I-TASSER results

I-TASSER results for job id Rv1227c

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

Input Sequence in FASTA format

>protein (177 residues)
MDHARNVPSATGPQRNHLALAEPAHRPSSQAPVMWALSASLGWILPVIAQLVWWAVHPQP
PWPHLAAAALTAVAMVVHIGVVPLWRYRVHRWEISPQAVFTRTGWLVQERRITPISRVQT
VDTYRGPMDRLFGLANVTVTTASSAGAVHIEALDTDVADRVVAQLTDIAALRGEDAT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDHARNVPSATGPQRNHLALAEPAHRPSSQAPVMWALSASLGWILPVIAQLVWWAVHPQPPWPHLAAAALTAVAMVVHIGVVPLWRYRVHRWEISPQAVFTRTGWLVQERRITPISRVQTVDTYRGPMDRLFGLANVTVTTASSAGAVHIEALDTDVADRVVAQLTDIAALRGEDAT
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEHCCEEEEEEEEEEEEEEEEHCCCEEEEEEHCCHHHHHHCCEEEEEEHCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHHCCCCC
Conf.Score	998778888888887777877776678877888899999999999999999999864665578999999999999999999999874568899989999999877999999995433688788769888765868999998899986899678999999999999999986556899
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MDHARNVPSATGPQRNHLALAEPAHRPSSQAPVMWALSASLGWILPVIAQLVWWAVHPQPPWPHLAAAALTAVAMVVHIGVVPLWRYRVHRWEISPQAVFTRTGWLVQERRITPISRVQTVDTYRGPMDRLFGLANVTVTTASSAGAVHIEALDTDVADRVVAQLTDIAALRGEDAT
Prediction	855566456455364552415535530344022123233333323333333221223433333332333333333333333333333321202035630312211023433403143024043433103222411403030235545040540557305402620362065466648
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEHCCEEEEEEEEEEEEEEEEHCCCEEEEEEHCCHHHHHHCCEEEEEEHCCCCCEEEEHCCCHHHHHHHHHHHHHHHHHHCCCCC
MDHARNVPSATGPQRNHLALAEPAHRPSSQAPVMWALSASLGWILPVIAQLVWWAVHPQPPWPHLAAAALTAVAMVVHIGVVPLWRYRVHRWEISPQAVFTRTGWLVQERRITPISRVQTVDTYRGPMDRLFGLANVTVTTASSAGAVHIEALDTDVADRVVAQLTDIAALRGEDAT

1p49A1

0.09

0.03

0.33

1.45

dPPAS2

----------------------------FTTGFKRLVFLPLQIVGVTLLTLAALNCLGLLHVPLGVFFSLLFLAALILTLFLGFLH-------------------------------------------------------------------------------------------

4ri2A

0.07

0.90

1.01

PPAS

AKAPKKVEKPKLKVEDGLFGTSGGIGFTKENELFVGRVAMIGFAASLLGEGITILSQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGRFVDE----PTFGFTKSNELF--GRLAQLGFAFSLIGEII-LAQLNIET----------GVPINEIEPLVLLNVVFFFIAAINPG

2axtZ

0.15

0.05

0.35

1.32

dPPAS2

----------------------------MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV---------------------------------------------------------------------------------------

1h2sB

0.08

0.03

0.34

1.31

dPPAS2

-----------------------------GAVFIFVGALTVLFGAIAYGEVTAAAATGDAAAVQEAAVSAILGLIILLGINLGLVAATL----------------------------------------------------------------------------------------

2l35A

0.06

0.02

0.36

1.26

dPPAS2

-----------------------CSTVSPGVLAGIVVGDLVLTVLIALAVYFLGRLGTAEVLGIISIVLVATVLKTIVLIPFLEQN-------------------------------------------------------------------------------------------

2yevC

0.11

0.04

0.35

1.13

dPPAS2

-----------------------------VYIALFALGAALVTLFFYLILPRVLTTEGETFDLRFVLFMLLLILLAAGTVALMLLIGKAHH--------------------------------------------------------------------------------------

5iitA

0.08

0.07

0.98

0.74

MUSTER

VQHTVRLLDSNNPPTQLEILEEELSDIIADVHDLAKFSRLNYTGFQKIIKKHDKKTGFILKPVFQVRLDSKPFFKENYDELVVKISQLYDIARTSGAGSDGF----TVLSTKSLFLGQKLQVVQADIASIDSDAVVHPTNTDFYIGGEVGNTLEKKGGKEFVEAVLELRKKNGPLEV

