I-TASSER results

I-TASSER results for job id Rv2418c

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

Input Sequence in FASTA format

>protein (247 residues)
MSSRRGRRPALLVFADSLAYYGPTGGLPADDPRIWPNIVASQLDWDLELIGRIGWTCRDV
WWAATQDPRAWAALPRAGAVIFATGGMDSLPSVLPTALRELIRYVRPSWLRRWVRDGYAW
VQPRLSPVARAALPPHLTAEYLEKTRGAIDFNRPGIPIIASLPSVHIAETYGKAHHGRAG
TVAAITEWAQHHDIPLVDLKAAVAEQILSGYGNRDGIHWNFEAHQAVAELMLKALAEAGV
PNEKSRG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MSSRRGRRPALLVFADSLAYYGPTGGLPADDPRIWPNIVASQLDWDLELIGRIGWTCRDVWWAATQDPRAWAALPRAGAVIFATGGMDSLPSVLPTALRELIRYVRPSWLRRWVRDGYAWVQPRLSPVARAALPPHLTAEYLEKTRGAIDFNRPGIPIIASLPSVHIAETYGKAHHGRAGTVAAITEWAQHHDIPLVDLKAAVAEQILSGYGNRDGIHWNFEAHQAVAELMLKALAEAGVPNEKSRG
Prediction	CCCCCCCCCEEEEEHCCCCHCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEEHCCCHHHHHHHHHCCCCCCEHCCCCCEEEEEHCCCCCCCCCCHHHHHHHCHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
Conf.Score	9877888877999975543437999999989987788999987996799987677445778887679854455467778999976888899866689998674358899999999999998777765467789964549999999999999888998899857765664457767896789999999999979988866888888875578998876777899999999999999997788777889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MSSRRGRRPALLVFADSLAYYGPTGGLPADDPRIWPNIVASQLDWDLELIGRIGWTCRDVWWAATQDPRAWAALPRAGAVIFATGGMDSLPSVLPTALRELIRYVRPSWLRRWVRDGYAWVQPRLSPVARAALPPHLTAEYLEKTRGAIDFNRPGIPIIASLPSVHIAETYGKAHHGRAGTVAAITEWAQHHDIPLVDLKAAVAEQILSGYGNRDGIHWNFEAHQAVAELMLKALAEAGVPNEKSRG
Prediction	8656646310000001100121272423374340013100541624030002121103100100153141013044040000000213312231131025203303164024103500320132025224421214000400440350054132600000002121305312403533440341034006636011020341035203545221100010140042005101510452424466678
	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

CCCCCCCCCEEEEEHCCCCHCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEEHCCCHHHHHHHHHCCCCCCEHCCCCCEEEEEHCCCCCCCCCCHHHHHHHCHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCHHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
MSSRRGRRPALLVFADSLAYYGPTGGLPADDPRIWPNIVASQLDWDLELIGRIGWTCRDVWWAATQDPRAWAALPRAGAVIFATGGMDSLPSVLPTALRELIRYVRPSWLRRWVRDGYAWVQPRLSPVARAALPPHLTAEYLEKTRGAIDFNRPGIPIIASLPSVHIAETYGKAHHGRAGTVAAITEWAQHHDIPLVDLKAAVAEQILSGYGNRDGIHWNFEAHQAVAELMLKALAEAGVPNEKSRG

3w7vA

0.19

0.15

0.83

1.33

MUSTER

MKIGSG--EKLLFIGDSITDCGRARPEGEGSGTGYVAYVVGLLQIRVVNKGISGNTVRDLKARWEED----VIAQKPDWVSIMIGINDVWRQYDLPFMKEKH------------------------------VYLDEYEATLRSLVLETKPLVKG--IILMTPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYLAWDRVHPSVAGHMILARAFLREIG---FEWVRSR-

