I-TASSER results

I-TASSER results for job id Rv1632c

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

Input Sequence in FASTA format

>protein (147 residues)
MRAVDEYTVHPWGLYLARPTPGRAQFHYLESWLLPSLGLRATVFHFNPSHKRDHDYYLDV
GEYTPGPSVWRSEDHYLDIEVRTGGGAELADVDELLDAVRHGLLTPTVAEQAVRHAVDAV
EGLARNGYDLTRWLATKGMELTWRSGS

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRAVDEYTVHPWGLYLARPTPGRAQFHYLESWLLPSLGLRATVFHFNPSHKRDHDYYLDVGEYTPGPSVWRSEDHYLDIEVRTGGGAELADVDELLDAVRHGLLTPTVAEQAVRHAVDAVEGLARNGYDLTRWLATKGMELTWRSGS
Prediction	CCCCEEEEEHCCEEEEHCCCCCCCCCCHHHHHHCCCCCCEEEEEHCCCCCCCCCCEEEEEEEEEHCCCEEEEEEEEEEEEEHCCCCEEEEEHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCEEEHCCCC
Conf.Score	987579998577577756889998754445444565598789875689745666568999999986988999986888999599968998678999999989999999999999999999999998999889887669757875789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRAVDEYTVHPWGLYLARPTPGRAQFHYLESWLLPSLGLRATVFHFNPSHKRDHDYYLDVGEYTPGPSVWRSEDHYLDIEVRTGGGAELADVDELLDAVRHGLLTPTVAEQAVRHAVDAVEGLARNGYDLTRWLATKGMELTWRSGS
Prediction	745355143442102021324733413211110034240200211244526352410010030347743020201000001247441301213102402743303473044014103300320253443144015734140314758
	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

CCCCEEEEEHCCEEEEHCCCCCCCCCCHHHHHHCCCCCCEEEEEHCCCCCCCCCCEEEEEEEEEHCCCEEEEEEEEEEEEEHCCCCEEEEEHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCEEEHCCCC
MRAVDEYTVHPWGLYLARPTPGRAQFHYLESWLLPSLGLRATVFHFNPSHKRDHDYYLDVGEYTPGPSVWRSEDHYLDIEVRTGGGAELADVDELLDAVRHGLLTPTVAEQAVRHAVDAVEGLARNGYDLTRWLATKGMELTWRSGS

2p12A

0.57

0.55

0.96

3.29

MUSTER

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

2p12A

0.57

0.55

0.96

5.68

dPPAS

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

2p12A

0.57

0.55

0.96

5.69

wdPPAS

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

2p12A

0.57

0.54

0.96

4.00

wMUSTER

VRHVDHYRVEPWGLYARTS--DHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIG-PIDWRG--

2p12A

0.57

0.54

0.96

5.00

wPPAS

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDELEAHT-TGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

2p12A

0.57

0.55

0.96

13.25

dPPAS2

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

2p12A

0.57

0.55

0.96

4.47

PPAS

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

2p12A

0.57

0.55

0.96

4.00

Env-PPAS

VRHVDHYRVEPWGLYAR--TSDHPQFHYLESWLLPDLGLRASIFHYHPYHQRDQDHYVDIGTFTRGDDVWKSEDHYLDLVVRTGRDTELLDVDE-LEAHTTGLLDTATAEQAILTATTAIDGIAAHGHDLGRWLASIGP-IDWRG--

3exmA

0.24

0.99

1.33

MUSTER

ARPVTVVRDDADLLAVWLAPADGTPVHLLATRKLARPGEAWSVWLFWDPGWRFKNWYVNLERPLT-EGGVDSEDHFLDISVHPDRTWHWRDEDEFAQALRDGLMDPASAGRVRRAGRSAVAEIRAWGDGWEHWRPDPAWPVDWRTPA

