I-TASSER results

I-TASSER results for job id Rv2728c

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

Input Sequence in FASTA format

>protein (231 residues)
MLSAIGIVPSAPVLVPELAGAAAAELADLGAAVIAAASLLPKSWIAVGTGRADDVVRPTD
VGTFAGFGADVRVGLAPQDGDGVAVPVELPLCALLTAWVRGQARPEARAQVHVYASDHGS
DAAVARGRQLRADIDREPDPIGVLVVADGLNTLTPRAPGGYDPDGAGMQRALDDALASGD
LAVLTRLPAQVLGRVAFQVLAGLAEPGPRSAKEFYRGAPHGVGYFAGVWQP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MLSAIGIVPSAPVLVPELAGAAAAELADLGAAVIAAASLLPKSWIAVGTGRADDVVRPTDVGTFAGFGADVRVGLAPQDGDGVAVPVELPLCALLTAWVRGQARPEARAQVHVYASDHGSDAAVARGRQLRADIDREPDPIGVLVVADGLNTLTPRAPGGYDPDGAGMQRALDDALASGDLAVLTRLPAQVLGRVAFQVLAGLAEPGPRSAKEFYRGAPHGVGYFAGVWQP
Prediction	CCEEEEHCCCCCEEHCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCEEEEEHCCCCCEEEEEEEHCC
Conf.Score	956999958997354445787578999999999999998899589996689887777878875344799768875777776677777887688889999887666788699986789999999999999999998769988999986777788999999999854999999999999799889986998886668899999986678874788875798865789999859
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MLSAIGIVPSAPVLVPELAGAAAAELADLGAAVIAAASLLPKSWIAVGTGRADDVVRPTDVGTFAGFGADVRVGLAPQDGDGVAVPVELPLCALLTAWVRGQARPEARAQVHVYASDHGSDAAVARGRQLRADIDREPDPIGVLVVADGLNTLTPRAPGGYDPDGAGMQRALDDALASGDLAVLTRLPAQVLGRVAFQVLAGLAEPGPRSAKEFYRGAPHGVGYFAGVWQP
Prediction	410000000200000011044426404401500340054026200000003232424562302023130413031445446545453402000000110144134514130202247132630240043025316647420000000000231376132223650450152015006623163026034610431002000000444625141114500000000003038
	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                 180                 200                 220

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCEEEEHCCCCCEEHCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEHCCCCCCCCCCCCCCCCCCCCCCEEEEHCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCEEEEEHCCCCCEEEEEEEHCC
MLSAIGIVPSAPVLVPELAGAAAAELADLGAAVIAAASLLPKSWIAVGTGRADDVVRPTDVGTFAGFGADVRVGLAPQDGDGVAVPVELPLCALLTAWVRGQARPEARAQVHVYASDHGSDAAVARGRQLRADIDREPDPIGVLVVADGLNTLTPRAPGGYDPDGAGMQRALDDALASGDLAVLTRLPAQVLGRVAFQVLAGLAEPGPRSAKEFYRGAPHGVGYFAGVWQP

5heeA

0.17

0.16

0.96

2.22

MUSTER

MLFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWLGFEGVELPGEWEFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.18

0.17

0.96

2.54

dPPAS

MLFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWLGFEGVEPTVDLHFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.18

0.17

0.96

3.68

wdPPAS

MLFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISDHAQHLISWLGFEIP-TVDLHFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.17

0.16

0.95

2.62

wMUSTER

-LFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWL-GFELPGEWETDFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.17

0.16

0.96

3.87

wPPAS

MLFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWL-GFELPGEWETDFASRSGRYSRWPLTWGELIPLQFLE----KKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.18

0.17

0.96

9.13

dPPAS2

MLFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWLGFEGVEPTVDLHFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.17

0.16

0.96

3.16

PPAS

MLFGIGLMPHNPALSPE-----DKETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWLGFEGVELPGEWEFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

5heeA

0.17

0.16

0.96

4.03

Env-PPAS

MLFGIGLMPHNPALSPED-----KETEKLAGVLKDIGKAFADSYVLISPHNVRISMAQHLISWLGFEGVELPGEWEFASRSGRYSRWPLTWGELIPLQFL----EKKPLVLLTPARRLSRETLIKAGEVLGEVLEGSEKKIALIVSADHGHAHDENGPYGYRKESEEYDRLIMELINESRLEELPEIPALPDSYWQMLIMLGAMHRVPVKLVESAYACPTYFGMAGALWVR

