I-TASSER results

I-TASSER results for job id Rv0804

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

Input Sequence in FASTA format

>protein (209 residues)
MSRLRALSLAAGLVGWSLVSPRLPAPWRIPLQAGLGSVLVLVTRATMGLWPPRLWAGLRL
GWAAGAAAATAIAATTPVPMVRLSMSARELPASVPVWLVWHIPGGTVWAEEAAFRGALAT
IGARAFGRSGGRILQAGAFGLSHIADARATGEPLVLTVLATGIAGWMFGWLADRSGSLAA
PLLTHLAINEAGAVAAVLVQRRSGISTRL

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSRLRALSLAAGLVGWSLVSPRLPAPWRIPLQAGLGSVLVLVTRATMGLWPPRLWAGLRLGWAAGAAAATAIAATTPVPMVRLSMSARELPASVPVWLVWHIPGGTVWAEEAAFRGALATIGARAFGRSGGRILQAGAFGLSHIADARATGEPLVLTVLATGIAGWMFGWLADRSGSLAAPLLTHLAINEAGAVAAVLVQRRSGISTRL
Prediction	CCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	97545667888888877655446665456788899999887644445886567889999999999999999999987678788765555545799999999999879999999999999999999796689999999999997466555546799999999999999999999989858999999999999999999999856776679
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSRLRALSLAAGLVGWSLVSPRLPAPWRIPLQAGLGSVLVLVTRATMGLWPPRLWAGLRLGWAAGAAAATAIAATTPVPMVRLSMSARELPASVPVWLVWHIPGGTVWAEEAAFRGALATIGARAFGRSGGRILQAGAFGLSHIADARATGEPLVLTVLATGIAGWMFGWLADRSGSLAAPLLTHLAINEAGAVAAVLVQRRSGISTRL
Prediction	65302020102112111121331345133303111121012222230203244123013313323333323112012123233213344233312132333323321220122011101320363243310011003100100022333343313212332233132012003224101100231333133012101203334514444
	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

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MSRLRALSLAAGLVGWSLVSPRLPAPWRIPLQAGLGSVLVLVTRATMGLWPPRLWAGLRLGWAAGAAAATAIAATTPVPMVRLSMSARELPASVPVWLVWHIPGGTVWAEEAAFRGALATIGARAFGRSGGRILQAGAFGLSHIADARATGEPLVLTVLATGIAGWMFGWLADRSGSLAAPLLTHLAINEAGAVAAVLVQRRSGISTRL

4cadC

0.11

0.99

1.48

MUSTER

F--LSTFVVTYILWFTGAYLSFSSTYIMLPGLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.11

0.99

1.18

dPPAS

F--LSTFVVTYILWFTGAYLSFSSTYIMLPGLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNRSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.11

0.99

2.76

wdPPAS

F--LSTFVVTYILWFTGAYLSFSSTY-GLMAPFIISTILIAKKKDFINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.12

0.11

0.99

1.92

wMUSTER

F--LSTFVVTYILWFTGAYLSFSSTYMLIMLPGLMAPFIISTILIAINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.13

0.12

0.97

3.69

wPPAS

F--LSTFVVTYILWFTGAYLSFSSTYLPGLMAPFIISTILIAKKKDFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSGG----DFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.11

0.99

2.71

dPPAS2

F--LSTFVVTYILWFTGAYLSFSSTYLIMLPGLMAPFIISTILIAKINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNRSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.12

0.11

0.99

2.47

PPAS

F--LSTFVVTYILWFTGAYLSFSSTYSGIYMLIMLPGLMAPFIIS-INRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4cadC

0.12

0.11

0.99

2.05

Env-PPAS

F--LSTFVVTYILWFTGAYLSFSSTYMLIMLPGLMAPFIISTILIAINRLFNLKLINLKTIPVVFLLMPAVILLSILLSIPFGGSISQFQFSGGDFVPVLFLLLLAATFEELGWRGYAFDSLQSRYSLFKASILFGIFWSLWHFEIFNQSIWYGLNFFLSILPMGIIITWMCLKNKSIILAIIFHFLINLNQELLAITQDTKIIETGVL

