I-TASSER results

I-TASSER results for job id Rv3351c

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

Input Sequence in FASTA format

>protein (264 residues)
MLASCPARSGAAVADAIKSAVGVQPSGVEHKTLRRMDLVRYLAGGHTTYPPEGFVAGSDV
IGTTNPAAAQAIVAAIGTWPPAAGRASALIDSLGGAVGDMDPEGSAFPWCRQSAVVQWYV
NTPSDGQVATANKWLSDAHHAVQHFSVGGYVNYLEANAAASQYFGANLSRLTTVRRKYDP
DRIMYSGLDFSTRQVAERLLPALGFRVRFGVLVIRCALCTDTVKRLGTLPNLTWSRLKVN
VAVTQEQAGVMDLPALPVRRTPRR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MLASCPARSGAAVADAIKSAVGVQPSGVEHKTLRRMDLVRYLAGGHTTYPPEGFVAGSDVIGTTNPAAAQAIVAAIGTWPPAAGRASALIDSLGGAVGDMDPEGSAFPWCRQSAVVQWYVNTPSDGQVATANKWLSDAHHAVQHFSVGGYVNYLEANAAASQYFGANLSRLTTVRRKYDPDRIMYSGLDFSTRQVAERLLPALGFRVRFGVLVIRCALCTDTVKRLGTLPNLTWSRLKVNVAVTQEQAGVMDLPALPVRRTPRR
Prediction	CCEHCCCCCHHHHHHHHHHHCCCCCCCEEEEEHCHHHHHHHHHCCCCCCCCCCEEHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHCCCCCEHCCCCCCCHHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHCCCCCCCCCCCCCCCCCCC
Conf.Score	955568887689999999975998864678886899999998578999998764554445789999999999999997788889779999856996668998889874458758999999858976789999999999999856678655678887657888756689999999988698887678889996567887646778556634456677765677777656787754456777776534565556777766778899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MLASCPARSGAAVADAIKSAVGVQPSGVEHKTLRRMDLVRYLAGGHTTYPPEGFVAGSDVIGTTNPAAAQAIVAAIGTWPPAAGRASALIDSLGGAVGDMDPEGSAFPWCRQSAVVQWYVNTPSDGQVATANKWLSDAHHAVQHFSVGGYVNYLEANAAASQYFGANLSRLTTVRRKYDPDRIMYSGLDFSTRQVAERLLPALGFRVRFGVLVIRCALCTDTVKRLGTLPNLTWSRLKVNVAVTQEQAGVMDLPALPVRRTPRR
Prediction	100002334045005203731525233332441313200210242443343432222221155035610430141036225533200010102111045146721010113010000000203467326303400420142033312000001132732334002621621240243031420021314064551144104324031100000010010251054223125131440303010346422224031123443578
	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                 220                 240                 260

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEHCCCCCHHHHHHHHHHHCCCCCCCEEEEEHCHHHHHHHHHCCCCCCCCCCEEHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEEHCCCCCCCCCCCCCCCCCCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHCCCCCEHCCCCCCCHHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCEEEEHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHCCCCCCCCCCCCCCCCCCC
MLASCPARSGAAVADAIKSAVGVQPSGVEHKTLRRMDLVRYLAGGHTTYPPEGFVAGSDVIGTTNPAAAQAIVAAIGTWPPAAGRASALIDSLGGAVGDMDPEGSAFPWCRQSAVVQWYVNTPSDGQVATANKWLSDAHHAVQHFSVGGYVNYLEANAAASQYFGANLSRLTTVRRKYDPDRIMYSGLDFSTRQVAERLLPALGFRVRFGVLVIRCALCTDTVKRLGTLPNLTWSRLKVNVAVTQEQAGVMDLPALPVRRTPRR

3w8wA

0.20

0.14

0.71

1.48

MUSTER

CAMSCWIGDPHEGERQLESILHAKPHGLTKATLPYRALQAY--SFPGAVVPDRIYTKSGYLNELSDEATDTVLEHAADIA--SPFTQLELLYLGGAVARVPDDATAYPNRQSPFVTNLAAAWMDPTEDARHTAWAREGYRALAGHLSGGYVNFMNPGRTREAYGAAKFERLQGVKAKYDPTNLFRLNQNIPP------------------------------------------------------------------------

2ipiA3

0.14

0.08

0.55

2.11

dPPAS

---------------------------------------------FDTGGFDRTKSKGAYRKPWTAAQAATLYRHLSA--DSQVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGTFINYPDGVPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRPP-----------------------------------------------------------------------

2ipiA3

0.14

0.08

0.55

3.39

wdPPAS

---------------------------------------------FDTGGFDRTKSKGAYLKPWTAAQAATLYRHLSADS--QVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGTFINYPDVDPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRPP-----------------------------------------------------------------------