3vsgA

0.14

0.13

0.98

1.81

MUSTER

TVVSAFLVPGTPLPQ----KPEVPSWGQLAAATERAGKALPDVVLVYSTQDQQWLTRPRSEGNWYEFGLAYDIRADTAARGVNYDGFPIDTGTITACTLMGIGTDAFPLVVGSNNLYHSGEITEKLAALAVDCAKDQNKRVAVVGVGGLSGSLFREEIDIANEEDDKWNRRVLKLIEAGDVSALREAMRVDMGFKHLHWILGALKGKFSGANVLGYGPSYGSGAAVIEFRL

3vsgA

0.12

0.99

1.96

dPPAS

TVVSAFLVPGTPLPQ--LKPEVGQLAAATERAGKALAASRPDVVLVYSTQTRPRSEGVHVDENWYEFGLAYDIRAGVHARGVNYDGFPIDTGTITACTLMGIGTDAFPLVVGSNNLYHSGEITEKLAALAVDCAKDQNKRVAVVGVGGLSGSLFREEDRIANEEDDKWNRRVLKLIEAGDVSALREAMRVDMGFKHLHWILGALKGKFSGANVLGYGPSYGSGAAVIEFRL

(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 3 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=0.83

Estimated TM-score = 0.83±0.08

Estimated RMSD = 4.0±2.7Å

Download Model 2

C-score=-2.19

Download Model 3

C-score=-2.65

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	5heeA	0.910	1.61	0.139	0.965
2	3vsgB	0.806	3.07	0.096	0.974
3	3vsgA	0.805	2.93	0.136	0.965
4	3wkuA	0.780	3.33	0.102	0.957
5	1bouB	0.775	3.21	0.098	0.952
6	3bczA	0.690	3.75	0.106	0.879
7	2pw6A	0.683	3.44	0.099	0.853
8	3b55A	0.479	4.67	0.056	0.688
9	2qgmA	0.476	4.70	0.037	0.688
10	3nvaA1	0.473	4.59	0.067	0.697

(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	0.12	3	5heeA	ZN	Rep, Mult	10,50,193
2	0.11	3	1b4uB	DHB	Rep, Mult	10,12,51,91,151,193,220,221,222
3	0.04	1	2yc5A	CU	Rep, Mult	42,70
4	0.04	1	3pyrI	MG	Rep, Mult	184,187
5	0.04	1	4awzA	MG	Rep, Mult	151,156
6	0.04	1	3mk0A	NPO	Rep, Mult	130,199,203,206
7	0.04	1	3k7tB	GP7	Rep, Mult	18,20,23
8	0.04	1	1zedA	PNP	Rep, Mult	168,172,176,192,193,196,197,200
9	0.04	1	2ch6D	GLC	Rep, Mult	145,149,151,158,160,162

