I-TASSER results

I-TASSER results for job id Rv2891

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

Input Sequence in FASTA format

>protein (249 residues)
MAKSPARRCTAKVRRVLSRSVLILCWSLLGAAPAHADDSRLGWPLRPPPAVVRQFDAASP
NWNPGHRGVDLAGRPGQPVYAAGSATVVFAGLLAGRPVVSLAHPGGLRTSYEPVVAQVRV
GQPVSAPTVIGALAAGHPGCQAAACLHWGAMWGPASGANYVDPLGLLKSTPIRLKPLSSE
GRTLHYRQAEPVFVNEAAAGALAGAGHRKSPKQGVFRGAAQGGDIVARQPPGRWVCPSSA
GGPIGWHRQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MAKSPARRCTAKVRRVLSRSVLILCWSLLGAAPAHADDSRLGWPLRPPPAVVRQFDAASPNWNPGHRGVDLAGRPGQPVYAAGSATVVFAGLLAGRPVVSLAHPGGLRTSYEPVVAQVRVGQPVSAPTVIGALAAGHPGCQAAACLHWGAMWGPASGANYVDPLGLLKSTPIRLKPLSSEGRTLHYRQAEPVFVNEAAAGALAGAGHRKSPKQGVFRGAAQGGDIVARQPPGRWVCPSSAGGPIGWHRQ
Prediction	CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCCCCCCCCCEHCCCCCCCEEEHCCCCEEEEEEEHCCCCEEEEEHCCCEEEEEEHCCCCCCCCEEEHCCEEEEEHCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCC
Conf.Score	998874554444555566777777764567777778888766668998757668899999887888866568899965897689799996765899789999699689998754689999889958878999779999988887656899988988888788577656678656788887654455544554455555556677766677665666666677654456788876454567888887789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MAKSPARRCTAKVRRVLSRSVLILCWSLLGAAPAHADDSRLGWPLRPPPAVVRQFDAASPNWNPGHRGVDLAGRPGQPVYAAGSATVVFAGLLAGRPVVSLAHPGGLRTSYEPVVAQVRVGQPVSAPTVIGALAAGHPGCQAAACLHWGAMWGPASGANYVDPLGLLKSTPIRLKPLSSEGRTLHYRQAEPVFVNEAAAGALAGAGHRKSPKQGVFRGAAQGGDIVARQPPGRWVCPSSAGGPIGWHRQ
Prediction	754435653334033003210121011123333343454300120434330112133344331423310102034311030254430000034342100102154132013030354054444054323103036223120000000000122444543101003105744020212447645434441552436554444444444443445453654442343225346242121433424431458
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEHCCCCCCCCCCCCCCCCEHCCCCCCCEEEHCCCCEEEEEEEHCCCCEEEEEHCCCEEEEEEHCCCCCCCCEEEHCCEEEEEHCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEHCCCCCCCCCCCC
MAKSPARRCTAKVRRVLSRSVLILCWSLLGAAPAHADDSRLGWPLRPPPAVVRQFDAASPNWNPGHRGVDLAGRPGQPVYAAGSATVVFAGLLAGRPVVSLAHPGGLRTSYEPVVAQVRVGQPVSAPTVIGALAAGHPGCQAAACLHWGAMWGPASGANYVDPLGLLKSTPIRLKPLSSEGRTLHYRQAEPVFVNEAAAGALAGAGHRKSPKQGVFRGAAQGGDIVARQPPGRWVCPSSAGGPIGWHRQ

4lxcA

0.23

0.20

0.84

2.28

MUSTER

---------------------------------AATHEHSAQW----LNNYKKGYGYGPYPLGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSYGGNQIGLIENDGHRQWYMHLSKNVKVGDYVKAGQIIGWS--GSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTPNTDIITRTTGPFRSMPQSGVLKAGQTHYDEVMKQDGHVWVGYTGNSGQRTWNKS

4lxcA

0.22

0.19

0.84

2.75

wMUSTER

-------------------------------------ATHEHSAQW-LNNYKKGYGYGPYPLGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSYGGGQIGLIENDGHRQWYMHLSKNVKVGDYVKAGQIIGWS--GSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTPNTDIITRTTGPFRSMPQSGVLKAGQTHYDEVMKQDGHVWVGYTGNSGQRTWNKS

2hsiB2

0.22

0.13

0.58

3.48

dPPAS

---------LPEDLKRIERELAEQTAAYRRFSPGLPSNLMLDKPVDGP--LSSPFG--------PHSGLDFAVPAGTPIKAPAAGKVILIGDYFFNGTVFVDHGQGFISMFCHLSIDVKLGQQVPRGGVLGKV--GATGRATGPHMHWNVSLNDAR----VDPAIFIGAF-------------------------------------------------------------------------------

