I-TASSER results

I-TASSER results for job id Rv0546c

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

Input Sequence in FASTA format

>protein (128 residues)
MEILASRMLLRPADYQRSLSFYRDQIGLAIAREYGAGTVFFAGQSLLELAGYGEPDHSRG
PFPGALWLQVRDLEATQTELVSRGVSIAREPRREPWGLHEMHVTDPDGITLIFVEVPEGH
PLRTDTRA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MEILASRMLLRPADYQRSLSFYRDQIGLAIAREYGAGTVFFAGQSLLELAGYGEPDHSRGPFPGALWLQVRDLEATQTELVSRGVSIAREPRREPWGLHEMHVTDPDGITLIFVEVPEGHPLRTDTRA
Prediction	CCEEEEEEEEHCCCHHHHHHHHHHHCCCEEEEHCCCEEEEHCCCCEEEEHCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHCCEEEHCCHCCCCCEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCC
Conf.Score	98678889986699999999988874995788758889997799789995799998898898679999959999999999998997875885579988999998899999999986888887656789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MEILASRMLLRPADYQRSLSFYRDQIGLAIAREYGAGTVFFAGQSLLELAGYGEPDHSRGPFPGALWLQVRDLEATQTELVSRGVSIAREPRREPWGLHEMHVTDPDGITLIFVEVPEGHPLRTDTRA
Prediction	85133120003154353024224734544133533300102244120101324457464443211000104303300530473506135424744423220103134413000101177223443668
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEEEEEHCCCHHHHHHHHHHHCCCEEEEHCCCEEEEHCCCCEEEEHCCCCCCCCCCCCCEEEEEHCCCHHHHHHHHHHHCCEEEHCCHCCCCCEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCC
MEILASRMLLRPADYQRSLSFYRDQIGLAIAREYGAGTVFFAGQSLLELAGYGEPDHSRGPFPGALWLQVRDLEATQTELVSRGVSIAREPRREPWGLHEMHVTDPDGITLIFVEVPEGHPLRTDTRA

4hc5A

0.23

0.20

0.89

2.81

MUSTER

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLPWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPP--EPWGQRATWFSDPDGNQFFLVEE------------

4hc5A

0.22

0.20

0.89

3.60

dPPAS

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLSWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPPE--PWGQRATWFSDPDGNQFFLVEE------------

4hc5A

0.23

0.20

0.89

3.19

wdPPAS

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLSWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPP--EPWGQRATWFSDPDGNQFFLVEE------------

4hc5A

0.23

0.20

0.89

3.18

wMUSTER

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLPWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPP--EPWGQRATWFSDPDGNQFFLVEE------------

4hc5A

0.23

0.20

0.89

3.11

wPPAS

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLSWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPP--EPWGQRATWFSDPDGNQFFLVEE------------

4hc5A

0.22

0.20

0.89

3.79

dPPAS2

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLSWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPPE--PWGQRATWFSDPDGNQFFLVEE------------

4hc5A

0.23

0.20

0.89

3.11

PPAS

LIAYVHSATIIVSDQEKALDFYVNTLGFEKVFDNQRFVTVVPAQTQVALGLSWYEDGRKPGGYTGISLITRDIDEAYKTLTERGVTFTKPP--EPWGQRATWFSDPDGNQFFLVEE------------

4jh1A

0.16

1.00

2.79

Env-PPAS

MLNGINHLCFSVSNLEDSIEFYEKVLEGELLVRGRKLAYFNICGVWVALNEIHIPRNEIYQSYTHIAFSVEDFESLLQRLEENDVHILKGRERDVRDCESIYFVDPDGHKFEFHSGTLQDRLNREDKP

1fa6A

0.26

0.23

0.90

2.62

MUSTER

MRL--LHTMLRVGDLQRSIDFYTKVLGMKLLRTSYKYSLAFVGEAVIELTYWGVDKYELGTAYGHIALSVDNAAEACEKIRQNGGNVTREAGPVKGGTVIAFVEDPDGYKIELIE-----------EG

2i7rA

0.14

0.12

0.88

3.39

dPPAS

---NLNQLDIIVSNVPQVCADLEHILDKKADYANDGFAQFTIGSHCLLSQNHLVPLENFQSGI-IIHIEVEDVDQNYKRLNELGIKVLHGPTVTDWGTESLLVQGPAGLVLDFYRK------------

