I-TASSER results

I-TASSER results for job id Rv1762c

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

Input Sequence in FASTA format

>protein (262 residues)
MQSSSLDPVASERLSHAEKSFTSDLSINEFALLHGAGFEPIELVMGVSVYHVGFQFSGMR
QQQELGVLTEATYRARWNAMARMQAEADALKADGIVGVRLNWRHHGEGGEHLEFMAVGTA
VRYTAKPGAFRRPNGQAFSSHLSGQDMVTLLRSGFAPVAFVMGNCVFHIAVQGFMQTLRQ
IGRNMEMPQWTQGNYQARELAMSRMQSEAERDGATGVVGVHFAISNYAWGVHTVEFYTAG
TAVRRTGSGETITPSFVLPMDS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MQSSSLDPVASERLSHAEKSFTSDLSINEFALLHGAGFEPIELVMGVSVYHVGFQFSGMRQQQELGVLTEATYRARWNAMARMQAEADALKADGIVGVRLNWRHHGEGGEHLEFMAVGTAVRYTAKPGAFRRPNGQAFSSHLSGQDMVTLLRSGFAPVAFVMGNCVFHIAVQGFMQTLRQIGRNMEMPQWTQGNYQARELAMSRMQSEAERDGATGVVGVHFAISNYAWGVHTVEFYTAGTAVRRTGSGETITPSFVLPMDS
Prediction	CCCCCCCHHHHHHCCCCCCEEEHCCCCCCEEEEEHCCCEEEEEEEEEEEEEHCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEHCCCCCEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEEEEEEEEHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEHCCEHCCCCCEEEEEEEEEEEEHCCCCCCCCCCCCCCCCC
Conf.Score	9866677678876577886788678888778887669588688986677764344444456765489999999999999999999999989988999987655655788779999998999997688877888899865678868999998867667789998899975456678999987568554799999999999999999999999899789999875444446787689999988888768888899875589999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 260 \| \| \| \| \| \| \| \| \| \| \| \| \| MQSSSLDPVASERLSHAEKSFTSDLSINEFALLHGAGFEPIELVMGVSVYHVGFQFSGMRQQQELGVLTEATYRARWNAMARMQAEADALKADGIVGVRLNWRHHGEGGEHLEFMAVGTAVRYTAKPGAFRRPNGQAFSSHLSGQDMVTLLRSGFAPVAFVMGNCVFHIAVQGFMQTLRQIGRNMEMPQWTQGNYQARELAMSRMQSEAERDGATGVVGVHFAISNYAWGVHTVEFYTAGTAVRRTGSGETITPSFVLPMDS
Prediction	7655614631473255541000014416424035134022112031101232132223333223053025104501540153036205724020000010114324442210000000000213555462645643311650444402301433130001021000203333311210331034340430251045015401530363047230200000001223333343100000001002435776524353414268
	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

CCCCCCCHHHHHHCCCCCCEEEHCCCCCCEEEEEHCCCEEEEEEEEEEEEEHCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEHCCCCCEEEEEEEEEEEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEEEEEEEEHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEHCCEHCCCCCEEEEEEEEEEEEHCCCCCCCCCCCCCCCCC
MQSSSLDPVASERLSHAEKSFTSDLSINEFALLHGAGFEPIELVMGVSVYHVGFQFSGMRQQQELGVLTEATYRARWNAMARMQAEADALKADGIVGVRLNWRHHGEGGEHLEFMAVGTAVRYTAKPGAFRRPNGQAFSSHLSGQDMVTLLRSGFAPVAFVMGNCVFHIAVQGFMQTLRQIGRNMEMPQWTQGNYQARELAMSRMQSEAERDGATGVVGVHFAISNYAWGVHTVEFYTAGTAVRRTGSGETITPSFVLPMDS

1y2iA

0.21

0.08

0.40

2.81

dPPAS

-------------------QFSTTPTLEGLTIVEYCGVVTGEAILGANIFRDFFAGIRDIVGGRSGAYEKELRKAREIAFEELGSQARALGADAVVGIDIDYETVGQNGS--LVSVSGTAVKTRRNI---------------------------------------------------------------------------------------------------------------------------------------

1y2iA

0.21

0.08

0.40

1.00

MUSTER

-------------------QFSTTPTLEGLTIVEYCGVVTGEAILGANIFRDFFAGIRDIVGGRSGAYEKELRKAREIAFEELGSQARALGADAVVGIDIDYETVGQNGS--LVSVSGTAVKTRRNI---------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.24

0.10

0.39

3.18

wdPPAS

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVRDG--MLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

