I-TASSER results

I-TASSER results for job id Rv0658c

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

Input Sequence in FASTA format

>protein (238 residues)
MEAGRADTVAPSHRWGLGAFLVVELVFLVASTSLAVVLTGHGPVSAGVLALALAAPTVVA
AGLAILITRLRGNGLRTDLRLRWSWRGLRLGLMFGFGGMLVTIPASLVYTAIVGPEANSA
VVRIFGGVRASWPWALVVFLVVVFVAPLCEEIIYRGLLWGAVDRRWGRWAALVVTTVVFA
LAHLEFARAPLLVVVAIPIALARFYSGGLLASIVTHQVTNLLPGIVLLLGLTGAISLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MEAGRADTVAPSHRWGLGAFLVVELVFLVASTSLAVVLTGHGPVSAGVLALALAAPTVVAAGLAILITRLRGNGLRTDLRLRWSWRGLRLGLMFGFGGMLVTIPASLVYTAIVGPEANSAVVRIFGGVRASWPWALVVFLVVVFVAPLCEEIIYRGLLWGAVDRRWGRWAALVVTTVVFALAHLEFARAPLLVVVAIPIALARFYSGGLLASIVTHQVTNLLPGIVLLLGLTGAISLP
Prediction	CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Conf.Score	9888888888755789999999999999999999999875456656899999999999999999999998677754444456655789999999999999999999999998677777568999998755658999999999999999999999999999999986768999999999999967888999999999999999999898489999999999999999999975677789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 \| \| \| \| \| \| \| \| \| \| \| MEAGRADTVAPSHRWGLGAFLVVELVFLVASTSLAVVLTGHGPVSAGVLALALAAPTVVAAGLAILITRLRGNGLRTDLRLRWSWRGLRLGLMFGFGGMLVTIPASLVYTAIVGPEANSAVVRIFGGVRASWPWALVVFLVVVFVAPLCEEIIYRGLLWGAVDRRWGRWAALVVTTVVFALAHLEFARAPLLVVVAIPIALARFYSGGLLASIVTHQVTNLLPGIVLLLGLTGAISLP
Prediction	8746555643231311211233333333333333122133333443221133333333333333332322244423441323343333231213333333333333333220233434442343144344333232233333133323323323321122203633321100221132323333343333312321220122012243321001013333331333331333342637
	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

CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
MEAGRADTVAPSHRWGLGAFLVVELVFLVASTSLAVVLTGHGPVSAGVLALALAAPTVVAAGLAILITRLRGNGLRTDLRLRWSWRGLRLGLMFGFGGMLVTIPASLVYTAIVGPEANSAVVRIFGGVRASWPWALVVFLVVVFVAPLCEEIIYRGLLWGAVDRRWGRWAALVVTTVVFALAHLEFARAPLLVVVAIPIALARFYSGGLLASIVTHQVTNLLPGIVLLLGLTGAISLP

4cadC

0.15

0.13

0.88

1.41

MUSTER

---------------NPKLYFLSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIP----FGGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFPLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.15

0.13

0.88

1.12

dPPAS

-----------------NPKLYFLSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKDFINRLFNL--KLINLKTIPVVFLLMPAVILLSILLSIPFGGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFPLNFFLSILPMGIIITWMCLKNRSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.15

0.13

0.88

2.92

wdPPAS

---------------NPKLYFLSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPF----GGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHF-LNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.15

0.13

0.88

1.93

wMUSTER

---------------NPKLYFLSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIP----FGGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFPLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.15

0.13

0.88

3.81

wPPAS

---------------NPKLYFLSTFVVTYILWFTGAYLSFSSTY--SGIYMLIMLPGLMAPFIISTILIAKKKDFINRL-FNLKLINLKTIPVV-FLLMPAVILLSILLSIPFGGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHF-LNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.15

0.13

0.88

2.36

dPPAS2

-----------------NPKLYFLSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKDFINRLFNL--KLINLKTIPVVFLLMPAVILLSILLSIPFGGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFPLNFFLSILPMGIIITWMCLKNRSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.15

0.13

0.88

2.47

PPAS

---------------NPKLYFLSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIP----FGGSIS---------QFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFPLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETG

4cadC

0.13

0.11

0.88

1.94

Env-PPAS

---------------NPKLYFLSTFVVTYILWFTGAYLSFSSTY--SGIYMLIMLPGLMAPFIISTILIAKKKDF---INRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQF--------SGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFPLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETG

4or2A2

0.10

0.95

1.02

MUSTER

VR------LEWSNIESIIAIAFSCLGILVTLFVTLIFVLYRDTPVVKSSSRELCYIILAGIFLGYVCPFTLIAKPTTTSCY---LQRLLVGLSSAMCYSALVTKTNRIARILARKPRFMSAWAQVIIASILISVQLTLVVTLIIMEPPMPILSY--YLNLGVVAPLGYNGLLIMSCTYYAFKTRNAFTMYTTCIIWLAFVPIYFGSNYKIITTCFAVSLSVTVALGCMFTPK-IIAKP

4ke2A

0.12

0.10

0.82

0.80

dPPAS

------MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSI-------------AAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-----------------------

(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=-0.61

Estimated TM-score = 0.64±0.13

Estimated RMSD = 7.0±4.1Å

Download Model 2

C-score=-2.29

Download Model 3

C-score=-1.25

Download Model 4

C-score=-1.23

Download Model 5

C-score=-4.15

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	4cadC	0.807	1.92	0.148	0.882
2	2ww9A	0.485	5.25	0.055	0.727
3	3kcrA	0.462	5.50	0.051	0.723
4	3hjbA	0.448	5.76	0.073	0.731
5	4iu8A	0.447	4.99	0.057	0.660
6	1gzdA1	0.444	5.73	0.053	0.727
7	3vvnA	0.440	5.28	0.075	0.685
8	3o0rB	0.439	4.81	0.073	0.643
9	3pr3A	0.438	5.52	0.052	0.710
10	4ka7A	0.438	5.13	0.058	0.698

(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	4	3s8gA	OLC	Rep, Mult	189,194,201
2	0.05	3	2nwlA	ASP	Rep, Mult	150,195,196,201,212,215,216,219
3	0.05	3	2nwwA	TB1	Rep, Mult	148,210,213,214,217
4	0.05	3	4x23F	III	Rep, Mult	148,151,152,155
5	0.05	3	1f51D	MG	Rep, Mult	216,220
6	0.04	2	3u32L	DCW	Rep, Mult	21,59,153,158
7	0.02	1	4ev6E	MG	Rep, Mult	25,181
8	0.02	1	3mk7A	CA	Rep, Mult	180,184,188
9	0.02	1	3bz1X	CLA	Rep, Mult	156,157,160,161
10	0.02	1	3qblA	22B	Rep, Mult	23,27,58,153
11	0.02	1	3gjcA	BOG	Rep, Mult	201,204
12	0.02	1	3aebC	EPH	Rep, Mult	139,181
13	0.02	1	3mk7D	CA	Rep, Mult	162,170,172,177
14	0.02	1	1e86A	CMO	Rep, Mult	25,28,154
15	0.02	1	2y00A	2CV	Rep, Mult	31,34,51,58
16	0.02	1	5etzA	22B	Rep, Mult	27,50,51,54,153,157