(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=0.50

Estimated TM-score = 0.78±0.10

Estimated RMSD = 3.5±2.4Å

Download Model 2

C-score=-2.39

Download Model 3

C-score=-4.16

Download Model 4

C-score=-3.81

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	4hc5A	0.804	1.44	0.219	0.891
2	1zswA	0.761	2.86	0.098	0.961
3	3hpvA	0.760	2.91	0.123	0.953
4	3zgjA	0.758	2.62	0.180	0.961
5	4huzA	0.758	2.80	0.097	0.969
6	3oajA	0.758	2.59	0.115	0.953
7	1mpyA	0.756	2.92	0.164	0.953
8	3r4qA	0.753	2.59	0.180	0.922
9	3zi1A	0.751	2.52	0.168	0.930
10	1lqkA	0.745	2.78	0.221	0.953

(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	0.18	22	4mtrA	ZN	Rep, Mult	7,48
2	0.07	10	1qipA	GNB	Rep, Mult	11,32,34,38,40,50,52
3	0.06	8	2p7pA	MN	Rep, Mult	65,102,112
4	0.05	7	2p7qA	GG6	Rep, Mult	63,65,97,102,112,114,121
5	0.04	6	1qinA	GIP	Rep, Mult	7,11,37,39,48,50,52
6	0.04	6	1lqoA	PO4	Rep, Mult	63,65,93,102,112,127
7	0.02	3	1froA	GSB	Rep, Mult	89,100,102,110,112
8	0.02	3	1lqoA	TL	Rep, Mult	93,95,96,97,100,102,114,127
9	0.02	3	3oa4A	ZN	Rep, Mult	7,48,65,112
10	0.01	1	2c210	III	Rep, Mult	5,6,7,8,9,11,26,31,32,33,34,42,45,46,65,66,67,68,69,70,71,109,112,116,119,120
11	0.01	2	1z0fA	MG	Rep, Mult	18,107
12	0.01	1	4zzbE	XE	Rep, Mult	21,26
13	0.01	1	2wl3A	CA	Rep, Mult	106
14	0.01	1	1ewjA	BLM	Rep, Mult	32,37,39,46
15	0.01	1	3oxhA	PMB	Rep, Mult	33,37,94,97,119
16	0.01	1	4nb0A	CYS	Rep, Mult	9,10,11,50
17	0.01	1	2p7pD	SO4	Rep, Mult	63,65

