I-TASSER results

I-TASSER results for job id Rv2762c

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

Input Sequence in FASTA format

>protein (139 residues)
MSAATAAWDRRAAVVVGGVAEPGSAGPIAGADRKRLISRIQVRQLDSAAVAAKRRHLYYV
RPLDGHPVARVDRKTDRAADSLPVAGVLGELDIPPVTVAEGLAGELASMASWLGLGGIAV
STRGDLAGELCAATKRTNG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSAATAAWDRRAAVVVGGVAEPGSAGPIAGADRKRLISRIQVRQLDSAAVAAKRRHLYYVRPLDGHPVARVDRKTDRAADSLPVAGVLGELDIPPVTVAEGLAGELASMASWLGLGGIAVSTRGDLAGELCAATKRTNG
Prediction	CCCCCCCCHHHCCCCCCCCHCCCCCCCCHHHHHHHHHHHHCCEEEEEEHCCCCCEEEEEEEHCCCEEEEEEEHCCCCCCCEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCHHHHHHHHHHHCC
Conf.Score	9988777455444556664547888865566689999985965899986765445657898659967899985445679979999998769988689999999999999999899959985788756999999987569
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MSAATAAWDRRAAVVVGGVAEPGSAGPIAGADRKRLISRIQVRQLDSAAVAAKRRHLYYVRPLDGHPVARVDRKTDRAADSLPVAGVLGELDIPPVTVAEGLAGELASMASWLGLGGIAVSTRGDLAGELCAATKRTNG
Prediction	7552554464314213532442423430244525313440514301011245424300000014641102021335366330303402334615475115402510540052160650403634612440253156488
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCHHHCCCCCCCCHCCCCCCCCHHHHHHHHHHHHCCEEEEEEHCCCCCEEEEEEEHCCCEEEEEEEHCCCCCCCEEEEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEHCCCCCHHHHHHHHHHHCC
MSAATAAWDRRAAVVVGGVAEPGSAGPIAGADRKRLISRIQVRQLDSAAVAAKRRHLYYVRPLDGHPVARVDRKTDRAADSLPVAGVLGELDIPPVTVAEGLAGELASMASWLGLGGIAVSTRGDLAGELCAATKRTNG

3lodA

0.12

0.11

0.87

1.22

dPPAS

-------------NAMYTITDIAPTDAEFIALIAALDAWQETLDLSQLPPQT--VIALAIRSPQGEAVGCGAIVLS-EEGFGEMKRVYIDPQHRGQQLGEKLLAALEAKARQRDCHTLRLETGIHQ--HAAIALYTRNG

1yx0A

0.08

0.07

0.88

1.08

wdPPAS

IKIDDLTGRQVVSEHLHSMTLMSPPESIHALGLEKLRG-----------PEI----TFWSAWEGDELAGCGALKE--DTRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKRGYERLSLETGSMASFEPARKLYESFG

1z4eA

0.14

0.13

0.91

1.02

wMUSTER

VTEATEGDLEQMADDVLGRKRERYEKPLPVSYVRAFKEIK-----------KDKNNELIVACNGEEIVGMLQV-TYQGSWRATIEGVRTHSAARGQGIGSQLVCWAIERAKERGCHLIQLTTDKQ-ALRFYEQLASHEG

1yx0A

0.09

0.08

0.88

1.78

dPPAS2

MHIDDLTGRQVVSEHLHSMTLMSPPESIHALGLEKLRG-----------PEI----TFWSAWEGDELAGCGALKEL-DTRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKRGYERLSLETGSMASFEPARKLYESFG

2r1iA

0.12

0.11

0.92

1.20

dPPAS

PRRATPADAATVAQLHDFNTEFGAPTPGTDELASRLSHLLAGEDVVVLLAGEP---------PTGLAVLSFRPNVWYPGPVAILDELYVRPGRRGHRLGSALLAASCGLVRSRGGALLEINVDGE--DTDARRFYEARG

2dxqA

0.14

0.12

0.89

1.00

wMUSTER

IS---AAGPGDLPGLLELYQVLNPSDPEL--TTQEAGAVFAA--------LAQPGLTIFVATENGKPVATATL-TRAARPYAFIENVVTLEARRGRGYGRTVVRHAIETAFGANCYKVLLTGRHD-VHAFYESCQNKTG

3lodA

0.12

0.10

0.87

1.70

dPPAS2

-------------NAMYTITDIAPTDAEFIALIAALDAWQETLDLSQLPPQT--VIALAIRSPQGEAVGCGAIVLS-EEGFGEMKRVYIDPQHRGQQLGEKLLAALEAKARQRDCHTLRLETGIHQHAAIALYTRN--G