4bwzA2

0.14

0.12

0.91

0.98

MUSTER

ILAVGKEAFLVAVLGVALPFLGGYLGFETLPALFLGTALVATSVGIT-LGVLSRPYSRIILGAAVIDDVLGLIVLACVNGVAETGQELSALASPVVLVAGTVVTVIAILGKVLGGFLGALTQG---------VRSALTVGCGMAPR----GEVGLIVAALGLKAGAVNEEEYAIV--LFMVVFTTLFAPFALKPLIAWTERERAAKE--

4ke2A

0.18

0.17

0.94

0.90

dPPAS

-MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATA------ADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP------

(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=0.01

Estimated TM-score = 0.71±0.11

Estimated RMSD = 5.4±3.4Å

Download Model 2

C-score=-3.98

Download Model 3

C-score=-1.63

Download Model 4

C-score=-3.76

Download Model 5

C-score=-1.18

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	0.942	1.48	0.120	1.000
2	2ww9A	0.542	5.03	0.050	0.813
3	3kcrA	0.507	5.39	0.081	0.823
4	2wwbA	0.497	5.10	0.051	0.761
5	2akhY	0.494	5.20	0.081	0.785
6	3o7pA	0.478	4.52	0.079	0.689
7	3vvnA	0.477	4.79	0.067	0.723
8	2iwhB	0.465	5.12	0.048	0.742
9	4mt1A	0.461	5.15	0.056	0.723
10	3wdoA	0.459	4.87	0.074	0.703

(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	0.10	5	4umjA	BFQ	Rep, Mult	139,168,172
2	0.10	5	1h16A	NA	Rep, Mult	132,133,134,138,139,164,165
3	0.06	3	4zjbG	PNS	Rep, Mult	177,178
4	0.04	2	2zt9G	III	Rep, Mult	178,186
5	0.04	2	3myrB	SF4	Rep, Mult	22,185
6	0.02	1	1i5aA	MN	Rep, Mult	185,189
7	0.02	1	4f88M	III	Rep, Mult	189,199
8	0.02	1	2wpnB	UUU	Rep, Mult	22,143
9	0.02	1	2y9wA	CU	Rep, Mult	139,143,185
10	0.02	1	1xmeC	HAS	Rep, Mult	155,159
11	0.02	1	1h18B	DTL	Rep, Mult	110,111,115,118
12	0.02	1	2h2pA	SEK	Rep, Mult	109,111
13	0.02	1	2b2jA	XE	Rep, Mult	118,131,134