2axtZ

0.15

0.05

0.35

0.73

dPPAS

----------------------------MTILFQLALAALVILSFVMVIGVPVAYASPQDWDRSKQLIFLGSGLWIALVLVVGVLNFFVV---------------------------------------------------------------------------------------

4chmA

0.13

0.08

0.63

1.01

wdPPAS

-----------------------------------------------------SMASPQVTAADIEDLHRRLLAGMAVLVLLQ----CILHYNEADSSLSISCE---DKVRVIPLSDIKALLHTRDQLQRV-NLVCVALHLLESGNCIPLRFDGVKDKTCFVDLLKKLKAAA-----

3jd8A

0.10

0.97

0.83

wMUSTER

VDEVTAPSIVCGPKPQPPPPPAPWTILGLDAMYVIMWITYMAFLLVFFGAFFAFEGCLRRLFTRWGSFCVRGCVIFFSLVFITACSSGLVFVRVTTNPVDLPSSQARLEKEYFPFFRTEQLIIRAP------LTDKHIYQPYPSGADVPFPPLDIQILHQVLDLQIAIENITYDNET

(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=-3.82

Estimated TM-score = 0.30±0.10

Estimated RMSD = 14.2±3.8Å

Download Model 2

C-score=-3.99

Download Model 3

C-score=-4.05

Download Model 4

C-score=-3.20

Download Model 5

C-score=-3.07

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	2ewgA	0.474	4.41	0.065	0.706
2	2gq3A3	0.471	4.47	0.061	0.695
3	4qbdA	0.471	4.96	0.055	0.768
4	2xtlA	0.469	5.09	0.063	0.746
5	4iggA	0.466	4.62	0.041	0.718
6	3lk5A	0.466	4.71	0.097	0.701
7	1d8cA3	0.465	4.99	0.043	0.729
8	3g4dA	0.464	4.20	0.062	0.689
9	5fbyA2	0.464	5.00	0.068	0.763
10	5do7B	0.463	4.59	0.052	0.701

(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	0.07	3	3hykB	A3P	Rep, Mult	117,130
2	0.07	3	2htnD	HEM	Rep, Mult	41,44,48,67,74,75
3	0.05	2	4zzcA	XE	Rep, Mult	33,36,81,84
4	0.05	2	3e5uC	3C4	Rep, Mult	70,73,74
5	0.05	2	5jqhA	CLR	Rep, Mult	51,67,70,71
6	0.02	1	1f35A	ZN	Rep, Mult	154,156
7	0.02	1	3lo1A	AZI	Rep, Mult	126,130,131
8	0.02	1	3qqvA	IPE	Rep, Mult	150,151,165
9	0.02	1	3n8bB	MG	Rep, Mult	141,143
10	0.02	1	1fbmD	RTL	Rep, Mult	41,48
11	0.02	1	3i8hH	NUC	Rep, Mult	115,117,132,161
12	0.02	1	2h9dD	PYR	Rep, Mult	117,118
13	0.02	1	3m50A	EBT	Rep, Mult	34,37,38
14	0.02	1	2hgrH	NUC	Rep, Mult	117,130,132
15	0.02	1	3i8gH	NUC	Rep, Mult	117,161