1yx0A

0.08

0.07

0.88

1.19

dPPAS

DDLTGRQVVSLVNEHLHSMTLMSPPESIHALGLEKLRG-----------PEI----TFWSAWEGDELAGCGALKEL-DTRHGEIKSMRTSASHLRKGVAKQVLQHIIEEAEKRGYERLSLETGSMASFEPARKLYESFG

1s5kA

0.11

0.10

0.89

1.00

wMUSTER

VPRGSQMNKTHLEHWRGLRKQLWPGHP-DDAHLADGEEIL-----------QADHLASFIAMADGVAIGFADASIRHDSPVVFLEGIFVLPSFRQRGVAKQLIAAVQRWGTNKGCREMASDTSPE---TISQKVHQALG

2r1iA

0.12

0.11

0.89

1.50

dPPAS2

PRRATPADAATVAQLHDFNTEFGAPTPGTDELASRLSHLLA--------GED-----VVVLLAGEPPTGLAVLSVWYPGPVAILDELYVRPGRRGHRLGSALLAASCGLVRSRGGALLEINVDGE--DTDARRFYEARG

(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=-1.37

Estimated TM-score = 0.54±0.15

Estimated RMSD = 7.5±4.3Å

Download Model 2

C-score=-3.92

Download Model 3

C-score=-3.44

Download Model 4

C-score=-3.13

Download Model 5

C-score=-2.00

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	2wpxA	0.738	2.42	0.109	0.892
2	3fixA	0.729	2.80	0.100	0.935
3	1qsmD	0.725	2.69	0.063	0.906
4	2vzzA	0.725	3.30	0.137	0.935
5	1z4eA	0.724	2.86	0.102	0.899
6	2r7hB	0.719	2.69	0.071	0.906
7	3g8wB	0.718	2.73	0.081	0.892
8	4e0aA	0.715	2.97	0.094	0.921
9	2q7bA	0.715	2.47	0.065	0.885
10	2fiaB	0.713	2.77	0.104	0.899

(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	0.36	25	1gheA	ACO	Rep, Mult	19,84,85,86,87,88,89,94,95,97,98,99,100,120,121,122,130,131,133,134,135,137
2	0.04	3	3n6hA	MG	Rep, Mult	72,90,121
3	0.01	1	3e25A	MG	Rep, Mult	72,76
4	0.01	1	1w0hA	MG	Rep, Mult	32,125
5	0.01	1	2dkiA	XE	Rep, Mult	45,60,67,68,82
6	0.01	1	1dxeA	MG	Rep, Mult	90,125
7	0.01	1	3zvwC	MG	Rep, Mult	62,63
8	0.01	1	3n1cA	F6P	Rep, Mult	53,54
9	0.01	1	1izcA	MG	Rep, Mult	46,72