1dexA

0.17

0.15

0.88

1.17

dPPAS

--------TTVYLAGDSTM----AKNGGGSGTNGWGEYLASYLSATVVNDAVAGRSARSYTREGRFE-NIADVVTAGDYVIVEFGHNDGG-SLSTDNGRTDCSGTGAEVC--------------YSVYDGVNETILTFPAYLENAAKLFTAK--GAKVILSSQTPNNPWETGTFVNSPTRFVEYAELAAEVAGVEYVDHWSYVDSIYETLGFPIDHTHTSPAGAEVVAEAFLKAVVCTGTSTTSFEG

3w7vA

0.20

0.17

0.81

1.24

wdPPAS

MKIGSGE--KLLFIGDSITDCGPEGGSFGALGTGYVAYVVGLLQLGIRVVNKGGNTVRDLKARWEED----VIAQKPDWVSIMIG----------------------------INDVWRQYDLPFMKEKHVY------DEYEATLRSLVLETKPVKGIILMTPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLY--WDRVH-SVAGHMILARAFLREIG---FEWVRSR-

3w7vA

0.20

0.17

0.82

1.18

wMUSTER

IGSGE----KLLFIGDSITDCGPEGGSFGALGTGYVAYVVGLLQIRVVNKGISGNTVRDLKARWEED----VIAQKPDWVSIMIGINDVWRQYDLPFMKEKH--VYLDEYEATLRSLVLETKPL------------------------------VKGIILMTPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYLAWDRVHPSVAGHMILARAFLREIG---FEWVRSR-

4tx1A

0.21

0.17

0.77

1.12

wPPAS

M--------TVLCYGDSLTWYDATGSHALED-R-WPSVLQKALGSDAHVIAEGGRTT--AYNGARVLPTVLHTHAPLDLIVFMLGSNDMKPII-AFGAVKGIERL--NLVRRHDWPTETEEGPEILIVSPPPLCETANSAFAAMFAGGVEQS--------------------------AMLAPLYRDLADELDCGFFDGGSVA-------RTTPDGVHLDAENTRAVGRGLEPVVRMM--------G

3w7vA

0.18

0.15

0.83

1.75

dPPAS2

MKIGSGE--KLLFIGDSIRARPEGEGSFGALGTGYVAYVVGLLQLGIRVVNKGGNTVRDLKARWEED----VIAQKPDWVSIMIG----------------------------INDVWRQYDLPFMKEKHVY-----LDEYEATLRSLVLETKPLVKGIILMPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYPAWDRVHPSVAGHMILARAFLREIG---FEWVRSR-

4tx1A

0.20

0.16

0.81

1.17

PPAS

M--------TVLCYGDSLTWYDATGSGRHALEDRWPSVLQKALGSDAHVIAEGGRTTAYDDNGARVLPTVLHTHAPLDLIVFMLGSNDMKPII-----------GTAFGAVKGIERLVNLVRRHDWPTETEEGPEILIVS-------------P--PPLCETANSAFAAMFAGGVEQSAMLAPLYRDLADELDCGFFDGGSV------ARTTPIDGVHLDAENTRAVGRGLEPVVRMM--------G

3w7vA

0.18

0.15

0.83

1.56

Env-PPAS

MKIGSGE--KLLFIGDSICGRARPEGEGSFGATGYVAYVVGLLQLGIRVVNKGGNTVRDLKARWEED----VIAQKPDWVSIMIGINDVW-RQYDLPFMKE-KHVYLDEYEATLRSLVLETKPL------------------------------VKGIILMTPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYPAWDRVHPSVAGHMILARAFLREIG---FEWVRSR-

1yzfA

0.17

0.13

0.75

1.29

MUSTER

MR-------KIVLFGDSITAGYLDEAVSP----VLVDLVKRDIAVAVINAGMPGDTTEDGLKRLNKE----VLIEKPDEVVIFFGANDAS--------------------------------------LDRNITVATFRENLETMIHEIGSEK----VILITPPYADSGRRPERPQTRKELVKVAQEVGAAHNLPVIDLYKAMTVY-TDEFLQADGLHFSQVGYELLGALIVREIKGRLKPKQA---