	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	3npkA	0.429	4.20	0.042	0.622	2.5.1.10	37
2	0.060	2ewgA	0.474	4.41	0.065	0.706	2.5.1.10	NA
3	0.060	2yyjA	0.429	5.04	0.026	0.712	1.14.13.3	NA
4	0.060	1gkzA	0.433	5.15	0.047	0.740	2.7.11.4,2.7.1.115	NA
5	0.060	3lomA	0.429	4.45	0.045	0.650	2.5.1.10	91
6	0.060	1no3A	0.428	4.96	0.083	0.695	1.13.11.12	NA
7	0.060	1vzoA	0.445	5.10	0.068	0.729	2.7.11.1,2.7.1.37	NA
8	0.060	2j1pB	0.431	4.44	0.070	0.655	2.5.1.1,2.5.1.10,2.5.1.29	NA
9	0.060	1ofdA	0.440	5.44	0.063	0.780	1.4.7.1	NA
10	0.060	2iukA	0.469	4.38	0.103	0.706	1.13.11.12	NA
11	0.060	2pnrB	0.433	5.18	0.031	0.757	2.7.11.2	78
12	0.060	1n1zA	0.435	4.86	0.043	0.701	5.5.1.8	43
13	0.060	3czkA	0.443	4.52	0.073	0.684	3.2.1.48	NA
14	0.060	3c2wC	0.441	4.41	0.063	0.655	2.7.13.3	72,74,79
15	0.060	3i39X	0.439	5.38	0.069	0.740	1.2.99.2	76,79,153
16	0.060	2iukB	0.469	4.40	0.096	0.706	1.13.11.12	89
17	0.060	1bxrA	0.431	5.25	0.060	0.740	6.3.5.5	NA
18	0.060	3lk5A	0.466	4.71	0.097	0.701	2.5.1.1	69
19	0.060	1wmwA	0.454	4.92	0.086	0.735	2.5.1.-	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	0.07	0.451	4.76	0.05	0.70	4jzbA	GO:0004161 GO:0004337 GO:0005737 GO:0005783 GO:0005829 GO:0006695 GO:0008299 GO:0016740 GO:0045337 GO:0046872
1	0.07	0.455	4.54	0.05	0.69	4lfgA	GO:0004337 GO:0008299 GO:0016740
2	0.07	0.367	5.68	0.06	0.68	4ex4B	GO:0003824 GO:0004474 GO:0005737 GO:0006097 GO:0006099 GO:0016740 GO:0046872
3	0.07	0.430	5.02	0.10	0.71	4gp2A	GO:0004311 GO:0008299 GO:0016740 GO:0033386
4	0.07	0.365	5.94	0.06	0.70	4ex4A	GO:0003824 GO:0004474 GO:0005737 GO:0006097 GO:0006099 GO:0016740 GO:0046872
5	0.07	0.460	4.67	0.02	0.71	4kk2A	GO:0004161 GO:0004337 GO:0008299 GO:0009507 GO:0009536 GO:0016740 GO:0033384 GO:0033849 GO:0033851 GO:0045337 GO:0046872
6	0.07	0.364	5.94	0.05	0.69	2gq3A	GO:0000287 GO:0003824 GO:0004474 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0006097 GO:0006099 GO:0015936 GO:0016740 GO:0030145 GO:0046872
7	0.06	0.404	5.04	0.02	0.66	3cc9C	GO:0008299 GO:0016020 GO:0016021 GO:0016740 GO:0046872
8	0.06	0.467	4.61	0.07	0.69	3lk5A	GO:0004161 GO:0008299 GO:0016740
9	0.06	0.378	5.76	0.04	0.72	2jqxA	GO:0003824 GO:0004474 GO:0005737 GO:0005829 GO:0006097 GO:0006099 GO:0009436 GO:0016740 GO:0046872
10	0.06	0.451	4.18	0.07	0.66	3q1oA	GO:0008299 GO:0016740
11	0.06	0.425	4.49	0.06	0.66	4wk5A	GO:0008299 GO:0016740
12	0.06	0.346	5.19	0.04	0.56	3cuzA	GO:0003824 GO:0004474 GO:0005737 GO:0006097 GO:0006099 GO:0016740
13	0.06	0.378	5.57	0.07	0.69	3wjkA	GO:0008299 GO:0016740
14	0.06	0.419	4.15	0.08	0.62	3zcdA	GO:0008299 GO:0016740 GO:0046872
15	0.06	0.443	4.75	0.04	0.68	3rbmB	GO:0008299 GO:0016020 GO:0016021 GO:0016740 GO:0046872
16	0.06	0.353	5.25	0.04	0.57	5e8kA	GO:0004161 GO:0004311 GO:0004337 GO:0005739 GO:0008299 GO:0016117 GO:0016740 GO:0033384 GO:0033386 GO:0045337 GO:0046872
17	0.06	0.474	4.41	0.07	0.71	2ewgA	GO:0008299 GO:0016740 GO:0046872
18	0.06	0.413	4.60	0.05	0.63	4jyxA	GO:0008299 GO:0016740 GO:0036422

Consensus prediction of GO terms

Molecular Function	GO:0003824	GO:0043169
GO-Score	0.40	0.37
Biological Processes	GO:0006720	GO:0044249	GO:0008610
GO-Score	0.37	0.37	0.37
Cellular Component	GO:0044424
GO-Score	0.37

(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.