4lxcA

0.21

0.18

0.84

4.71

wdPPAS

------------------------------------AATHEHSAQW-LNNYKKGYGYGPYPLGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNGGGQIGLIENDGHRQWYMHLSKNVKVGDYVKAGQIIGWS--GSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDG-WVGYTGNSGQRNKSTN

2hsiB2

0.22

0.13

0.58

4.90

wdPPAS

---------LPEDLKRIERELAEQTAAYRRFSPGLPSNLMLDKPVDGP--LSSPFG--------PHSGLDFAVPAGTPIKAPAAGKVILIGDYFFNGTVFVDHGQGFISMFCHLSKDVKLGQQVPRGGVLGKV--GATGRATGPHMHWNVSLNDAR----VDPAIFIGAF-------------------------------------------------------------------------------

4lxcA

0.22

0.18

0.84

4.29

Env-PPAS

---------------------------------------AATHEHSALNNYKKGYGYGPYPNGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNGGNQIGLIENDGHRQWYMHLSYNVKVGDYVKAGQIIGWS--GSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNASFTPNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHWVGYTGNSGQRIWNKS

2hsiB2

0.21

0.12

0.58

3.69

wPPAS

---------LPEDLKRIERELAEQTAAYRRFSPGLPSNLMLDKPVDG--PLSSPFG--------PHSGLDFAVPAGTPIKAPAAGKVILIGDYFFNGTVFVDHGQGFISMFCHLSKDVKLGQQVPRGGVLGKV--GATGRATGPHMHWNVSLNDAR----VDPAIFIGAF-------------------------------------------------------------------------------

4lxcA

0.22

0.19

0.84

3.01

dPPAS

---------------------------------AATHEHSAQW----LNNYKKGYGYGPYPNGGMHYGVDFFMNIGTPVKAISSGKIVEAGWSNYGGQIGLIENDGHRQWYMHLSYNVKVGDYVKAGQIIGWS--GSTGYSTAPHLHFQRMVNSFSNSTAQDPMPFLKSAGYGKAGGTVTPTPNTGWKTNKYGTNTDIITRTTGPFRSMPQSGVLKAGQTIHYDEVMKQDGHVWVGYTGNSGQRTWNKS

2hsiB2

0.22

0.13

0.58

5.13

dPPAS2

---------LPEDLKRIERELAEQTAAYRRFSPGLPSNLMLDKPVDGP--LSSPFG--------PHSGLDFAVPAGTPIKAPAAGKVILIGDYFFNGTVFVDHGQGFISMFCHLSIDVKLGQQVPRGGVLGKV--GATGRATGPHMHWNVSLNDAR----VDPAIFIGAF-------------------------------------------------------------------------------

4bh5A

0.23

0.12

0.51

3.06

PPAS

--------------------------------GLGAPRGQAFWPVRG--PTLHRYGEQLQG-ELRWKGMVIGASEGTEVKAIADGRVILADWLQGYGVVVVEHGKGDMSLYGYNQSLVSVGSQVRAGQPIALV--GSSGGQGRPSLYFEIRRQGQA----VNPQPWLGR--------------------------------------------------------------------------------

(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=-0.00

Estimated TM-score = 0.71±0.11

Estimated RMSD = 5.8±3.6Å

Download Model 2

C-score=-1.66

Download Model 3

C-score=-0.01

Download Model 4

C-score=-4.52

Download Model 5

C-score=-5.00

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	4lxcA	0.714	2.68	0.224	0.823
2	2hsiB	0.534	1.93	0.188	0.582
3	2gu1A	0.511	3.27	0.160	0.615
4	1qwyA	0.502	3.03	0.196	0.590
5	3nyyA	0.462	3.42	0.136	0.562
6	4rnyA	0.455	4.28	0.165	0.582
7	3tufB	0.454	2.39	0.219	0.514
8	3sluA	0.450	3.70	0.176	0.546
9	4bh5A	0.445	2.28	0.234	0.494
10	3it7A	0.444	3.47	0.217	0.546

(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	0.56	16	5j1lC	ZN	Rep, Mult	66,70,147
2	0.03	1	1qwyA	ZN	Rep, Mult	5,66,70,147
3	0.02	1	2e26A	UUU	Rep, Mult	88,90,91,120
4	0.02	1	1piiA	PO4	Rep, Mult	73,76,78,132,133
5	0.02	1	5j1lA	ZN	Rep, Mult	70,113,145,147