3exmA

0.26

0.22

0.88

1.75

dPPAS

YTKPRTVQRDQWVLKLARPGEA------------------WSVWLFWDPGWRFKNWYVNLERPLTREGGVDSEDHFLDISVHPDRTWHWRDEDEFAQALRDGLMDPASAGRVRRAGRSAVAEIRAWGSPFADGWEHWRPDPAWPVPS

(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=1.50

Estimated TM-score = 0.92±0.06

Estimated RMSD = 1.9±1.6Å

Download Model 2

C-score=-2.74

Download Model 3

C-score=-2.66

Download Model 4

C-score=-3.18

Download Model 5

C-score=-4.70

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	2p12A	0.936	0.74	0.589	0.959
2	3exmA	0.741	2.98	0.199	0.925
3	1v7vA1	0.488	4.31	0.055	0.735
4	3d8kB	0.487	4.73	0.039	0.823
5	1tlbA	0.487	4.93	0.059	0.850
6	1n7qA3	0.486	4.58	0.045	0.735
7	4nnzA	0.486	4.91	0.046	0.816
8	2aexA	0.475	4.87	0.081	0.809
9	2qt8B	0.474	4.89	0.051	0.816
10	5eo6A	0.474	4.83	0.051	0.816

(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	0.24	7	3exmA	CA	Rep, Mult	57,59,74,78
2	0.13	4	3exmA	CA	Rep, Mult	76,78,91
3	0.07	3	4ku8A	GLY	Rep, Mult	108,112
4	0.05	2	3jcuH	CLA	Rep, Mult	112,119
5	0.05	2	3exmA	GP2	Rep, Mult	22,23,27,57,59,74,78,90,91
6	0.02	1	2xgxA	AKG	Rep, Mult	117,121
7	0.02	1	2d2cA	CLA	Rep, Mult	92,120
8	0.02	1	1gzmA	C8E	Rep, Mult	120,123

