I-TASSER results

I-TASSER results for job id Rv2630

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

Input Sequence in FASTA format

>protein (179 residues)
MLHRDDHINPPRPRGLDVPCARLRATNPLRALARCVQAGKPGTSSGHRSVPHTADLRIEA
WAPTRDGCIRQAVLGTVESFLDLESAHAVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVG
ETPVDLRLRDVDGGVDVTFATTDASTLVQVGAVPKAVSLNELRFSQGRHGWRCAVTLDV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MLHRDDHINPPRPRGLDVPCARLRATNPLRALARCVQAGKPGTSSGHRSVPHTADLRIEAWAPTRDGCIRQAVLGTVESFLDLESAHAVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVGETPVDLRLRDVDGGVDVTFATTDASTLVQVGAVPKAVSLNELRFSQGRHGWRCAVTLDV
Prediction	CCCCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHCCCCCCCCCCCEEEHCCCCEEEEEEEHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCEEEEEEEEEEHCCEEEEEEEEEHCCCCCCCCCCEEEEEHCCCEEEEHCCEEEEEEEEHC
Conf.Score	98877888888887555676545546656777764456788878885775777648999996999999999999999998568878885899999985997899999999999998646856899999996999999999986676655676555776467589996999999999969
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MLHRDDHINPPRPRGLDVPCARLRATNPLRALARCVQAGKPGTSSGHRSVPHTADLRIEAWAPTRDGCIRQAVLGTVESFLDLESAHAVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVGETPVDLRLRDVDGGVDVTFATTDASTLVQVGAVPKAVSLNELRFSQGRHGWRCAVTLDV
Prediction	74446651537434435343542454444543364365566636231321413010001020631530022003000110032651546442504052732340013102200022304410124030444653030202236166335451301000223030465752020100004
	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

CCCCCCCCCCCCCCCCCCCCCHHHCCCHHHHHHHHCCCCCCCCCCCEEEHCCCCEEEEEEEHCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEHCCCHHHHHHHHHHHHHHHHHHCCEEEEEEEEEEHCCEEEEEEEEEHCCCCCCCCCCEEEEEHCCCEEEEHCCEEEEEEEEHC
MLHRDDHINPPRPRGLDVPCARLRATNPLRALARCVQAGKPGTSSGHRSVPHTADLRIEAWAPTRDGCIRQAVLGTVESFLDLESAHAVHTRLRRLTADRDDDLLVAVLEEVIYLLDTVGETPVDLRLRDVDGGVDVTFATTDASTLVQVGAVPKAVSLNELRFSQGRHGWRCAVTLDV

1jw3A

0.18

0.14

0.76

2.93

MUSTER

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.18

0.14

0.76

6.14

dPPAS

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.18

0.14

0.76

7.18

wdPPAS

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.19

0.14

0.75

3.70

wMUSTER

--------------------------------------------KGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.18

0.14

0.76

5.29

wPPAS

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.18

0.14

0.76

9.59

dPPAS2

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.18

0.14

0.76

4.51

PPAS

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

1jw3A

0.18

0.14

0.76

4.75

Env-PPAS

-------------------------------------------MKGFEFFDVTADAGFWAYGHDLEEVFENAALAMFEVMTDTSLVEAAEERRVEITSEDRVSLLYDWLDELLFIHDTEFILFSKFKVKIDEKHLTGTAMGEEIKEGHERRDEVKAVTFHMMEILDEDGLIKARVILDL

4n2pA

0.14

0.11

0.75

2.66

MUSTER

-------------------------------------------LKKWEHYEHTADIGIRGYGDSLEEAFEAVAIALFDVV-NVNKVEKKEVREIEVEAEDLEALLYSFLEELLVIHDIEGLVFRDFEVKIERVRLRAKAYGEKLDLKHEPKEEVKAITYHD-KIERLPNGKWAQLVPDI

4n2pA

0.14

0.11

0.75

5.41

dPPAS

-------------------------------------------LKKWEHYEHTADIGIRGYGDSLEEAFEAVAIALFDVV-NVNKVEKKEVREIEVEAEDLEALLYSFLEELLVIHDIEGLVFRDFEVKIERVRLRAKAYGEKLDKKHEPKEEVKAITYHDKIER-LPNGKWAQLVPDI

(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=-0.71

Estimated TM-score = 0.62±0.14

Estimated RMSD = 6.6±4.0Å

Download Model 2

C-score=-2.05

Download Model 3

C-score=-2.10

Download Model 4

C-score=-2.86

Download Model 5

C-score=-2.33

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	2jadA1	0.445	4.96	0.065	0.732
2	1xmzB	0.443	4.80	0.065	0.715
3	2pbhA	0.431	5.41	0.046	0.765
4	2uv9D	0.430	5.26	0.040	0.715
5	7pckA	0.423	5.62	0.060	0.776
6	2fa0A	0.422	5.32	0.041	0.715
7	2vviC	0.421	5.19	0.058	0.721
8	1cs8A	0.421	5.58	0.053	0.760
9	2h5rA	0.417	5.05	0.073	0.721
10	3juvA	0.416	5.15	0.055	0.693

(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	0.26	3	1j5uA	CA	Rep, Mult	55,178,179
2	0.06	1	3ld6B	BCD	Rep, Mult	56,57,58,59,60,79
3	0.06	1	3ls3C	SPD	Rep, Mult	66,98,134,135
4	0.06	1	3k24A	III	Rep, Mult	67,69,72,108,109,163
5	0.06	1	3k24B	III	Rep, Mult	69,72,73,108,113,157
6	0.06	1	3nedA	NA	Rep, Mult	78,122,123,124

