I-TASSER results

I-TASSER results for job id Rv0966c

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

Input Sequence in FASTA format

>protein (200 residues)
MSNSAQRDARNSRDESARASDTDRIQIAQLLAYAAEQGRLQLTDYEDRLARAYAATTYQE
LDRLRADLPGAAIGPRRGGECNPAPSTLLLALLGGFERRGRWNVPKKLTTFTLWGSGVLD
LRYADFTSTEVDIRAYSIMGAQTILLPPEVNVEIHGHRVMGGFDRKVVGEGTRGVPTVRI
RGFSLWGDVGIKRKPRKPRK

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSNSAQRDARNSRDESARASDTDRIQIAQLLAYAAEQGRLQLTDYEDRLARAYAATTYQELDRLRADLPGAAIGPRRGGECNPAPSTLLLALLGGFERRGRWNVPKKLTTFTLWGSGVLDLRYADFTSTEVDIRAYSIMGAQTILLPPEVNVEIHGHRVMGGFDRKVVGEGTRGVPTVRIRGFSLWGDVGIKRKPRKPRK
Prediction	CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCEEEEEEEEHCEEEHCCCEHCCCCEEEEEEEEEEHCEEEEHCCCEEEEEEEEEEHCCEEHCCCCCCCCCCCEEEEEEEEEEHCEEEEHCCCCCCC
Conf.Score	99888899999998778998899999999999999989999999999999999956888999997688888888877778888887654445565577656677866899998756589856557579879999999985779996899799998777766778767889999987899999999856899957888789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSNSAQRDARNSRDESARASDTDRIQIAQLLAYAAEQGRLQLTDYEDRLARAYAATTYQELDRLRADLPGAAIGPRRGGECNPAPSTLLLALLGGFERRGRWNVPKKLTTFTLWGSGVLDLRYADFTSTEVDIRAYSIMGAQTILLPPEVNVEIHGHRVMGGFDRKVVGEGTRGVPTVRIRGFSLWGDVGIKRKPRKPRK
Prediction	86645655475564441213363044005204601441303362045014302414335204402333544433444343333443443443334343444243443132313213330102404155530202020210403020156040314021201314344565455511202020202004040324555668
	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

CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCEEEEEEEEHCEEEHCCCEHCCCCEEEEEEEEEEHCEEEEHCCCEEEEEEEEEEHCCEEHCCCCCCCCCCCEEEEEEEEEEHCEEEEHCCCCCCC
MSNSAQRDARNSRDESARASDTDRIQIAQLLAYAAEQGRLQLTDYEDRLARAYAATTYQELDRLRADLPGAAIGPRRGGECNPAPSTLLLALLGGFERRGRWNVPKKLTTFTLWGSGVLDLRYADFTSTEVDIRAYSIMGAQTILLPPEVNVEIHGHRVMGGFDRKVVGEGTRGVPTVRIRGFSLWGDVGIKRKPRKPRK

4qrkA

0.13

0.12

0.91

1.29

MUSTER

---KPKEEIKIVEPNGAEKTK---------LNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGFSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.13

0.12

0.91

1.24

dPPAS

---KPKEEIKIVEPNGAE---------KTKLNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGFSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.13

0.12

0.91

2.27

wdPPAS

-----------KPKEEIKIVEPNGAEKTK-LNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGNSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.12

0.10

0.90

1.52

wMUSTER

KEEIKIVEPNGAEKTKLNLN--------------FGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGFSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.13

0.12

0.91

2.27

wPPAS

-----------KPKEEIKIVEPNGAEKTK-LNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGNSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.13

0.12

0.91

2.99

dPPAS2

---KPKEEIKIVEPNGAE---------KTKLNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGFSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.13

0.12

0.91

1.79

PPAS

-----------KPKEEIKIVEPNGAEKTK-LNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGFSQYGKSKNSIEVNIEAGVGAINIKQK------

4qrkA

0.13

0.12

0.91

Env-PPAS

-----------KPKEEIKIVEPNGAEKTK-LNLNFGVGKLNISGNEEKLKGKFIYSENEWKPEIKYEVKDKDGELEISQPGLKSGNVSLNNKRNEWNINLNEKIPTEIKLSLGTGEFKADLSKINLYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANKNSQYGKSKNSIEVNIEAGVGAINIKQK------

4ghnA1

0.12

0.95

0.81

MUSTER

FYNDKQIDVENFYIAELPLTPSQFEEDFKEIHQIVEN-HLNDSLYQACDARVRQAQTTTDYGLIVQALQCAHAITCYKRYTANQRVAFIEDFLKPNDYLTEYGFQDKDRIIAINGLPY-QNEKYTEASTVPHRRLRTAYDAFRSYADTLRNYTLLRDTLTVTLPLKQRDYFPGNGPRPFCTKQRTYFRIPTR--------

