764666645566666678644678899988765677655788886566569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MPVVTAVGRRRGFAMPWVSTARSGAVMLANYSAGVCGRVSSPGLNVRKMCLKANTPGAVTWLDTPKRFLSTQTASRCMAVNSSDVVTGRIDPQVLHTPLNTDVDGYAHAMHSSINSGPLEYLPATFSVFPALGDVGDLGGGVGAATYALDRLSNMRSGACVGGGESPWRSLMT
Prediction	74224222444420231133244111101423231123154442403420242634210311423441144532430231445411324143511423143415320412343155331431333131023224235323222103211430452442213233643144247
	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

CCCEEHCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCCCCCCEEEHHHCCCCCCEEEHCCCHHHHHHHHHHHEEHCCCCCEEEHCCCCCEHCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCC
MPVVTAVGRRRGFAMPWVSTARSGAVMLANYSAGVCGRVSSPGLNVRKMCLKANTPGAVTWLDTPKRFLSTQTASRCMAVNSSDVVTGRIDPQVLHTPLNTDVDGYAHAMHSSINSGPLEYLPATFSVFPALGDVGDLGGGVGAATYALDRLSNMRSGACVGGGESPWRSLMT

4yt2A1

0.21

0.20

0.97

0.57

MUSTER

MKVVYGAGNQNGGEPPYIEFAEAGDVVLAEPNKNIMSKVEDAGVKVVSDDVEAAKHGEIHVLFTPFGKATFRIAKTIIHVPENAVICNTVSPVVLYYSLETKRKDVGSSMHPA--AVPGTPQHGHYVIGGKTTDGKELAT--EQIKKAVELAKSAGKEAYVVPADVSSVVAD-

4cfiA2

0.23

0.13

0.58

0.56

dPPAS

----------------MVQTGQTGTIKVAIDSSGAAWSSGSTGQETTQINVVSDGKGGFTFTDQNNQALSSTAVTAVFGSSTAGTGTA-ASPSFQTLALSTSATSNATAMVAQINAKP-------------------------------------------------------

4yskA1

0.25

0.16

0.64

0.53

wdPPAS

---------------------EDEGFRIGNLQARA---LHTPG----------HTPACMSFM--------------IEDAGEIAVFVG--D--TLFMPARCDFPG-ARTLYRSIR---LLAFPDQTRLFMC--DYLPGGRMQYVTTVAEQRASNIH----IHQGID-FVAMRE

3x1dA

0.18

0.17

0.91

0.55

wMUSTER

RFVVSVAGARKGFLLDFFLRYMYS-----KYVHH--ATERDTGILMWSDIFLHDYPIAIILLDTQGAFALSTMLSSVQIY----NLSQNIQEDDLQH-LQL-FTEYGRLALADTGKKPFQRL--QFLVRDWSFPYEAEYGALGGDKILKRRLVSDKQHPELQSLRRHISSCFT

3gr6D2

0.29

0.22

0.76

0.48

wPPAS

--VYHSIGRREGFAQ--ISSPEGGSIVATTYLGGE--FAV-QNYNV--MVAKA----S---LEANVKYLALDLGPDNIRVNA--ISAGPIR-----TLSAKGVGGFNTILKEIEERAPLKRN-VD----Q---EVG------KTAAYLLD-LSSGVTGENVDSG----FHAIK

4cfiA2

0.23

0.13

0.58

0.55

dPPAS2

----------------MVQTGQTGTIKVAIDSSGAAWSSGSTGQETTQINVVSDGKGGFTFTDQNNQALSSTAVTAVFGSSTAGTGTA-ASPSFQTLALSTSATSNATAMVAQINAKP-------------------------------------------------------