	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	0.104	1bouB	0.775	3.21	0.098	0.952	1.13.11.8	NA
2	0.104	1b4uB	0.775	3.31	0.097	0.957	1.13.11.8	NA
3	0.060	2vz9B	0.441	5.65	0.069	0.740	2.3.1.85	NA
4	0.060	2aebA	0.447	5.27	0.094	0.710	3.5.3.1	NA
5	0.060	1vcnA	0.461	4.72	0.076	0.680	6.3.4.2	NA
6	0.060	2fknB	0.450	4.92	0.058	0.671	4.2.1.49	45,62
7	0.060	1alkA	0.463	5.32	0.064	0.732	3.1.3.1	28,218
8	0.060	3e2dA	0.456	5.44	0.065	0.727	3.1.3.1	194
9	0.060	1e1eB	0.420	5.06	0.066	0.636	3.2.1.21	151
10	0.060	1zedA	0.460	5.34	0.080	0.727	3.1.3.1	NA
11	0.060	1cevA	0.444	5.13	0.090	0.680	3.5.3.1	NA
12	0.060	1cz1A	0.439	5.78	0.055	0.727	3.2.1.58	17
13	0.060	2e3zA	0.453	5.49	0.074	0.736	3.2.1.21	NA
14	0.060	2w5vA	0.453	5.35	0.055	0.727	3.1.3.1	NA
15	0.060	3igyB	0.443	5.42	0.090	0.710	5.4.2.1	NA
16	0.060	1myrA	0.458	5.67	0.063	0.762	3.2.1.147	NA
17	0.060	2gftB	0.458	5.30	0.059	0.719	3.2.1.89	NA
18	0.060	1hqfA	0.447	5.27	0.084	0.710	3.5.3.1	NA
19	0.060	2vz8A	0.441	5.77	0.064	0.749	2.3.1.85	225
20	0.060	2pw6A	0.683	3.44	0.099	0.853	1.13.-.-	NA
21	0.060	1s1mB	0.461	4.65	0.075	0.680	6.3.4.2	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	0.23	0.805	2.93	0.14	0.97	3vsgA	GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0055114
1	0.22	0.806	3.07	0.10	0.97	3vsgB	GO:0006725 GO:0008198 GO:0016491 GO:0019439 GO:0046872 GO:0051213 GO:0055114
2	0.16	0.788	3.01	0.10	0.95	3wr9A	GO:0006725 GO:0008198 GO:0016491 GO:0046872 GO:0051213 GO:0055114
3	0.15	0.775	3.31	0.10	0.96	1b4uB	GO:0006725 GO:0008198 GO:0016491 GO:0018579 GO:0019439 GO:0051213 GO:0055114
4	0.13	0.712	3.48	0.09	0.89	2pw6A	GO:0005737 GO:0005886 GO:0006725 GO:0008198 GO:0008270 GO:0016491 GO:0016701 GO:0046872 GO:0050297 GO:0051213 GO:0055114
5	0.06	0.400	5.29	0.06	0.61	2wskA	GO:0003824 GO:0004133 GO:0004135 GO:0004553 GO:0005975 GO:0005977 GO:0005980 GO:0006974 GO:0008152 GO:0016787 GO:0016798
6	0.06	0.391	5.92	0.06	0.68	4ymzA	GO:0003824 GO:0004807 GO:0005737 GO:0005829 GO:0006094 GO:0006096 GO:0006098 GO:0008152 GO:0016853 GO:0019563 GO:0046166
7	0.06	0.366	5.21	0.10	0.58	3pl1A	GO:0003824 GO:0005506 GO:0006769 GO:0008152 GO:0008936 GO:0016787 GO:0016811 GO:0016999 GO:0030145 GO:0034355 GO:0046872
8	0.06	0.365	5.17	0.07	0.57	2c44C	GO:0003824 GO:0005737 GO:0005829 GO:0006520 GO:0006568 GO:0006569 GO:0009034 GO:0009072 GO:0016020 GO:0016829 GO:0016830 GO:0030170 GO:0030955 GO:0042802 GO:0060187 GO:0080146
9	0.06	0.361	5.92	0.05	0.63	4qoyC	GO:0003824 GO:0004739 GO:0008152 GO:0016491 GO:0055114
10	0.06	0.356	5.02	0.06	0.53	3io5B	GO:0000166 GO:0003677 GO:0003697 GO:0005524 GO:0006259 GO:0006260 GO:0006281 GO:0006310 GO:0006974 GO:0008094
11	0.06	0.404	4.97	0.10	0.61	4fn4A	GO:0000166 GO:0016491 GO:0055114
12	0.06	0.337	4.86	0.03	0.52	5cxkA	GO:0004089 GO:0008270 GO:0015976 GO:0016829
13	0.06	0.328	5.71	0.07	0.55	2qmmA	GO:0005737 GO:0008033 GO:0008168 GO:0008175 GO:0008757 GO:0016740 GO:0030488 GO:0032259
14	0.06	0.312	6.02	0.10	0.53	3w6zA	GO:0000166 GO:0004616 GO:0016491 GO:0051287 GO:0055114
15	0.06	0.300	5.81	0.03	0.52	4up2D	GO:0003824 GO:0006520 GO:0006568 GO:0006569 GO:0009034 GO:0009072 GO:0016829 GO:0016830
16	0.06	0.314	6.64	0.04	0.59	4w1yB	GO:0003824 GO:0005737 GO:0005829 GO:0006520 GO:0006568 GO:0006569 GO:0009034 GO:0009072 GO:0016020 GO:0016829 GO:0016830 GO:0030170 GO:0030955 GO:0042802 GO:0060187 GO:0080146
17	0.06	0.304	5.46	0.09	0.51	2r77A	GO:0008429 GO:0016301 GO:0016310 GO:0019887 GO:0045859
18	0.06	0.268	6.27	0.05	0.49	4chlB	GO:0005506 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005759 GO:0006749 GO:0016491 GO:0046872 GO:0050313 GO:0051213 GO:0055114 GO:0070221 GO:0070813
19	0.06	0.322	4.95	0.09	0.48	5butA	GO:0005886 GO:0006810 GO:0006811 GO:0006813 GO:0008324 GO:0016020 GO:0098655

Consensus prediction of GO terms

Molecular Function	GO:0008198	GO:0016702
GO-Score	0.63	0.30
Biological Processes	GO:0055114	GO:0019439
GO-Score	0.63	0.49
Cellular Component	GO:0005737	GO:0005886
GO-Score	0.13	0.13

(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.