3w8wA

0.20

0.14

0.71

1.80

wMUSTER

CAMSCWIGDPHEGERQLESILHAKPHGLTKATLPYRALQAYS--FPGAVVPDRIYTKSGYLNELSDEATDTVLEHAADIA--SPFTQLELLYLGGAVARVPDDATAYPNRQSPFVTNLAAAWMDPTEDARHTAWAREGYRALAGHLSGGYVNFMNPGRTREAYGAAKFERLQGVKAKYDPTNLFRLNQNIPP------------------------------------------------------------------------

2ipiA3

0.15

0.08

0.55

2.84

wPPAS

---------------------------------------------FDTGGFDRTKSKGAYLKPWTAAQAATLYRHLSADS--QVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGTFINYPDVDPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRP--------P---------------------------------------------------------------

2ipiA3

0.14

0.08

0.55

3.83

dPPAS2

---------------------------------------------FDTGGFDRTKSKGAYLKPWTAAQAATLYRHLSA--DSQVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGTFINYPDVDPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRPP-----------------------------------------------------------------------

2ipiA3

0.14

0.08

0.55

2.09

PPAS

---------------------------------------------FDTGGFDRTKSKGAYLKPWTAAQAATLYRHLSADS--QVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGTFINYPDGVPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRPP-----------------------------------------------------------------------

2ipiA3

0.14

0.08

0.55

2.04

Env-PPAS

---------------------------------------------FDTGGFDRTKSKGAYLRKWTAAQAATLYRHLSADS--QVWGEVSLYSYGGKVNSVPETATATAQRDSIIKVWMSATWMDPAHDDANLAWIREIYREIFATTGGTFINYPDVDPWYTLYYKGNYPRLQKVKARWDPRDVFRHALSVRPP-----------------------------------------------------------------------

3w8wA2

0.21

0.15

0.71

1.47

MUSTER

CAMSCWIGDPHEGERQLESILHAKPHGLTKATLPYRALQAY--SFPGAVVPDRIYTKSGYLNELSDEATDTVLEHAADI--ASPFTQLELLYLGGAVARVPDDATAYPNRQSPFVTNLAAAWMDPTEDARHTAWAREGYRALAGHLSGGYVNFMEADRTREAYGAAKFERLQGVKAKYDPTNLFRLNQNIPP------------------------------------------------------------------------

3w8wA2

0.19

0.14

0.71

1.78

dPPAS

CAMSCWIGDPHEGERQLESILHAGKHGLTKATLPYRALQAY--SFPGAVVPDRIYTKSGYLNELSDEATDTVLEHAADIASPFT--QLELLYLGGAVARVPDDATAYPNRQSPFVTNLAAAWMDPTEDARHTAWAREGYRALAGHLSGGYVNFMNPDRTREAYGAAKFERLQGVKAKYDPTNLFRLNQNIPP------------------------------------------------------------------------

(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=-2.50

Estimated TM-score = 0.42±0.14

Estimated RMSD = 11.7±4.5Å

Download Model 2

C-score=-3.18

Download Model 3

C-score=-3.30

Download Model 4

C-score=-3.46

Download Model 5

C-score=-3.55

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	3w8wA2	0.672	1.54	0.202	0.712
2	2y08A	0.626	2.85	0.124	0.735
3	3popA	0.622	2.78	0.136	0.724
4	3d2dA2	0.622	2.73	0.147	0.716
5	2ipiA	0.618	2.66	0.138	0.716
6	5d79A	0.607	2.89	0.136	0.708
7	1zr6A	0.606	3.15	0.149	0.727
8	4ud8A	0.605	2.94	0.151	0.712
9	2bvgA	0.604	2.80	0.149	0.712
10	3vteA	0.603	3.18	0.148	0.724

(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	0.10	5	4oalA	245	Rep, Mult	56,58,89,115,119,150,154
2	0.08	4	1zr6A	FAD	Rep, Mult	150,152,153
3	0.04	2	2y3rA	TIR	Rep, Mult	49,50,51,54,56,89,119,121,153
4	0.04	2	3rjaA	ABL	Rep, Mult	44,89,117,119,121,153
5	0.04	2	4rku4	CLA	Rep, Mult	132,135
6	0.04	2	2qlaA	ZN	Rep, Mult	140,144
7	0.02	1	1g291	MG	Rep, Mult	178,179
8	0.02	1	5awvB	3MY	Rep, Mult	170,173
9	0.02	1	1nqeA	C8E	Rep, Mult	88,118
10	0.02	1	2wdxA	BMA	Rep, Mult	39,43,44
11	0.02	1	4rku4	CLA	Rep, Mult	131,132
12	0.02	1	4il6R	HEM	Rep, Mult	138,142
13	0.02	1	2dyo1	III	Rep, Mult	125,129,131,132,133,135,136,139,140,141,142,143,145,146,147,161,162,163
14	0.02	1	3rj8A	FAD	Rep, Mult	49,150,152,153