1y2iA

0.21

0.08

0.40

1.27

wMUSTER

-------------------QFSTTPTLEGLTIVEYCGVVTGEAILGANIFRDFFAGIRDIVGGRSGAYEKELRKAREIAFEELGSQARALGADAVVGIDIDYETVGQNGS--LVSVSGTAVKTRRNI---------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.24

0.10

0.39

2.40

wPPAS

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVRDG--MLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.24

0.10

0.39

9.01

dPPAS2

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVRDG--MLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.23

0.09

0.39

1.96

PPAS

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVR--DGMLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.23

0.09

0.39

2.88

Env-PPAS

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVR--DGMLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.24

0.10

0.39

0.98

MUSTER

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVRDG--MLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

1vr4A

0.24

0.10

0.39

2.80

dPPAS

------------------MIVTTTSGIQGKEIIEYIDIVNGEAIMGANIVRDLFASVRDVVGGRAGSYESKLKEARDIAMDEMKELAKQKGANAIVGVDVDYEVVRDG--MLMVAVSGTAVRI-------------------------------------------------------------------------------------------------------------------------------------------

(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=-3.61

Estimated TM-score = 0.32±0.11

Estimated RMSD = 14.7±3.6Å

Download Model 2

C-score=-4.13

Download Model 3

C-score=-4.12

Download Model 4

C-score=-3.90

Download Model 5

C-score=-3.68

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	2glfA	0.406	6.08	0.070	0.676
2	3ehnA	0.404	6.23	0.061	0.710
3	4a01A	0.403	5.80	0.039	0.653
4	4he8L	0.402	5.44	0.075	0.622
5	2gljX	0.396	6.20	0.047	0.668
6	3cghA	0.396	6.24	0.049	0.702
7	4pucA	0.394	6.16	0.067	0.695
8	4emeA	0.392	6.26	0.064	0.672
9	4r8fA	0.392	6.23	0.050	0.676
10	3sghA	0.392	6.14	0.053	0.679

(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	1o5qA	MG	Rep, Mult	24,99
2	0.04	2	1izlM	CLA	Rep, Mult	80,87
3	0.04	2	3c67A	GLC	Rep, Mult	200,201,207,208,212,240
4	0.04	2	4llhA	CM5	Rep, Mult	70,74
5	0.04	2	4mhlA	ARF	Rep, Mult	72,76
6	0.04	2	4pydB	8CS	Rep, Mult	88,91
7	0.04	2	3ak1D	EDO	Rep, Mult	83,90
8	0.02	1	1q0kE	THJ	Rep, Mult	76,79
9	0.02	1	2e2tA	PHZ	Rep, Mult	113,114,115,240
10	0.02	1	4gqtA	ZN	Rep, Mult	82,86
11	0.02	1	3s8gA	OLC	Rep, Mult	171,175,236,237,238
12	0.02	1	2xs4A	MG	Rep, Mult	23,26
13	0.02	1	3b2sA	MG	Rep, Mult	225,226
14	0.02	1	2zalA	ASP	Rep, Mult	185,186
15	0.02	1	1lt6P	GAA	Rep, Mult	36,37
16	0.02	1	4a5aA	MG	Rep, Mult	199,235
17	0.02	1	3u33B	FAD	Rep, Mult	59,63,66,69,164
18	0.02	1	3nmvB	MG	Rep, Mult	113,163
19	0.02	1	3u33K	FAD	Rep, Mult	181,198,201