4qrkA2

0.19

0.07

0.39

0.84

dPPAS

------------------------------------------------------------------------------------------------------------------GKVDLDISG--NYKNNVKVNIEGGVGEATVYLPKSIGVKIKAEKGVGAVNANGNSQYGKSKNSIEVNIEAGVGAINIKQK------

(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=-1.20

Estimated TM-score = 0.56±0.15

Estimated RMSD = 8.0±4.4Å

Download Model 2

C-score=-1.43

Download Model 3

C-score=-3.90

Download Model 4

C-score=-2.88

Download Model 5

C-score=-4.73

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	4qrkA	0.840	1.81	0.121	0.910
2	3lycA	0.552	4.28	0.060	0.770
3	3petA	0.552	3.89	0.065	0.770
4	3jx8A	0.550	3.91	0.065	0.775
5	3ljyA	0.531	4.38	0.048	0.780
6	4yguA	0.519	3.84	0.130	0.720
7	4dn7A	0.490	5.11	0.057	0.795
8	2zu0A	0.488	5.03	0.061	0.790
9	5awfA	0.482	4.89	0.048	0.785
10	3vstA	0.480	5.19	0.046	0.775

(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	6	3rqiA	CA	Rep, Mult	44,120,122
2	0.04	2	3uomA	CA	Rep, Mult	21,23
3	0.04	2	1x06A	FPS	Rep, Mult	121,145,178,180
4	0.04	2	2iq7A	UUU	Rep, Mult	116,120,141
5	0.02	1	1y66B	DIO	Rep, Mult	42,45,49
6	0.02	1	1d4m1	MYR	Rep, Mult	187,188
7	0.02	1	1ia5A	MAN	Rep, Mult	127,128,131
8	0.02	1	1cm5B	NA	Rep, Mult	144,146,152,192
9	0.02	1	1kj4B	III	Rep, Mult	176,178
10	0.02	1	2izxA	DTD	Rep, Mult	45,48,49,52
11	0.02	1	4x4qA	MG	Rep, Mult	132,179
12	0.02	1	2jigB	ZN	Rep, Mult	155,157
13	0.02	1	4as8A	EDO	Rep, Mult	63,65,76
14	0.02	1	5tglA	HEE	Rep, Mult	116,184
15	0.02	1	3cf4A	SF4	Rep, Mult	20,22,23,29,71
16	0.02	1	1rmgA	MAN	Rep, Mult	34,36,37,38,40
17	0.02	1	3sjqC	PHU	Rep, Mult	67,68