	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	1pn0C	0.397	6.31	0.059	0.697	1.14.13.7	NA
2	0.060	2ckpB	0.325	5.60	0.040	0.504	2.7.1.32	NA
3	0.060	2pywA	0.391	6.21	0.063	0.678	2.7.1.100	137
4	0.060	3dq0A	0.560	3.51	0.092	0.701	1.5.99.12	NA
5	0.060	1kv9A	0.400	6.27	0.055	0.697	1.1.99.-	NA
6	0.060	3f2sA	0.400	6.04	0.065	0.659	2.7.1.32	NA
7	0.060	1lrwC	0.402	6.43	0.036	0.716	1.1.99.8	154
8	0.060	2exrA	0.536	3.64	0.105	0.686	1.5.99.12	NA
9	0.060	2c4mC	0.397	6.53	0.066	0.705	2.4.1.1	NA
10	0.060	2zuwC	0.394	6.12	0.047	0.670	2.4.1.211	153
11	0.060	2pffD	0.420	6.14	0.056	0.720	2.3.1.86	72
12	0.060	2d0vA	0.400	6.44	0.041	0.712	1.1.99.8	NA
13	0.060	1ahuA	0.491	4.43	0.082	0.689	1.1.3.38,1.1.3.13	NA
14	0.060	3l4uA	0.410	5.97	0.054	0.705	3.2.1.20,3.2.1.3	NA
15	0.060	2pffA	0.416	6.16	0.048	0.724	2.3.1.41,2.3.1.86	NA
16	0.060	2o1xC	0.377	6.56	0.058	0.693	2.2.1.7	NA
17	0.060	1zy9A	0.400	6.49	0.056	0.708	3.2.1.22	135,137
18	0.060	2uxwA	0.405	6.11	0.016	0.670	1.3.99.-	77
19	0.060	2ppqA	0.403	5.60	0.038	0.625	2.7.1.39	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	0.09	0.675	1.55	0.20	0.72	3w8wB	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
1	0.07	0.622	2.78	0.14	0.72	3popA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
2	0.07	0.626	2.84	0.12	0.73	2y08B	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
3	0.07	0.618	2.66	0.14	0.72	2ipiA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0017000 GO:0050660 GO:0055114
4	0.07	0.605	2.71	0.15	0.71	2bvfA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0018530 GO:0050660 GO:0055114
5	0.07	0.605	2.94	0.15	0.71	4ud8A	GO:0000166 GO:0003824 GO:0005618 GO:0009506 GO:0009793 GO:0010197 GO:0016491 GO:0016614 GO:0045551 GO:0050660 GO:0055114
6	0.07	0.602	3.13	0.14	0.71	4pveA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
7	0.07	0.607	2.89	0.14	0.71	5d79A	GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
8	0.07	0.603	3.18	0.15	0.72	3vteA	GO:0003824 GO:0005576 GO:0016491 GO:0016614 GO:0048046 GO:0050660 GO:0055114
9	0.07	0.617	2.90	0.14	0.72	3d2jA	GO:0003824 GO:0009820 GO:0016023 GO:0016491 GO:0016614 GO:0031410 GO:0050468 GO:0050660 GO:0055114
10	0.07	0.598	3.09	0.17	0.71	4dnsA	GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
11	0.07	0.594	3.04	0.17	0.70	5awvA	GO:0003824 GO:0004497 GO:0016491 GO:0016614 GO:0016746 GO:0016757 GO:0050660 GO:0055114
12	0.07	0.560	3.57	0.11	0.71	4o95A	GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
13	0.07	0.560	3.51	0.09	0.70	3s1eA	GO:0003824 GO:0005576 GO:0005615 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
14	0.07	0.550	3.29	0.10	0.68	4oalA	GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
15	0.07	0.549	3.61	0.10	0.70	2exrA	GO:0003824 GO:0009690 GO:0009823 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
16	0.07	0.561	3.58	0.12	0.71	4ml8A	GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
17	0.07	0.559	3.58	0.12	0.71	4mlaB	GO:0000166 GO:0003824 GO:0009690 GO:0016491 GO:0016614 GO:0019139 GO:0050660 GO:0055114
18	0.07	0.478	4.39	0.14	0.66	4p8lA	GO:0003824 GO:0003885 GO:0016020 GO:0016491 GO:0016614 GO:0045227 GO:0050660 GO:0055114 GO:0071555

Consensus prediction of GO terms

Molecular Function	GO:0050660	GO:0016614
GO-Score	0.32	0.32
Biological Processes	GO:0055114
GO-Score	0.32
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.