	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	0.255	2b44A	0.451	2.16	0.248	0.502	3.4.24.75	90,139
2	0.060	2gprA	0.384	4.01	0.096	0.494	2.7.1.69	147,149
3	0.060	2ok5A	0.371	6.18	0.038	0.647	3.4.21.47	NA
4	0.060	2q2eB	0.371	6.25	0.038	0.671	5.99.1.3	75
5	0.060	1piiA	0.389	6.37	0.081	0.687	4.1.1.48,5.3.1.24	NA
6	0.060	1rtkA	0.314	6.50	0.040	0.586	3.4.21.47	NA
7	0.060	1jxaA	0.294	6.57	0.045	0.542	2.6.1.16	NA
8	0.060	3ixzA	0.386	6.14	0.061	0.667	3.6.3.10	NA
9	0.060	3lxuX	0.410	5.96	0.081	0.699	3.4.14.10	93
10	0.060	2pplA	0.375	6.26	0.043	0.675	3.1.1.3	NA
11	0.060	1gytJ	0.377	5.60	0.065	0.602	3.4.11.1	98,158
12	0.060	2pffA	0.399	6.48	0.075	0.743	2.3.1.41,2.3.1.86	NA
13	0.060	2pffD	0.400	6.48	0.030	0.739	2.3.1.86	73
14	0.060	1ei1A	0.373	5.82	0.050	0.623	5.99.1.3	NA
15	0.060	1rs0A	0.310	6.01	0.018	0.534	3.4.21.47	NA
16	0.060	1m7xB	0.369	6.41	0.039	0.671	2.4.1.18	70
17	0.060	1glaF	0.379	4.09	0.098	0.486	2.7.1.69	NA
18	0.060	1jcmP	0.288	6.40	0.065	0.514	4.1.1.48,5.3.1.24	NA
19	0.060	1lf6A	0.385	5.95	0.055	0.647	3.2.1.3	NA
20	0.060	1rp1A	0.366	6.51	0.052	0.683	3.1.1.3	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	0.31	0.714	2.68	0.22	0.82	4lxcA	GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0071555
1	0.29	0.511	3.27	0.16	0.61	2gu1A	GO:0046872
2	0.26	0.534	1.93	0.19	0.58	2hsiB	GO:0046872
3	0.17	0.454	2.39	0.22	0.51	3tufB	GO:0016020 GO:0016021 GO:0030435 GO:0042601
4	0.16	0.435	3.76	0.20	0.55	3it5A	GO:0004175 GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872
5	0.11	0.445	2.28	0.23	0.49	4bh5A	GO:0000920 GO:0001896 GO:0005886 GO:0007049 GO:0009273 GO:0016787 GO:0030288 GO:0032153 GO:0042493 GO:0042597 GO:0051301 GO:0051345
6	0.07	0.502	3.03	0.20	0.59	1qwyA	GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872 GO:0071555
7	0.06	0.296	6.69	0.03	0.55	4bbjA	GO:0000166 GO:0005886 GO:0006812 GO:0016020 GO:0016021 GO:0016787 GO:0019829 GO:0046872 GO:0098655
8	0.06	0.281	6.03	0.04	0.49	4dk0A	GO:0016020 GO:0042802 GO:0055085
9	0.06	0.259	6.59	0.04	0.48	1bzlA	GO:0005737 GO:0015036 GO:0015042 GO:0016491 GO:0016668 GO:0045454 GO:0050660 GO:0055114
10	0.06	0.264	6.02	0.06	0.45	4yaiA	GO:0016491 GO:0055114
11	0.06	0.455	4.28	0.17	0.58	4rnyA	GO:0016020 GO:0016021 GO:0046872
12	0.06	0.469	3.51	0.13	0.57	3nyyA	GO:0016020 GO:0016021
13	0.06	0.231	5.87	0.04	0.39	4h67C	GO:0009228 GO:0009229
14	0.06	0.228	6.62	0.06	0.41	4h65B	GO:0009228 GO:0009229
15	0.06	0.240	5.99	0.07	0.41	3rysA	GO:0000034 GO:0006146 GO:0008270 GO:0009117 GO:0016787 GO:0019239 GO:0043103 GO:0046872
16	0.06	0.464	3.59	0.17	0.57	3sluB	GO:0016020 GO:0016021
17	0.06	0.213	5.90	0.06	0.36	1c41A	GO:0000906 GO:0009231 GO:0009349 GO:0016740 GO:1902444
18	0.06	0.245	3.79	0.11	0.32	2mk5A	GO:0008745 GO:0009253 GO:0044659 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0046872	GO:0008237
GO-Score	0.70	0.42
Biological Processes	GO:0006508	GO:0043934	GO:0048646	GO:0030154	GO:0071555	GO:0051704
GO-Score	0.42	0.33	0.33	0.33	0.31	0.31
Cellular Component	GO:0005576	GO:0042763
GO-Score	0.42	0.33

(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.