	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	1airA	0.475	5.35	0.087	0.795	4.2.2.2	NA
2	0.060	1hg8A	0.463	5.56	0.064	0.805	3.2.1.15	NA
3	0.060	2z8gB	0.458	5.76	0.092	0.790	3.2.1.57	NA
4	0.060	1wmrA	0.454	5.56	0.071	0.815	3.2.1.57	NA
5	0.060	3maxA	0.437	5.04	0.056	0.685	3.5.1.98	120
6	0.060	2pecA	0.472	5.33	0.063	0.805	4.2.2.2	111
7	0.060	1jtaA	0.475	5.23	0.054	0.825	4.2.2.2	NA
8	0.060	1rmgA	0.467	5.13	0.044	0.795	3.2.1.-	NA
9	0.060	2pflA	0.442	5.25	0.048	0.725	2.3.1.54	185
10	0.060	1pclA	0.447	5.66	0.056	0.795	4.2.2.2	NA
11	0.060	1ru4A	0.440	5.79	0.029	0.750	4.2.2.2	NA
12	0.060	3h09B	0.431	5.50	0.083	0.700	3.4.21.72	NA
13	0.060	1bn8A	0.471	5.16	0.056	0.810	4.2.2.2	NA
14	0.060	1idjA	0.477	5.36	0.043	0.805	4.2.2.10	NA
15	0.060	1omjA	0.444	4.66	0.056	0.685	3.4.24.40	170
16	0.060	1ogmX	0.457	5.69	0.065	0.780	3.2.1.11	NA
17	0.060	1ib4A	0.456	5.29	0.053	0.770	3.2.1.15	115
18	0.060	1wcgA	0.433	5.83	0.041	0.785	3.2.1.147	NA
19	0.060	1ogoX	0.459	5.72	0.065	0.785	3.2.1.11	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	0.06	0.381	5.70	0.05	0.67	4w8jA	GO:0005102 GO:0006952 GO:0009405 GO:0030435
1	0.06	0.286	5.77	0.02	0.51	4b4uB	GO:0000105 GO:0000166 GO:0003824 GO:0004477 GO:0004488 GO:0006164 GO:0006730 GO:0008152 GO:0008652 GO:0009086 GO:0009396 GO:0016491 GO:0016787 GO:0035999 GO:0055114
2	0.06	0.286	5.79	0.05	0.49	4g41A	GO:0003824 GO:0008152 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0016798 GO:0019509
3	0.06	0.342	5.68	0.04	0.59	3zh3A	GO:0003824 GO:0005737 GO:0005829 GO:0007049 GO:0008360 GO:0008760 GO:0009252 GO:0016740 GO:0016765 GO:0019277 GO:0051301 GO:0071236 GO:0071555
4	0.06	0.273	5.09	0.04	0.44	1lr5A	GO:0004872 GO:0005783 GO:0005788 GO:0008270 GO:0009734 GO:0010011 GO:0046872
5	0.06	0.253	6.31	0.01	0.48	2be3A	GO:0015969
6	0.06	0.261	4.55	0.02	0.40	3rofA	GO:0004721 GO:0004725 GO:0006470 GO:0016787 GO:0035335
7	0.06	0.281	5.87	0.03	0.52	1i9rH
8	0.06	0.225	5.33	0.06	0.39	2di7A	GO:0005783 GO:0005788 GO:0006664 GO:0046527
9	0.06	0.249	5.27	0.04	0.41	4bz4B	GO:0046872
10	0.06	0.226	5.58	0.03	0.40	3wo4C	GO:0004872 GO:0005886 GO:0006954 GO:0006955 GO:0007165 GO:0007166 GO:0016020 GO:0016021 GO:0070301 GO:0071345
11	0.06	0.248	6.06	0.03	0.46	4cl1D	GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004197 GO:0004252 GO:0004386 GO:0005198 GO:0005524 GO:0006508 GO:0008026 GO:0008236 GO:0008270 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0017111 GO:0019012 GO:0019028 GO:0019031 GO:0019079 GO:0019087 GO:0039694 GO:0046872
12	0.06	0.274	5.56	0.04	0.48	4av2A	GO:0006810 GO:0008565 GO:0009279 GO:0009297 GO:0009306 GO:0015031 GO:0016020 GO:0019867 GO:0030420
13	0.06	0.261	5.13	0.06	0.42	3mvkG	GO:0005996 GO:0016853 GO:0048029
14	0.06	0.222	5.55	0.03	0.39	3t8nB	GO:0004769 GO:0006629 GO:0008202 GO:0016853
15	0.06	0.254	5.12	0.04	0.43	4aqzA	GO:0006810 GO:0008565 GO:0009279 GO:0009297 GO:0009306 GO:0015031 GO:0016020 GO:0019867 GO:0030420
16	0.06	0.202	5.10	0.03	0.32	1jpyA	GO:0005125 GO:0005126 GO:0005576 GO:0005615 GO:0006954 GO:0016525 GO:0017015 GO:0019955 GO:0042089 GO:0042109 GO:0042803 GO:0045076 GO:0045408 GO:0045414 GO:0045423 GO:0045944 GO:0051216 GO:1900017 GO:2000778
17	0.06	0.209	5.67	0.07	0.38	2i85A	GO:0001525 GO:0001618 GO:0001945 GO:0002042 GO:0005102 GO:0005886 GO:0005887 GO:0005925 GO:0007155 GO:0007267 GO:0007275 GO:0007399 GO:0007411 GO:0009653 GO:0009887 GO:0010839 GO:0016020 GO:0016021 GO:0016032 GO:0030154 GO:0031295 GO:0046718 GO:0046875 GO:0048013 GO:0048514 GO:0050920 GO:0072178 GO:2000727
18	0.06	0.239	4.76	0.09	0.38	4v9fY	GO:0000166 GO:0003677 GO:0003723 GO:0003735 GO:0005622 GO:0005840 GO:0006281 GO:0006412 GO:0019843 GO:0030529

Consensus prediction of GO terms

Molecular Function	GO:0000166	GO:0004488	GO:0004477	GO:0005102	GO:0008782	GO:0008930	GO:0008270	GO:0010011	GO:0008760	GO:0004872
GO-Score	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06
Biological Processes	GO:0006164	GO:0009405	GO:0006952	GO:0009164	GO:0030435	GO:0019509	GO:0035999	GO:0000105	GO:0009396	GO:0055114	GO:0009734	GO:0019277	GO:0007049	GO:0009252	GO:0008360	GO:0071555	GO:0071236	GO:0051301
GO-Score	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06	0.06
Cellular Component	GO:0005788	GO:0005829
GO-Score	0.06	0.06

(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.