	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	1bgxT	0.422	4.99	0.080	0.670	2.7.7.7	NA
2	0.060	3ljkA	0.419	5.40	0.039	0.689	5.3.1.9	NA
3	0.060	2zbzA	0.421	4.98	0.050	0.632	1.14.14.1	168,190
4	0.060	1p2yA	0.389	5.28	0.040	0.632	1.14.15.1	NA
5	0.060	3bjxA	0.400	5.54	0.026	0.684	3.8.1.10	119
6	0.060	2pflA	0.440	5.29	0.061	0.713	2.3.1.54	171
7	0.060	3hjbA	0.418	5.61	0.066	0.703	5.3.1.9	NA
8	0.060	1iduA	0.415	5.45	0.103	0.699	1.11.1.10	185
9	0.060	1i1iP	0.413	4.54	0.073	0.632	3.4.24.16	NA
10	0.060	1h16A	0.438	5.39	0.042	0.727	2.3.1.54	NA
11	0.060	3czoB	0.454	4.35	0.070	0.655	4.3.1.3	NA
12	0.060	2c6fA	0.409	5.66	0.036	0.655	3.4.15.1	NA
13	0.060	1iriA	0.422	5.61	0.065	0.699	5.3.1.9	NA
14	0.060	2vdcA	0.420	5.94	0.066	0.756	1.4.1.13	NA
15	0.060	2z36B	0.419	5.05	0.040	0.641	1.-.-.-	168,190
16	0.060	1ea0A	0.420	5.94	0.066	0.756	1.4.1.13	NA
17	0.060	2vdcF	0.419	5.94	0.060	0.756	1.4.1.13	2,6
18	0.060	2qnoA	0.393	5.41	0.030	0.665	3.2.1.4	182
19	0.060	2wu8A	0.418	5.82	0.041	0.727	5.3.1.9	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	0.34	0.925	1.83	0.12	1.00	4cadI	GO:0004175 GO:0004662 GO:0005886 GO:0005887 GO:0006508 GO:0008233 GO:0016020 GO:0016021 GO:0016787 GO:0071586
1	0.07	0.521	5.15	0.08	0.82	2yxrA	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
2	0.07	0.542	5.03	0.05	0.81	2ww9A	GO:0005048 GO:0005783 GO:0005789 GO:0006614 GO:0006810 GO:0008320 GO:0015031 GO:0016020 GO:0016021 GO:0071261 GO:0071806
3	0.07	0.448	5.43	0.07	0.76	5awwY	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
4	0.06	0.373	6.02	0.09	0.67	3bo0A	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
5	0.06	0.324	6.23	0.06	0.63	5eulY	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
6	0.06	0.339	5.43	0.04	0.54	3mp7A	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
7	0.06	0.497	5.10	0.05	0.76	2wwbA	GO:0005783 GO:0005789 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0030176 GO:0045047
8	0.06	0.312	5.88	0.04	0.54	3twbC	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0016052 GO:0016829 GO:0046872 GO:0047929
9	0.06	0.321	5.94	0.04	0.58	3t6cA	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0016052 GO:0016829 GO:0046872 GO:0047929
10	0.06	0.324	5.97	0.05	0.57	4ihcB	GO:0000287 GO:0003824 GO:0008152 GO:0008927 GO:0009063 GO:0016052 GO:0016829 GO:0046872 GO:0047929
11	0.06	0.324	5.90	0.07	0.56	5ahzA	GO:0005216 GO:0005886 GO:0006810 GO:0006811 GO:0007602 GO:0009881 GO:0016020 GO:0016021 GO:0018298 GO:0034220 GO:0050896
12	0.06	0.465	5.30	0.05	0.73	3jc21	GO:0005783 GO:0005789 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0030176 GO:0045047
13	0.06	0.434	5.67	0.08	0.75	3dinC	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
14	0.06	0.312	5.71	0.04	0.54	1xvlA	GO:0005886 GO:0006810 GO:0007155 GO:0010043 GO:0030001 GO:0046872
15	0.06	0.328	5.89	0.03	0.59	4jooA	GO:0001540 GO:0004175 GO:0004190 GO:0005768 GO:0005770 GO:0005771 GO:0005783 GO:0005788 GO:0005794 GO:0005802 GO:0005886 GO:0005887 GO:0006508 GO:0006509 GO:0008233 GO:0008798 GO:0009986 GO:0010008 GO:0016020 GO:0016021 GO:0016787 GO:0019899 GO:0030163 GO:0030424 GO:0030659 GO:0031410 GO:0044267 GO:0045121 GO:0050435 GO:0070931
16	0.06	0.451	5.42	0.07	0.74	3dl8G	GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
17	0.06	0.453	5.47	0.05	0.77	5abbA	GO:0005622 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
18	0.06	0.278	5.39	0.06	0.46	5bq1A	GO:0004089 GO:0008270 GO:0015976 GO:0016829

Consensus prediction of GO terms

Molecular Function	GO:0004175	GO:0004662
GO-Score	0.34	0.34
Biological Processes	GO:0006886	GO:1902582	GO:0071806	GO:0071586
GO-Score	0.37	0.37	0.37	0.34
Cellular Component	GO:0005887
GO-Score	0.34

(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.