3llsA1

0.18

0.15

0.83

0.50

PPAS

QPET----RRYRAGEPPLT----GSLLIGGAGRVV-DYDLVGNDSFGGLVFDATGITEPAGLKGLHEFFTP--VLRNLGRCGRVVVVGGT-PEAAASTNER-LEGFTRSLGKELRRG------ATALVYLSPDAKPAATGLESTMRFLLAK-SAYVDG--VGADDS-------

3iqcA

0.22

0.14

0.64

0.68

Env-PPAS

---------------------------YANYQA-Y--QHESPAKLI-EMLYE----GILRFSSQAKRCIENDIEKKIYYINVTDIFTE------LLNILDYEKGGVAVYLTG------L-Y---THQIK-VLTQA-NVENDASKIDLVLNVARGLLEA---------WREIHS

3on5A2

0.22

0.18

0.83

0.57

MUSTER

KERLIIFG--AGDVPPLVTFASNGYTVVTD------WR---PN-----QCEKHFFPDADEIIVDPADFLRKFLIRPDDFV----LITFQKDQEILHFLLEKELRGSKERTRRLLQNKPPDHLYS-----PVGLSIDAQGPEEIAISIVAQLIQLIRSRK---QASSPFSYLF-

3ihgA2

0.15

0.12

0.79

0.54

dPPAS

SAVLATDDDPARVENPLTPSGRPGFRG-------PHVLVSRHG---ERLSTVDLFGDGWTLLAGELGADWVAAAEAVSAELGVPVRAYRVGAGL------TDPESAVSERYGIGKAGASLVRPDGIVAWRTDEAAADA---AQTLEGVLRRVLDR------------------

(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=-3.41

Estimated TM-score = 0.34±0.11

Estimated RMSD = 13.0±4.2Å

Download Model 2

C-score=-3.89

Download Model 3

C-score=-4.54

Download Model 4

C-score=-4.15

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	2o2sA	0.538	3.84	0.163	0.780
2	4q9nA	0.534	3.81	0.128	0.769
3	3gr6D	0.532	3.85	0.119	0.775
4	5koiA	0.531	3.82	0.135	0.769
5	3f4bB	0.531	3.84	0.158	0.769
6	1qsgG	0.525	3.81	0.107	0.757
7	2p91A	0.524	3.81	0.122	0.757
8	1uluB	0.523	3.93	0.136	0.763
9	2qioA2	0.522	3.79	0.099	0.757
10	1ipfA	0.514	4.20	0.104	0.775

(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	0.15	8	1qg6A	TCL	Rep, Mult	46,99,100,103,106
2	0.07	4	4d45C	GLU	Rep, Mult	103,104,105,106
3	0.04	2	3ak3D	EDO	Rep, Mult	149,152
4	0.04	2	1izlA	CLA	Rep, Mult	113,117
5	0.04	2	2xctB	CPF	Rep, Mult	11,12,166
6	0.04	2	3hrdF	NIO	Rep, Mult	59,60,61
7	0.02	1	2o9eA	HG	Rep, Mult	120,153,161
8	0.02	1	4pr7A	ADA	Rep, Mult	10,89
9	0.02	1	4af5A	MG	Rep, Mult	34,170
10	0.02	1	1yb1A	AE2	Rep, Mult	66,152,155
11	0.02	1	1zxyD	MG	Rep, Mult	8,19
12	0.02	1	1bn8A	CA	Rep, Mult	104,134,137
13	0.02	1	3mjlB	2AI	Rep, Mult	96,108

