I-TASSER results

I-TASSER results for job id Rv1532c

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

Input Sequence in FASTA format

>protein (144 residues)
MSDPLTAQEQHKRRQAVRELMPRTPFIGGLGIVFERYEPDDVVIRLPFRTDLTNDGTYFH
GGVIASVMDTAGAAAAWSNHDFDRGTRAATVAMSIQYTGAAKRCDLLCHARTARRRKELT
FTEITATDPDGNIVAHAVQTYRIV

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSDPLTAQEQHKRRQAVRELMPRTPFIGGLGIVFERYEPDDVVIRLPFRTDLTNDGTYFHGGVIASVMDTAGAAAAWSNHDFDRGTRAATVAMSIQYTGAAKRCDLLCHARTARRRKELTFTEITATDPDGNIVAHAVQTYRIV
Prediction	CCCCCCCCCHHHHHHHHHHHHHCCHHHHHHCCEEEEEHCCEEEEEEHCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEHCCCCCCEEEEEEEEEHCCCCEEEEEEEEHCCCCCEEEEEEEEEEHC
Conf.Score	999999887999999999998659688987999999989999999987878778899865799999999999999998788888756788999888856898876999999998689699999999959998899999999989
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSDPLTAQEQHKRRQAVRELMPRTPFIGGLGIVFERYEPDDVVIRLPFRTDLTNDGTYFHGGVIASVMDTAGAAAAWSNHDFDRGTRAATVAMSIQYTGAAKRCDLLCHARTARRRKELTFTEITATDPDGNIVAHAVQTYRIV
Prediction	876444674364035204621763201420402034145530202030445134431100002100000300010010234365433011131303213325744020303033344310101020225743200202022344
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCHHHHHHHHHHHHHCCHHHHHHCCEEEEEHCCEEEEEEHCCHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEHCCCCCCEEEEEEEEEHCCCCEEEEEEEEHCCCCCEEEEEEEEEEHC
MSDPLTAQEQHKRRQAVRELMPRTPFIGGLGIVFERYEPDDVVIRLPFRTDLTNDGTYFHGGVIASVMDTAGAAAAWSNHDFDRGTRAATVAMSIQYTGAAKRCDLLCHARTARRRKELTFTEITATDPDGNIVAHAVQTYRIV

3e1eC

0.24

0.22

0.94

3.57

MUSTER

--EPRFA----GYAQKVRDSFARQPVMATLGARIDTLLPGRVELCMPYDRALTQQHGFLHAGIVSTVLDSACGYAAFSL--MEEEAAVLTVEFKVNFLNPAEGERFAFRAEVVKPGRTLTVATATAYAGEERAIATMTATLMAL

3e1eC

0.22

0.21

0.94

4.52

dPPAS

------EPRFAGYAQKVRDSFARQPVMATLGARIDTLLPGRVELCMPYDRALTQQHGFLHAGIVSTVLDSACGYAAFSL--MEEEAAVLTVEFKVNFLNPAEGERFAFRAEVVKPGRTLTVATATAYAGEERAIATMTATLMAL

1vh9A

0.15

0.14

0.94

4.39

wdPPAS

LI--KRHLTLDELNATSD-----NTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMM--TRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVL

1vh9A

0.15

0.14

0.93

4.32

wMUSTER

L---KRHLTLDELNATSD-----NTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMM--TRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVL

3e1eC

0.23

0.22

0.94

4.21

wPPAS

--EPRF----AGYAQKVRDSFARQPVMATLGARIDTLLPGRVELCMPYDRALTQQHGFLHAGIVSTVLDSACGYAAFSL--MEEEAAVLTVEFKVNFLNPAEGERFAFRAEVVKPGRTLTVATATAYAGEERAIATMTATLMAL

3e1eC

0.22

0.21

0.94

4.96

dPPAS2

------EPRFAGYAQKVRDSFARQPVMATLGARIDTLLPGRVELCMPYDRALTQQHGFLHAGIVSTVLDSACGYAAFSL--MEEEAAVLTVEFKVNFLNPAEGERFAFRAEVVKPGRTLTVATATAYAGEERAIATMTATLMAL

3e1eC

0.23

0.22

0.94

4.13

PPAS

--EPRF----AGYAQKVRDSFARQPVMATLGARIDTLLPGRVELCMPYDRALTQQHGFLHAGIVSTVLDSACGYAAFSL--MEEEAAVLTVEFKVNFLNPAEGERFAFRAEVVKPGRTLTVATATAYAGEERAIATMTATLMAL

1vh9A

0.15

0.14

0.94

3.74

Env-PPAS

LI-WKRHLTLDELNATSD-----NTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMM--TRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVL

1vh9A

0.15

0.14

0.94

3.52

MUSTER

L--WKRHLTLDELNATSD-----NTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMM--TRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVL

1vh9A

0.15

0.14

0.95

4.51

dPPAS

SLIWKRHLTLDELNATSD-----NTMVAHLGIVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMM--TRDGQCVVGTELNATHHRPVSEGKVRGVCQPLHLGRQNQSWEIVVFDEQGRRCCTCRLGTAVL

(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=1.06

Estimated TM-score = 0.86±0.07

Estimated RMSD = 2.6±2.0Å

Download Model 2

C-score=-3.78

Download Model 3

C-score=-4.82

Download Model 4

C-score=-3.90

Download Model 5

C-score=-0.99

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	3e1eC	0.875	1.41	0.221	0.944
2	1vh9A	0.844	1.91	0.147	0.944
3	1vi8B	0.838	1.94	0.147	0.944
4	3e8pA	0.825	1.97	0.191	0.931
5	1sc0A	0.820	1.87	0.129	0.917
6	2fs2B	0.806	1.64	0.203	0.889
7	4qd7A	0.797	2.19	0.149	0.931
8	3lmbA	0.797	2.08	0.113	0.917
9	3e29B	0.792	1.61	0.238	0.875
10	3f5oA	0.784	2.17	0.227	0.917

(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	0.41	54	4qd8D	0FQ	Rep, Mult	54,55,56,59,60,61,97,98,99,100,133
2	0.20	29	1wn3A	HXC	Rep, Mult	69,73,88,89,90,91,142
3	0.18	32	3r35B	4CO	Rep, Mult	69,70,73,74,87,89,90,91,142,144
4	0.04	8	3f5oA	UUU	Rep, Mult	113,115,117,118,119,121
5	0.02	4	4k4bA	UOQ	Rep, Mult	18,22,27,69,73,74,89,90,91,144
6	0.02	5	3kuwB	FAH	Rep, Mult	69,90,91,92,93,139
7	0.01	2	1q4sA	PHB	Rep, Mult	54,56,60,61
8	0.01	2	1vh50	III	Rep, Mult	21,25,26,29,30,50,51,53,55,60,61,62,63,65,66,69,70,90,91,92,93,94,95,96,97
9	0.01	3	3r3aA	PHB	Rep, Mult	1,69,70,73,74,89,90
10	0.01	2	5t02A	GDP	Rep, Mult	41,109,110,111,113,123,124,125,133,136,138
11	0.00	1	3f5oC	UUU	Rep, Mult	94,95,96,137,138,140
12	0.00	1	3cf9C	AGI	Rep, Mult	65,68,69,96,125
13	0.00	1	2f410	III	Rep, Mult	60,62,65,66,90,91,92,93,94,95,96,97
14	0.00	1	2glpB	BDE	Rep, Mult	44,46,110