	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	0.107	1qsmD	0.725	2.69	0.063	0.906	2.3.1.48	101
2	0.105	2cntD	0.702	2.23	0.121	0.835	2.3.1.128	113
3	0.086	1i1dD	0.682	3.33	0.080	0.885	2.3.1.4	NA
4	0.073	2vezA	0.663	3.27	0.090	0.863	2.3.1.4	NA
5	0.067	3d3sA	0.660	2.87	0.119	0.849	2.3.1.178	101
6	0.067	3igrA	0.702	3.30	0.092	0.921	2.3.1.128	119
7	0.067	2z11A	0.639	3.31	0.090	0.863	2.3.1.128	NA
8	0.060	2vqyA	0.680	3.41	0.094	0.899	2.3.1.82	NA
9	0.060	1fy7A	0.604	3.27	0.108	0.799	2.3.1.48	NA
10	0.060	2o28A	0.648	3.23	0.124	0.856	2.3.1.4	87
11	0.060	1q2yA	0.672	2.38	0.132	0.820	2.3.1.-	NA
12	0.060	1bobA	0.632	2.87	0.096	0.827	2.3.1.48	NA
13	0.060	1vhsA	0.669	3.17	0.120	0.892	2.3.1.183	NA
14	0.060	2r8vA	0.669	2.72	0.147	0.835	2.3.1.1	NA
15	0.060	2beiB	0.669	3.35	0.081	0.885	2.3.1.57	107
16	0.060	2jevB	0.679	3.30	0.087	0.906	2.3.1.57	NA
17	0.060	1yvoB	0.689	3.21	0.110	0.899	2.3.-.-	NA
18	0.060	2pq8A	0.599	3.14	0.100	0.784	2.3.1.48	NA
19	0.060	1yghA	0.655	2.83	0.050	0.856	2.3.1.48	NA
20	0.060	1z4rA	0.662	2.69	0.068	0.842	2.3.1.48	NA
21	0.060	2ou2A	0.586	2.90	0.109	0.791	2.3.1.48	NA
22	0.060	1iykA	0.681	3.25	0.063	0.914	2.3.1.97	NA
23	0.060	1nmtA	0.679	3.26	0.055	0.914	2.3.1.97	99
24	0.060	2rc4A	0.587	3.00	0.099	0.799	2.3.1.48,	NA
25	0.060	1cm0A	0.668	2.67	0.068	0.842	2.3.1.48	NA
26	0.060	1k4jA	0.569	3.28	0.094	0.763	2.3.1.184	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	0.25	0.710	2.95	0.17	0.91	2euiA	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0031248
1	0.21	0.701	3.21	0.14	0.93	2cy2A	GO:0008080 GO:0016740
2	0.18	0.636	3.37	0.10	0.84	1bo4A	GO:0008080 GO:0016740
3	0.17	0.650	2.59	0.14	0.80	1y9kB	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0031248
4	0.14	0.717	2.99	0.09	0.92	4e0aA	GO:0008080
5	0.14	0.738	2.56	0.11	0.90	2wpwA	GO:0008080 GO:0033050
6	0.13	0.718	2.51	0.07	0.90	3d8pB	GO:0008080
7	0.13	0.721	2.99	0.11	0.91	1gheB	GO:0008080 GO:0016740 GO:0016746
8	0.13	0.725	2.69	0.06	0.91	1qsmD	GO:0004402 GO:0008080 GO:0016568 GO:0016573 GO:0016740 GO:0016746 GO:0042802 GO:0042803 GO:0051289
9	0.13	0.735	2.80	0.10	0.94	3fixA	GO:0004145 GO:0008080 GO:0016740 GO:0016746 GO:0043939
10	0.13	0.706	3.16	0.12	0.93	2i79A	GO:0008080 GO:0016740
11	0.13	0.724	2.86	0.10	0.90	1z4eA	GO:0008080
12	0.12	0.702	3.20	0.09	0.91	4mbuA	GO:0008080 GO:0016740
13	0.12	0.693	2.92	0.07	0.89	1wwzA	GO:0008080
14	0.12	0.688	2.37	0.13	0.83	5isvA	GO:0005737 GO:0006474 GO:0008080 GO:0008999 GO:0016407 GO:0016740 GO:0016746
15	0.12	0.728	2.76	0.07	0.92	2r7hB	GO:0008080 GO:0016740
16	0.12	0.694	3.01	0.12	0.90	4yfjB	GO:0008080 GO:0016740
17	0.11	0.687	2.59	0.08	0.86	1yx0A	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0031248
18	0.11	0.683	2.79	0.13	0.85	4qusB	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0016747 GO:0031248
19	0.11	0.683	3.38	0.12	0.92	2fe7B	GO:0008080 GO:0016740
20	0.11	0.680	3.11	0.12	0.90	1vhsA	GO:0004596 GO:0006474 GO:0008080 GO:0009635 GO:0016740 GO:0016746 GO:0031248 GO:0046677
21	0.11	0.680	2.99	0.07	0.88	5f47B	GO:0008080
22	0.10	0.692	3.23	0.10	0.91	1yr0A	GO:0008080 GO:0016740
23	0.10	0.690	2.81	0.07	0.87	1b87A	GO:0008080
24	0.10	0.727	2.46	0.06	0.90	2q7bA	GO:0008080 GO:0016740
25	0.09	0.685	2.92	0.07	0.87	3ld2B	GO:0008080 GO:0016740
26	0.08	0.679	2.93	0.09	0.89	2q0yA	GO:0008080 GO:0016740 GO:0046872
27	0.08	0.631	2.61	0.12	0.79	2atrA	GO:0008080 GO:0016740
28	0.07	0.718	2.88	0.11	0.93	1tiqA	GO:0004145 GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0030435 GO:0031248 GO:0043939
29	0.07	0.654	2.50	0.10	0.81	1yvkA	GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0031248
30	0.07	0.627	3.17	0.05	0.80	3t9yA	GO:0008080 GO:0016740

Consensus prediction of GO terms

Molecular Function	GO:0004596
GO-Score	0.38
Biological Processes	GO:0006474
GO-Score	0.38
Cellular Component	GO:0031248
GO-Score	0.38

(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.