	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	1w27A	0.394	5.75	0.031	0.672	4.3.1.24	NA
2	0.060	1j36A	0.392	6.41	0.042	0.714	3.4.15.1	NA
3	0.060	3hjbA	0.448	5.76	0.073	0.731	5.3.1.9	NA
4	0.060	2p0mA	0.394	6.25	0.066	0.693	1.13.11.33	NA
5	0.060	2wu8A	0.432	5.76	0.089	0.723	5.3.1.9	NA
6	0.060	3czoB	0.422	5.06	0.063	0.651	4.3.1.3	NA
7	0.060	1b8fA	0.392	5.28	0.058	0.622	4.3.1.3	NA
8	0.060	2yr4A	0.394	5.84	0.059	0.655	1.13.12.9	NA
9	0.060	3bkkA	0.399	5.78	0.042	0.655	3.4.15.1	NA
10	0.060	1ygeA	0.412	6.35	0.048	0.756	1.13.11.12	NA
11	0.060	1wgzA	0.412	5.17	0.050	0.651	3.4.24.66	NA
12	0.060	1ci8A	0.396	6.10	0.065	0.706	3.1.1.1	NA
13	0.060	2vkzG	0.395	6.11	0.062	0.698	2.3.1.38,3.1.2.14	NA
14	0.060	2o2dB	0.435	5.74	0.064	0.731	5.3.1.9	NA
15	0.060	2uv8G	0.394	5.99	0.068	0.693	2.3.1.86	NA
16	0.060	1no3A	0.391	6.60	0.056	0.735	1.13.11.12	NA
17	0.060	2pgiA	0.391	5.51	0.057	0.622	5.3.1.9	154
18	0.060	1i1iP	0.408	5.82	0.059	0.698	3.4.24.16	24
19	0.060	1pgjA	0.406	5.09	0.074	0.609	1.1.1.44	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	0.30	0.818	1.81	0.15	0.89	4cadI	GO:0004175 GO:0004662 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0016020 GO:0016021 GO:0016787 GO:0071586
1	0.07	0.485	5.25	0.06	0.73	2ww9A	GO:0005048 GO:0005783 GO:0005789 GO:0006614 GO:0006810 GO:0008320 GO:0015031 GO:0016020 GO:0016021 GO:0071261 GO:0071806
2	0.07	0.467	5.61	0.07	0.75	4qfhB	GO:0004347 GO:0006094 GO:0006096 GO:0016853
3	0.07	0.464	5.41	0.05	0.72	2yxrA	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
4	0.07	0.429	5.69	0.06	0.71	4em6A	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
5	0.07	0.435	5.74	0.06	0.73	2o2dB	GO:0004347 GO:0005777 GO:0006094 GO:0006096 GO:0016853 GO:0020015
6	0.07	0.437	5.81	0.06	0.71	1iriA	GO:0001525 GO:0001701 GO:0001707 GO:0004347 GO:0005125 GO:0005576 GO:0005615 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0006959 GO:0007599 GO:0007611 GO:0008083 GO:0016020 GO:0016853 GO:0016866 GO:0019242 GO:0031625 GO:0034101 GO:0042593 GO:0043005 GO:0043154 GO:0043209 GO:0043524 GO:0046185 GO:0048029 GO:0051156 GO:0060170 GO:0061621 GO:0070062
7	0.07	0.440	5.79	0.06	0.72	4wmjB	GO:0004347 GO:0006094 GO:0006096 GO:0016853
8	0.07	0.448	5.76	0.07	0.73	3hjbA	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
9	0.07	0.432	5.76	0.09	0.72	2wu8A	GO:0004347 GO:0005737 GO:0005886 GO:0006094 GO:0006096 GO:0016853 GO:0040007
10	0.07	0.436	5.78	0.04	0.74	3nbuB	GO:0004347 GO:0005737 GO:0005829 GO:0006094 GO:0006096 GO:0016853 GO:0034599 GO:0042802
11	0.07	0.440	5.58	0.06	0.71	3ljkA	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
12	0.07	0.433	5.67	0.06	0.71	1q50A	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
13	0.07	0.438	5.52	0.05	0.71	3pr3A	GO:0004347 GO:0006094 GO:0006096 GO:0006098 GO:0016853
14	0.06	0.386	5.95	0.07	0.66	3dl8G	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
15	0.06	0.387	5.12	0.09	0.59	1zzgA	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
16	0.06	0.293	6.46	0.04	0.55	3ff1A	GO:0004347 GO:0005737 GO:0006094 GO:0006096 GO:0016853
17	0.06	0.382	6.01	0.06	0.66	3dinC	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
18	0.06	0.462	5.39	0.05	0.72	3bo0A	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002

Consensus prediction of GO terms

Molecular Function	GO:0004661	GO:0070011
GO-Score	0.59	0.59
Biological Processes	GO:0080120	GO:0016485
GO-Score	0.59	0.59
Cellular Component	GO:0031226	GO:0016021
GO-Score	0.59	0.39

(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.