	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	0.218	1tbuB	0.588	1.93	0.094	0.667	3.1.2.2	61,109
2	0.205	2qq2C	0.672	1.99	0.174	0.750	3.1.2.2	61,63,90
3	0.160	1mkaA	0.699	3.14	0.075	0.917	4.2.1.60	61
4	0.115	2gllA	0.717	3.03	0.150	0.917	4.2.1.-	NA
5	0.106	1u1zB	0.698	3.04	0.122	0.896	4.2.1.-	NA
6	0.060	2d0vA	0.473	4.57	0.060	0.792	1.1.99.8	NA
7	0.060	3khpA	0.562	3.64	0.096	0.771	1.-.-.-	109,124
8	0.060	3b7kC	0.648	2.35	0.104	0.736	3.1.2.1	61,70
9	0.060	1vlbA	0.469	4.79	0.106	0.750	1.2.99.7	62,108
10	0.060	2hx5A	0.549	3.37	0.132	0.736	3.1.2.-	136
11	0.060	2ownB	0.575	3.12	0.093	0.743	3.1.2.14	NA
12	0.060	3kvnX	0.475	2.86	0.043	0.611	3.1.1.1	129
13	0.060	2v1oE	0.640	1.57	0.158	0.701	3.1.2.2	62,73
14	0.060	3khpC	0.566	3.44	0.104	0.764	1.-.-.-	NA
15	0.060	1lrwA	0.471	4.61	0.068	0.792	1.1.99.8	NA
16	0.060	1z6bA	0.681	2.90	0.087	0.861	4.2.1.-	NA
17	0.060	2c2iA	0.574	3.10	0.080	0.736	4.2.1.17	NA
18	0.060	3el6A	0.591	3.18	0.130	0.792	4.2.1.61	60
19	0.060	3ir3A	0.591	2.57	0.107	0.701	4.2.1.-	NA
20	0.060	1s9cD	0.566	2.98	0.083	0.729	4.2.1.107	NA
21	0.060	1iq6B	0.615	2.30	0.076	0.708	4.2.1.17	NA
22	0.060	2vkzG	0.619	3.22	0.075	0.826	2.3.1.38,3.1.2.14	NA
23	0.060	1lo8A	0.608	2.49	0.075	0.736	3.1.2.23	NA
24	0.060	3c7oA	0.475	4.87	0.065	0.833	3.2.1.55	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	0.47	0.763	1.49	0.20	0.83	4k02A	GO:0005777 GO:0016787 GO:0042372 GO:0051289
1	0.43	0.758	1.64	0.20	0.83	3s4kA	GO:0016787
2	0.41	0.833	2.24	0.12	0.94	2b6eD	GO:0016787
3	0.40	0.758	2.52	0.13	0.89	4gahB	GO:0005737 GO:0005739 GO:0005743 GO:0005758 GO:0005759 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006915 GO:0016020 GO:0016290 GO:0016787 GO:0032587 GO:0035338 GO:0042995 GO:0043491 GO:0047617 GO:1902108
4	0.39	0.777	2.15	0.20	0.90	2cy9B	GO:0005634 GO:0005737 GO:0005739 GO:0005819 GO:0005829 GO:0005856 GO:0016787 GO:0047617 GO:0051289 GO:0070062
5	0.39	0.832	1.63	0.20	0.92	2fs2B	GO:0010124 GO:0016289 GO:0016787 GO:0016790
6	0.39	0.784	2.17	0.23	0.92	3f5oA	GO:0005634 GO:0005737 GO:0005739 GO:0005819 GO:0005829 GO:0005856 GO:0016787 GO:0035338 GO:0047617 GO:0051289 GO:0070062
7	0.37	0.738	1.51	0.20	0.81	1wluA	GO:0016790
8	0.33	0.817	2.18	0.15	0.95	4qd7A	GO:0016787
9	0.32	0.756	2.31	0.13	0.88	4ae8A	GO:0005737 GO:0005739 GO:0005743 GO:0005758 GO:0005759 GO:0005829 GO:0005886 GO:0006629 GO:0006631 GO:0006915 GO:0016020 GO:0016290 GO:0016787 GO:0032587 GO:0035338 GO:0042995 GO:0043491 GO:0047617 GO:1902108
10	0.32	0.838	1.94	0.15	0.94	1vi8B	GO:0009234 GO:0016289 GO:0016787 GO:0016790 GO:0061522
11	0.30	0.693	2.68	0.14	0.82	2gvhB	GO:0016787
12	0.29	0.781	2.26	0.12	0.90	1q4sA	GO:0016787 GO:0018739
13	0.26	0.844	1.91	0.15	0.94	1vh9A	GO:0005737 GO:0005829 GO:0009239 GO:0016289 GO:0016787 GO:0016788 GO:0016790 GO:0042802
14	0.06	0.243	2.80	0.02	0.31	1af8A	GO:0017000
15	0.06	0.271	4.37	0.06	0.44	2dm7A	GO:0000166 GO:0004672 GO:0004674 GO:0005085 GO:0005089 GO:0005516 GO:0005524 GO:0005737 GO:0005829 GO:0006468 GO:0007275 GO:0008307 GO:0016301 GO:0016310 GO:0016740 GO:0030016 GO:0030018 GO:0030154 GO:0030506 GO:0031430 GO:0031432 GO:0035023 GO:0036309 GO:0043065 GO:0043547 GO:0045214 GO:0046872 GO:0051056 GO:0098779
16	0.06	0.715	1.82	0.21	0.78	3lbbA
17	0.06	0.728	1.58	0.11	0.80	3gekA
18	0.06	0.875	1.41	0.22	0.94	3e1eC
19	0.06	0.792	1.61	0.24	0.88	3e29B
20	0.06	0.756	1.64	0.32	0.83	3dkzA

Consensus prediction of GO terms

Molecular Function	GO:0016290
GO-Score	0.40
Biological Processes	GO:0051289	GO:0042372	GO:0035338	GO:0006631	GO:0043491	GO:1902108
GO-Score	0.68	0.47	0.40	0.40	0.40	0.40
Cellular Component	GO:0005829	GO:0005777	GO:0005743	GO:0005759	GO:0032587	GO:0005758	GO:0005819	GO:0070062	GO:0005634
GO-Score	0.63	0.47	0.40	0.40	0.40	0.40	0.39	0.39	0.39

(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.