	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	0.408	2c21A	0.731	2.58	0.189	0.891	4.1.1.-	48
2	0.280	1fa7B	0.678	2.46	0.217	0.852	4.4.1.5	10,48,64,68,106,108
3	0.162	1lqkA	0.745	2.78	0.221	0.953	2.5.1.18	48
4	0.060	1b76A	0.445	4.84	0.063	0.750	6.1.1.14	NA
5	0.060	1npbA	0.741	2.70	0.207	0.945	2.5.1.18	27,85,106
6	0.060	2uv8G	0.444	5.03	0.077	0.828	2.3.1.86	NA
7	0.060	1f1uA	0.732	3.16	0.171	0.961	1.13.11.15	NA
8	0.060	1q78A	0.452	4.12	0.073	0.711	2.7.7.19	NA
9	0.060	1mpyA	0.756	2.92	0.164	0.953	1.13.11.2	NA
10	0.060	1wleB	0.446	4.77	0.039	0.750	6.1.1.11	33
11	0.060	3hpvA	0.760	2.91	0.123	0.953	1.13.11.2	NA
12	0.060	1qipB	0.725	2.90	0.192	0.906	4.4.1.5	48
13	0.060	1nj6A	0.447	4.42	0.063	0.727	6.1.1.15	9
14	0.060	2vkzG	0.444	5.03	0.077	0.828	2.3.1.38,3.1.2.14	NA
15	0.060	2fu3B	0.443	3.90	0.052	0.664	2.7.7.-	28
16	0.060	1lqoB	0.744	2.80	0.221	0.953	2.5.1.18	27,106,108
17	0.060	1yvjA	0.446	4.89	0.115	0.773	2.7.10.2	NA
18	0.060	3f2bA	0.461	4.72	0.050	0.820	2.7.7.7	104
19	0.060	2zi8A	0.711	3.17	0.106	0.953	1.13.11.39	NA
20	0.060	1f9zA	0.680	2.44	0.217	0.852	4.4.1.5	48
21	0.060	1cjxA	0.570	4.22	0.095	0.938	1.13.11.27	NA
22	0.060	1nj1A	0.446	4.33	0.063	0.719	6.1.1.15	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	0.36	0.715	2.36	0.25	0.87	3l7tA	GO:0004462 GO:0046872
1	0.36	0.691	2.68	0.20	0.88	2p25A
2	0.36	0.809	1.54	0.22	0.91	4hc5D	GO:0051213 GO:0055114
3	0.36	0.725	2.90	0.19	0.91	1qipB	GO:0004462 GO:0005737 GO:0005829 GO:0005975 GO:0006090 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0030316 GO:0043066 GO:0046872 GO:0070062
4	0.34	0.741	2.70	0.21	0.95	1npbA	GO:0004364 GO:0005737 GO:0016740 GO:0046677 GO:0046872
5	0.33	0.739	2.42	0.15	0.91	3hnqA	GO:0009405
6	0.32	0.674	2.54	0.25	0.85	4n04A	GO:0051213 GO:0055114
7	0.32	0.745	2.59	0.15	0.92	3ey7A	GO:0003824 GO:0051213 GO:0055114
8	0.32	0.761	1.97	0.16	0.89	4g6xA	GO:0051213 GO:0055114
9	0.31	0.731	2.87	0.14	0.96	4mymA	GO:0051213 GO:0055114
10	0.31	0.702	2.92	0.15	0.90	4nazA	GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
11	0.29	0.725	2.89	0.20	0.91	4kykA	GO:0004462 GO:0005975 GO:0006357 GO:0006749 GO:0008270 GO:0009438 GO:0016829 GO:0019243 GO:0030316 GO:0043066 GO:0046872 GO:0070062
12	0.28	0.719	3.31	0.15	0.98	4jd1B	GO:0000287 GO:0004364 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
13	0.26	0.719	3.06	0.13	0.97	4jh1A	GO:0000287 GO:0005737 GO:0016740 GO:0016765 GO:0046677 GO:0046872
14	0.25	0.705	2.74	0.22	0.88	3kolA	GO:0004462 GO:0046872 GO:0051213 GO:0055114
15	0.24	0.711	2.90	0.17	0.91	2rk0A	GO:0051213 GO:0055114
16	0.23	0.758	2.80	0.10	0.97	4huzA	GO:0016491 GO:0046872 GO:0051213 GO:0055114
17	0.15	0.758	2.59	0.12	0.95	3oajA	GO:0005737 GO:0009636 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
18	0.14	0.712	3.26	0.15	0.95	1kmyA	GO:0003824 GO:0005506 GO:0006725 GO:0008198 GO:0016491 GO:0018583 GO:0019439 GO:0042178 GO:0046872 GO:0051213 GO:0055114
19	0.14	0.740	2.68	0.12	0.96	2r5vA	GO:0003868 GO:0005506 GO:0009072 GO:0016491 GO:0016701 GO:0017000 GO:0033072 GO:0046872 GO:0050585 GO:0055114
20	0.14	0.761	2.86	0.10	0.96	1zswA	GO:0046872
21	0.13	0.717	2.86	0.13	0.95	1sqiB	GO:0000139 GO:0003868 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0006559 GO:0006572 GO:0009072 GO:0016020 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114
22	0.12	0.606	3.95	0.12	0.94	5ec3A	GO:0003868 GO:0005829 GO:0006559 GO:0006572 GO:0009072 GO:0016491 GO:0016701 GO:0046872 GO:0051213 GO:0055114 GO:0070062
23	0.07	0.760	2.91	0.12	0.95	3hpvA	GO:0003824 GO:0006725 GO:0008198 GO:0016491 GO:0018577 GO:0019439 GO:0046872 GO:0051213 GO:0055114
24	0.06	0.390	4.32	0.07	0.63	4jwtA	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
25	0.06	0.380	5.13	0.06	0.71	3tsdB	GO:0000166 GO:0003824 GO:0003938 GO:0006164 GO:0006177 GO:0016491 GO:0046872 GO:0055114
26	0.06	0.388	4.45	0.08	0.65	4lobA	GO:0008299 GO:0016740

Consensus prediction of GO terms

Molecular Function	GO:0004462	GO:0051213	GO:0008270	GO:0004364
GO-Score	0.59	0.36	0.36	0.34
Biological Processes	GO:0055114	GO:0006090	GO:0006749	GO:0005975	GO:0009438	GO:0030316	GO:0043066	GO:0006357	GO:0046677
GO-Score	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.36	0.34
Cellular Component	GO:0005829	GO:0070062
GO-Score	0.36	0.36

(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.