	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	1tu5A	0.370	6.01	0.076	0.634	1.4.3.21	NA
2	0.060	2gmjA	0.374	6.22	0.045	0.641	1.5.5.1	NA
3	0.060	1e1yA	0.364	6.35	0.030	0.626	2.4.1.1	91
4	0.060	3kalA	0.368	5.55	0.053	0.592	6.3.2.3	NA
5	0.060	1fvoB	0.367	6.21	0.034	0.641	2.1.3.3	NA
6	0.060	1z8lA	0.364	6.02	0.069	0.615	3.4.17.21	NA
7	0.060	2cseW	0.371	6.51	0.045	0.676	3.6.4.13	NA
8	0.060	2vuaA	0.268	6.40	0.030	0.481	3.4.24.69	NA
9	0.060	3ig5A	0.366	6.30	0.042	0.637	6.3.2.2	NA
10	0.060	2qllA	0.350	6.34	0.045	0.618	2.4.1.1	NA
11	0.060	2hgsA	0.371	5.65	0.059	0.599	6.3.2.3	NA
12	0.060	1vlvA	0.376	6.00	0.051	0.622	2.1.3.3	99
13	0.060	1tgoA	0.353	5.95	0.038	0.580	2.7.7.7	179,216,218
14	0.060	1duvG	0.383	5.88	0.046	0.637	2.1.3.3	245
15	0.060	1ortI	0.370	6.27	0.055	0.626	2.1.3.3	214,242
16	0.060	2fpqA	0.375	5.48	0.053	0.592	3.4.24.69	NA
17	0.060	1a1sA	0.372	6.15	0.050	0.637	2.1.3.3	245
18	0.060	3kakB	0.353	5.59	0.051	0.573	6.3.2.3	NA
19	0.060	1fa9A	0.367	6.52	0.052	0.645	2.4.1.1	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	0.06	0.396	6.19	0.05	0.67	2gljA	GO:0004177 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
1	0.06	0.383	6.19	0.06	0.66	5jm6A	GO:0004177 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
2	0.06	0.385	6.30	0.06	0.67	3vatA	GO:0004177 GO:0005576 GO:0005634 GO:0005654 GO:0005737 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872 GO:0070006 GO:0072562
3	0.06	0.391	6.05	0.05	0.65	4njrA	GO:0004177 GO:0005737 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872 GO:0070006
4	0.06	0.394	6.34	0.06	0.68	4emeC	GO:0004177 GO:0005737 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872 GO:0070006
5	0.06	0.387	6.07	0.07	0.65	2ijzA	GO:0004177 GO:0005737 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872 GO:0070006
6	0.06	0.382	6.43	0.06	0.67	3varA	GO:0004177 GO:0005576 GO:0005634 GO:0005654 GO:0005737 GO:0006508 GO:0006518 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872 GO:0070006 GO:0072562
7	0.06	0.384	6.25	0.06	0.65	1y7eA	GO:0004177 GO:0006508 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0046872
8	0.06	0.395	6.24	0.05	0.71	4pucB	GO:0046872
9	0.06	0.333	6.39	0.04	0.60	3mx3A	GO:0046872
10	0.06	0.308	6.08	0.06	0.52	4mpqA	GO:0003824 GO:0008152 GO:0016829
11	0.06	0.300	6.24	0.04	0.52	4ks0B	GO:0000287 GO:0003824 GO:0004743 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0030955
12	0.06	0.392	6.23	0.05	0.68	5jm9A	GO:0000324 GO:0004177 GO:0005576 GO:0005773 GO:0006508 GO:0006518 GO:0006810 GO:0007039 GO:0008233 GO:0008237 GO:0008270 GO:0015031 GO:0016787 GO:0042802 GO:0046872 GO:0070006
13	0.06	0.398	6.21	0.04	0.71	3cghA	GO:0046872
14	0.06	0.253	5.30	0.03	0.40	3tr4B	GO:0000287 GO:0004427 GO:0005737 GO:0006796 GO:0016787 GO:0046872
15	0.06	0.260	4.45	0.03	0.35	5b2kA	GO:0000166 GO:0000287 GO:0001934 GO:0004672 GO:0004674 GO:0004702 GO:0004708 GO:0004713 GO:0005524 GO:0005634 GO:0005737 GO:0005829 GO:0006468 GO:0006915 GO:0006970 GO:0007165 GO:0007254 GO:0007257 GO:0008022 GO:0008545 GO:0009408 GO:0009411 GO:0016301 GO:0016310 GO:0016740 GO:0018108 GO:0019899 GO:0019901 GO:0019903 GO:0031435 GO:0032212 GO:0034612 GO:0035897 GO:0038095 GO:0043525 GO:0046872 GO:0051403 GO:0051973 GO:0072709 GO:1904355
16	0.06	0.256	7.08	0.06	0.50	3qv9B	GO:0000287 GO:0003824 GO:0004743 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0030955
17	0.06	0.293	5.93	0.05	0.48	1a0iA	GO:0000166 GO:0003677 GO:0003909 GO:0003910 GO:0005524 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0016874 GO:0046872 GO:0051103
18	0.06	0.275	6.23	0.03	0.46	4ks0A	GO:0000287 GO:0003824 GO:0004743 GO:0006096 GO:0016301 GO:0016310 GO:0016740 GO:0030955

Consensus prediction of GO terms

Molecular Function	GO:0046914	GO:0008235
GO-Score	0.57	0.36
Biological Processes	GO:0019538	GO:1901564	GO:0043603
GO-Score	0.57	0.36	0.36
Cellular Component	GO:0044424
GO-Score	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.