3w7vA

0.18

0.15

0.83

1.16

dPPAS

MKIGSGE--KLLFIGDSIRARPEGEGSFGALGTGYVAYVVGLLQLGIRVVNKGGNTVRDLKARWEED----VIAQKPDWVSIMIG----------------------------INDVWRQYDLPFMKEKHVY-----LDEYEATLRSLVLETKPLVKGIILMPFYIEGNEQDPMRRTMDQYGRVVKQIAEETNSLFVDTQAAFNEVLKTLYPAWDRVHPSVAGHMILARAFLREIG---FEWVRSR-

(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=-1.41

Estimated TM-score = 0.54±0.15

Estimated RMSD = 8.9±4.6Å

Download Model 2

C-score=-3.43

Download Model 3

C-score=-3.76

Download Model 4

C-score=-1.47

Download Model 5

C-score=-4.09

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	3w7vA	0.733	2.44	0.166	0.830
2	5jd3A	0.726	2.45	0.163	0.822
3	3rjtA	0.690	2.36	0.161	0.777
4	4q9aA	0.683	2.56	0.113	0.781
5	1escA	0.667	3.72	0.128	0.850
6	3kvnX	0.652	3.63	0.129	0.826
7	3milA	0.645	3.01	0.140	0.757
8	4q7qA	0.640	3.35	0.138	0.781
9	4hyqA	0.638	3.50	0.100	0.789
10	1dexA	0.634	3.70	0.159	0.793

(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	0.25	13	3dt9A	GD7	Rep, Mult	16,17,86,87,217,218
2	0.04	2	3bqmB	BQM	Rep, Mult	11,35,39,46,81,157,159,160,161,195,196,197,198,232
3	0.04	2	2hsjA	MG	Rep, Mult	189,192,194
4	0.04	2	4aljF	GLU	Rep, Mult	9,78,157,194,235
5	0.02	1	3lsjA	COA	Rep, Mult	218,219,224
6	0.02	1	3dc7C	NA	Rep, Mult	194,195,196,233
7	0.02	1	3anvA	2RA	Rep, Mult	22,218
8	0.02	1	1xp3A	ZN	Rep, Mult	166,215,218
9	0.02	1	1y10C	CA	Rep, Mult	212,215
10	0.02	1	1r3nA	BIB	Rep, Mult	175,213