	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	2b35C	0.391	5.41	0.073	0.711	1.3.1.9	NA
2	0.060	3enkA	0.498	4.92	0.112	0.832	5.1.3.2	NA
3	0.060	1iy8A	0.499	4.37	0.104	0.775	1.1.1.-	106
4	0.060	1cydD	0.495	4.31	0.165	0.769	1.1.1.184	6
5	0.060	1sb8A	0.501	4.89	0.054	0.838	5.1.3.7	NA
6	0.060	1bvrA	0.492	4.21	0.083	0.757	1.3.1.9	NA
7	0.060	1qsgG	0.525	3.81	0.107	0.757	1.3.1.9	147
8	0.060	3fnhA	0.501	4.21	0.075	0.775	1.3.1.9	90
9	0.060	1nhdD	0.176	4.48	0.088	0.272	1.3.1.9	NA
10	0.060	2cfcC	0.489	4.26	0.100	0.751	1.1.1.268	88,97
11	0.060	2cfcA	0.493	4.21	0.100	0.751	1.1.1.268	NA
12	0.060	1ipeA	0.512	4.24	0.089	0.775	1.1.1.236	NA
13	0.060	1xhlA	0.493	4.87	0.074	0.809	1.1.1.236	52
14	0.060	3gr6D	0.532	3.85	0.119	0.775	1.3.1.9	147
15	0.060	1z45A	0.505	5.02	0.092	0.850	5.1.3.2,5.1.3.3	NA
16	0.060	2o2sA	0.538	3.84	0.163	0.780	1.3.1.9	NA
17	0.060	1uluB	0.523	3.93	0.136	0.763	1.3.1.10	NA
18	0.060	1gegE	0.507	4.23	0.097	0.775	1.1.1.5	NA
19	0.060	1ipeB	0.511	4.24	0.089	0.775	1.1.1.236	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	0.532	3.89	0.14	0.77	2wywA	GO:0000166 GO:0004318 GO:0006633 GO:0016491 GO:0055114
1	0.07	0.499	4.94	0.08	0.84	3m1aD	GO:0016491 GO:0055114
2	0.07	0.510	4.21	0.12	0.77	2dknA	GO:0000166 GO:0016491 GO:0047042 GO:0055114
3	0.07	0.494	5.10	0.06	0.83	2ntvA	GO:0004318 GO:0006633 GO:0016491 GO:0055114
4	0.07	0.504	4.41	0.13	0.78	4ituA	GO:0000166 GO:0016491 GO:0055114
5	0.07	0.482	4.58	0.11	0.77	4ureA	GO:0016491 GO:0055114
6	0.07	0.490	4.82	0.08	0.79	2pd3A	GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0030497 GO:0051289 GO:0055114
7	0.07	0.467	4.67	0.12	0.75	4yqzA	GO:0016491 GO:0055114
8	0.07	0.512	4.28	0.11	0.78	1ae1B	GO:0009710 GO:0016491 GO:0050356 GO:0055114
9	0.07	0.472	4.50	0.13	0.74	1hdcA	GO:0006629 GO:0008202 GO:0008207 GO:0016491 GO:0047044 GO:0055114
10	0.07	0.499	4.37	0.10	0.77	1iy8A	GO:0016491 GO:0055114
11	0.07	0.486	4.98	0.09	0.81	4yaiA	GO:0016491 GO:0055114
12	0.07	0.469	5.21	0.07	0.79	2ph3A	GO:0004316 GO:0006633 GO:0016491 GO:0051287 GO:0055114
13	0.07	0.493	4.46	0.12	0.77	3tscA	GO:0000166 GO:0016491 GO:0055114
14	0.07	0.531	3.86	0.12	0.77	4nr0C	GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0016631 GO:0030497 GO:0051289 GO:0055114
15	0.07	0.489	4.50	0.10	0.76	4e4yA	GO:0016491 GO:0016853 GO:0055114
16	0.07	0.458	5.04	0.06	0.76	4lvuA	GO:0016491 GO:0055114
17	0.07	0.480	5.05	0.07	0.81	4rlhB	GO:0004318 GO:0006633 GO:0016491 GO:0055114
18	0.07	0.478	4.90	0.08	0.78	3ojfA	GO:0000166 GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0030497 GO:0051289 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0003824	GO:1901265	GO:0036094
GO-Score	0.41	0.38	0.38
Biological Processes	GO:0044710
GO-Score	0.59
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.