	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	2nqdB	0.382	5.26	0.056	0.654	3.4.22.15	NA
2	0.060	1mirA	0.428	5.43	0.046	0.771	3.4.22.1	NA
3	0.060	1ksdA	0.407	5.23	0.059	0.676	3.2.1.4	100
4	0.060	1jpzB	0.392	5.37	0.019	0.676	1.14.14.1,1.6.2.4	NA
5	0.060	1xqdA	0.385	5.71	0.033	0.698	1.7.99.7	162
6	0.060	7pckA	0.423	5.62	0.060	0.776	3.4.22.38	75
7	0.060	1egyA	0.405	5.12	0.037	0.682	1.14.-.-	49,78
8	0.060	1ftrD	0.391	4.32	0.033	0.564	2.3.1.101	112,135
9	0.060	1p2yA	0.380	5.68	0.034	0.693	1.14.15.1	76
10	0.060	2ghuA	0.410	5.49	0.075	0.726	3.4.22.-	NA
11	0.060	1csbE	0.279	5.87	0.038	0.520	3.4.22.1	107
12	0.060	2c7yB	0.402	5.17	0.113	0.659	2.3.1.16	NA
13	0.060	1dkpA	0.405	5.06	0.034	0.665	3.1.3.2,3.1.3.26	103
14	0.060	3i3kA	0.408	5.06	0.046	0.665	1.14.13.70	NA
15	0.060	1gkpA	0.400	5.50	0.058	0.710	3.5.2.2	NA
16	0.060	1oxaA	0.396	5.44	0.073	0.687	3.4.23.23	30,83
17	0.060	3hf2A	0.390	5.28	0.020	0.659	1.14.14.1,1.6.2.4	NA
18	0.060	2c7zA	0.395	5.12	0.095	0.648	2.3.1.16	NA
19	0.060	1xpmC	0.410	5.48	0.048	0.715	2.3.3.10	61,175

(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	0.17	0.439	5.12	0.03	0.75	3ai5A
1	0.07	0.438	5.31	0.01	0.77	4u2vB	GO:0001776 GO:0001782 GO:0001783 GO:0001836 GO:0001974 GO:0002262 GO:0002352 GO:0005622 GO:0005739 GO:0005741 GO:0005783 GO:0005829 GO:0006091 GO:0006915 GO:0006919 GO:0006987 GO:0007420 GO:0007568 GO:0008053 GO:0008218 GO:0008283 GO:0008285 GO:0008630 GO:0008635 GO:0009620 GO:0010046 GO:0010225 GO:0010248 GO:0010332 GO:0010524 GO:0010629 GO:0014070 GO:0016020 GO:0016021 GO:0018298 GO:0019835 GO:0031018 GO:0031072 GO:0031100 GO:0031307 GO:0031966 GO:0032469 GO:0032471 GO:0033137 GO:0034644 GO:0035108 GO:0042493 GO:0042542 GO:0042802 GO:0042803 GO:0042981 GO:0043065 GO:0043496 GO:0043497 GO:0044325 GO:0044346 GO:0045471 GO:0045862 GO:0046872 GO:0046902 GO:0046930 GO:0046982 GO:0048597 GO:0048872 GO:0051087 GO:0051400 GO:0051726 GO:0051881 GO:0060068 GO:0070059 GO:0070242 GO:0071260 GO:0090200 GO:0097190 GO:0097192 GO:0097202 GO:1900103 GO:1901030 GO:1902262 GO:1903896
2	0.07	0.439	5.01	0.02	0.74	2jadA	GO:0004364 GO:0004602 GO:0005737 GO:0006091 GO:0008218 GO:0009055 GO:0010731 GO:0015035 GO:0015036 GO:0018298 GO:0034599 GO:0045454 GO:0055114 GO:0098869
3	0.07	0.459	5.08	0.06	0.77	4ndjA	GO:0006091 GO:0008218 GO:0018298
4	0.07	0.458	4.73	0.05	0.73	4gf6B	GO:0006091 GO:0008218 GO:0018298
5	0.07	0.438	5.30	0.03	0.77	4jrbA	GO:0006091 GO:0008218 GO:0018298
6	0.07	0.441	5.14	0.07	0.75	3ls3D
7	0.06	0.445	5.04	0.04	0.75	3pibB	GO:0008218
8	0.06	0.423	5.01	0.04	0.71	4q9wA	GO:0006091 GO:0008218 GO:0018298
9	0.06	0.432	4.71	0.07	0.69	4ohsB	GO:0008218
10	0.06	0.427	4.77	0.06	0.69	2whsB	GO:0008218
11	0.06	0.430	4.99	0.06	0.72	2arlA	GO:0008218 GO:0010117 GO:0018298 GO:0018995
12	0.06	0.434	5.19	0.06	0.75	2hpwA	GO:0006091 GO:0008218
13	0.06	0.423	4.84	0.02	0.69	4dkmA	GO:0008218
14	0.06	0.443	4.80	0.07	0.72	1xmzB	GO:0008218 GO:0018298
15	0.06	0.431	4.95	0.06	0.72	2icrC	GO:0008218 GO:0018298
16	0.06	0.418	5.02	0.03	0.70	4jeoA	GO:0008218
17	0.06	0.419	5.16	0.06	0.72	3cglA	GO:0006091 GO:0008218 GO:0018298
18	0.06	0.446	4.87	0.07	0.72	5fguA	GO:0003676 GO:0006091 GO:0008218 GO:0016787 GO:0018298 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0051400	GO:0046982	GO:0042803	GO:0004602	GO:0004364	GO:0046872	GO:0015035	GO:0031072	GO:0044325	GO:0051087	GO:0009055
GO-Score	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07
Biological Processes	GO:0006464
GO-Score	0.47
Cellular Component	GO:0005829	GO:0046930	GO:0005783	GO:0031307
GO-Score	0.07	0.07	0.07	0.07

(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.