	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	0.154	2q0sH	0.593	3.35	0.122	0.721	3.1.1.2	218
2	0.090	1ivnA	0.573	3.32	0.189	0.709	3.1.1.5,	17,218
3	0.067	1bwpA	0.577	3.28	0.100	0.700	3.1.1.47	17,86,215,218
4	0.067	1vyhA	0.576	3.30	0.124	0.700	3.1.1.47	17,215,218
5	0.060	1a4uB	0.538	4.11	0.091	0.717	1.1.1.1	85,142,159
6	0.060	1ahiA	0.540	4.52	0.097	0.737	1.1.1.159	144
7	0.060	3gr6D	0.538	4.59	0.049	0.741	1.3.1.9	NA
8	0.060	3kvnX	0.652	3.63	0.129	0.826	3.1.1.1	18,85
9	0.060	1ae1B	0.538	4.37	0.084	0.737	1.1.1.206	NA
10	0.060	1zemA	0.542	4.41	0.073	0.733	1.1.1.9	161
11	0.060	1pp4A	0.633	3.76	0.159	0.798	3.1.1.-	NA
12	0.060	1xg5C	0.542	4.49	0.091	0.765	1.-.-.-	164
13	0.060	1ipeA	0.540	4.49	0.068	0.745	1.1.1.236	NA
14	0.060	1aknA	0.537	4.61	0.075	0.769	3.1.1.13,3.1.1.3	NA
15	0.060	1deoA	0.632	3.60	0.159	0.789	3.1.1.-	17,215,218
16	0.060	1k2wA	0.542	4.24	0.058	0.729	1.1.1.14	164
17	0.060	1ahiB	0.542	4.42	0.098	0.737	1.1.1.159	85,225
18	0.060	2dtdA	0.537	4.47	0.093	0.733	1.1.1.118	164,174
19	0.060	2p91A	0.539	4.72	0.045	0.745	1.3.1.9	NA
20	0.060	2waaA	0.576	3.49	0.164	0.721	3.1.1.72	49,226,228
21	0.060	2vptA	0.577	3.00	0.162	0.684	3.1.1.72	218
22	0.060	2b4qA	0.539	4.41	0.089	0.741	1.1.1.100	NA
23	0.060	1h5qA	0.539	4.39	0.074	0.729	1.1.1.138	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	0.28	0.734	2.43	0.17	0.83	4jhlA	GO:0000272 GO:0005737 GO:0005975 GO:0016787 GO:0045493 GO:0046555 GO:0052689
1	0.23	0.690	2.36	0.16	0.78	3rjtA
2	0.15	0.583	2.87	0.17	0.69	3x0hA	GO:0004553 GO:0005576 GO:0005975 GO:0030248
3	0.14	0.591	2.77	0.16	0.69	4rshA	GO:0016020 GO:0016021
4	0.07	0.617	3.46	0.14	0.76	2o14A	GO:0016787
5	0.07	0.614	3.12	0.16	0.72	1yzfA	GO:0016787
6	0.07	0.615	3.45	0.15	0.76	3dc7A
7	0.07	0.601	3.24	0.15	0.72	4ppyA	GO:0016787
8	0.07	0.594	3.10	0.15	0.70	4hf7A	GO:0016787
9	0.07	0.612	3.28	0.13	0.74	1z8hA
10	0.07	0.573	3.32	0.19	0.71	1ivnA	GO:0004620 GO:0004622 GO:0006508 GO:0006629 GO:0008233 GO:0016290 GO:0016298 GO:0016787 GO:0030288 GO:0042597 GO:0042802 GO:0047617
11	0.07	0.572	3.30	0.15	0.68	3p94A
12	0.06	0.423	5.67	0.09	0.66	4zrxA	GO:0004560 GO:0005975
13	0.06	0.412	3.61	0.09	0.53	4m1sC	GO:0000165 GO:0000166 GO:0001934 GO:0002223 GO:0003924 GO:0005525 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0005925 GO:0007165 GO:0007173 GO:0007264 GO:0007265 GO:0007411 GO:0008284 GO:0008542 GO:0010628 GO:0016020 GO:0019002 GO:0019003 GO:0019221 GO:0021897 GO:0030036 GO:0030275 GO:0031234 GO:0031647 GO:0032228 GO:0032403 GO:0035022 GO:0035176 GO:0038002 GO:0038095 GO:0038128 GO:0043406 GO:0043524 GO:0045121 GO:0045596 GO:0048169 GO:0048873 GO:0050900 GO:0051000 GO:0051092 GO:0051146 GO:0051384 GO:0051385 GO:0060441
14	0.06	0.430	4.02	0.07	0.59	2mscB	GO:0000166 GO:0005525 GO:0005622 GO:0007165 GO:0007264 GO:0016020 GO:0046872
15	0.06	0.350	5.64	0.06	0.56	4e3qA	GO:0003824 GO:0008483 GO:0030170
16	0.06	0.318	6.07	0.04	0.55	1dk5A	GO:0005509 GO:0005544
17	0.06	0.287	6.41	0.04	0.52	2i99A	GO:0000122 GO:0003714 GO:0005634 GO:0005737 GO:0005739 GO:0005782 GO:0006554 GO:0007605 GO:0016491 GO:0042403 GO:0042562 GO:0042803 GO:0047127 GO:0050661 GO:0055114 GO:0070062 GO:0070324 GO:0070327
18	0.06	0.254	5.16	0.09	0.38	4rckA	GO:0016020 GO:0016021 GO:0046872

Consensus prediction of GO terms

Molecular Function	GO:0052689
GO-Score	0.55
Biological Processes	GO:0045491	GO:0000272
GO-Score	0.55	0.55
Cellular Component	GO:0044424
GO-Score	0.55

(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.