	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	3c6bA	0.459	4.53	0.065	0.735	3.1.2.12	115
2	0.060	1vb3A	0.463	4.95	0.063	0.789	4.2.3.1	NA
3	0.060	1rqxC	0.458	5.16	0.022	0.823	3.5.99.7	NA
4	0.060	1rw9A	0.468	4.86	0.056	0.782	4.2.2.5	NA
5	0.060	3exmA	0.741	2.98	0.199	0.925	3.6.1.6	57,73,94
6	0.060	1tzmC	0.463	4.85	0.015	0.803	3.5.99.7	NA
7	0.060	1c8bA	0.471	4.01	0.031	0.673	3.4.24.78	39
8	0.060	2de6B	0.457	5.15	0.047	0.775	1.14.12.-	NA
9	0.060	1kb9A	0.456	5.07	0.068	0.803	1.10.2.2	NA
10	0.060	1tlbA	0.487	4.93	0.059	0.850	1.3.3.3	93,100,108
11	0.060	1sqbB	0.461	5.10	0.061	0.830	1.10.2.2	NA
12	0.060	2v5aB	0.453	4.98	0.062	0.782	6.3.4.14	123
13	0.060	1aupA	0.348	5.01	0.039	0.626	1.4.1.2	NA
14	0.060	3cxhL	0.419	5.36	0.052	0.803	1.10.2.2	NA
15	0.060	2vqdA	0.456	5.08	0.076	0.796	6.3.4.14,6.4.1.2	82
16	0.060	1larA	0.462	4.79	0.054	0.769	3.1.3.48	115
17	0.060	1ojnA	0.490	4.11	0.055	0.701	4.2.2.1	NA
18	0.060	1pa1A	0.472	4.93	0.042	0.789	3.1.3.48	74
19	0.060	1wgzA	0.456	4.67	0.047	0.755	3.4.24.66	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	0.30	0.735	2.85	0.20	0.91	3cbtA	GO:0046872
1	0.07	0.461	4.97	0.06	0.80	3d8kC	GO:0003824 GO:0004722 GO:0006470
2	0.07	0.487	4.93	0.06	0.85	1tlbA	GO:0004109 GO:0005737 GO:0005829 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0042803 GO:0055114
3	0.07	0.474	4.83	0.05	0.82	5eo6A	GO:0004109 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0055114
4	0.07	0.478	5.03	0.07	0.84	3dwrB	GO:0004109 GO:0005737 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0042803 GO:0055114
5	0.07	0.474	4.93	0.06	0.82	3dwsB	GO:0004109 GO:0005737 GO:0006779 GO:0006782 GO:0006783 GO:0016491 GO:0042803 GO:0055114
6	0.07	0.475	4.87	0.08	0.81	2aexA	GO:0004109 GO:0005212 GO:0005737 GO:0005739 GO:0005743 GO:0005758 GO:0006779 GO:0006782 GO:0006783 GO:0010035 GO:0010039 GO:0010288 GO:0016020 GO:0016491 GO:0017085 GO:0042802 GO:0042803 GO:0046685 GO:0051597 GO:0055114
7	0.07	0.420	4.51	0.03	0.64	3rt0A	GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005737 GO:0006470 GO:0009738 GO:0016787 GO:0043169 GO:0046872
8	0.07	0.413	4.97	0.02	0.67	1a6qA	GO:0000122 GO:0000287 GO:0003824 GO:0004721 GO:0004722 GO:0004871 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006470 GO:0006499 GO:0007050 GO:0010991 GO:0016020 GO:0016055 GO:0016311 GO:0016787 GO:0030145 GO:0030177 GO:0030512 GO:0030514 GO:0033192 GO:0035970 GO:0042347 GO:0043123 GO:0043124 GO:0043169 GO:0045893 GO:0046827 GO:0046872 GO:0070412 GO:0071560
9	0.07	0.399	5.35	0.07	0.71	3acsA	GO:0003824 GO:0005975 GO:0030246
10	0.07	0.443	4.94	0.06	0.79	3nmnD	GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005737 GO:0005886 GO:0006470 GO:0009408 GO:0009409 GO:0009737 GO:0009738 GO:0009787 GO:0009788 GO:0010119 GO:0016020 GO:0016787 GO:0019901 GO:0043169 GO:0046872
11	0.06	0.385	4.83	0.05	0.67	4n0gA	GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005829 GO:0006470 GO:0009409 GO:0009414 GO:0009737 GO:0009738 GO:0009788 GO:0010119 GO:0010360 GO:0016787 GO:0019901 GO:0043169 GO:0046872
12	0.06	0.435	4.89	0.06	0.78	2p8eB	GO:0000287 GO:0003824 GO:0004721 GO:0004722 GO:0005737 GO:0005829 GO:0006470 GO:0006499 GO:0016020 GO:0016787 GO:0030145 GO:0032688 GO:0035970 GO:0042347 GO:0043124 GO:0043169 GO:0046872 GO:0050687
13	0.06	0.387	5.13	0.06	0.71	4da1A	GO:0003824 GO:0004721 GO:0004722 GO:0005739 GO:0005759 GO:0006470 GO:0009083 GO:0016787 GO:0043169 GO:0046872
14	0.06	0.398	5.39	0.07	0.71	3rrsA	GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738
15	0.06	0.423	5.28	0.07	0.79	2isnA
16	0.06	0.401	5.00	0.06	0.70	1v7vA	GO:0003824 GO:0005975 GO:0016740 GO:0030246 GO:0046872
17	0.06	0.441	4.94	0.03	0.79	4lg5B	GO:0003824 GO:0004721 GO:0004722 GO:0005634 GO:0005737 GO:0006470 GO:0009738 GO:0016787 GO:0043169 GO:0046872
18	0.06	0.373	5.52	0.07	0.71	3qdeA	GO:0003824 GO:0005975 GO:0016740 GO:0016757 GO:0030246 GO:0047738

Consensus prediction of GO terms

Molecular Function	GO:0016634	GO:0046872
GO-Score	0.37	0.30
Biological Processes	GO:0006783	GO:0046501
GO-Score	0.37	0.37
Cellular Component	GO:0005829
GO-Score	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.