I-TASSER results

I-TASSER results for job id Rv1287

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

Input Sequence in FASTA format

>protein (161 residues)
MRMSAKAEYAVRAMVQLATAASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRG
REGGYELARPGTEISIADVLRCIDGPLASVRDIGLGDLPYSGPTTALTDVWRALRASMRS
VLEETTLADVAGGALPEHVAQLADDYRAQESTRHGASRHGD

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRMSAKAEYAVRAMVQLATAASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGGYELARPGTEISIADVLRCIDGPLASVRDIGLGDLPYSGPTTALTDVWRALRASMRSVLEETTLADVAGGALPEHVAQLADDYRAQESTRHGASRHGD
Prediction	CCCCCHHHHHHHHHHHHHHCCCCCCHCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEHCCCCCCEEHCCCHHHCCHHHHHHHHCCCCCHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Conf.Score	98776556899999999986899865899999998999999999999999989889885899976758996679999999998698754456788888777787749999999999999999858999998676789999998878988876566776789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MRMSAKAEYAVRAMVQLATAASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGGYELARPGTEISIADVLRCIDGPLASVRDIGLGDLPYSGPTTALTDVWRALRASMRSVLEETTLADVAGGALPEHVAQLADDYRAQESTRHGASRHGD
Prediction	74425303000000000043488431304300663713461033004404643103034147100301340750201100311246142240345774166464030340054026204513662234201575356415623653554567546555668
	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

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCHHHHHHHHHHHHHHCCCCCCHCHHHHHHHHCCCHHHHHHHHHHHHHHCCEEEHCCCCCCEEHCCCHHHCCHHHHHHHHCCCCCHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCCCCC
MRMSAKAEYAVRAMVQLATAASGTVVKTDDLAAAQGIPPQFLVDILTNLRTDRLVRSHRGREGGYELARPGTEISIADVLRCIDGPLASVRDIGLGDLPYSGPTTALTDVWRALRASMRSVLEETTLADVAGGALPEHVAQLADDYRAQESTRHGASRHGD

4cicA

0.33

0.27

0.83

2.48

MUSTER

LKVSTKGHYGVQAMFDLAQHFGEGPVSLKSIAERQGLSEPYLEQLIAVLRKAGLVKSVRGAQGGYILAREPRDIKVGDIIRVLEGSLKFDF-------------SVTKSVWEKVKKSIEEVLDSITLADMLKDAEEAQMAQGYMYYI--------------

4hf0A

0.30

0.22

0.75

5.94

dPPAS

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4hf0A

0.30

0.22

0.75

5.70

wdPPAS

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4cicA

0.32

0.26

0.81

2.97

wMUSTER

LKVSTKGHYGVQAMFDLAQHFGEGPVSLKSIAERQGLSEPYLEQLIAVLRKAGLVKSVRGAQGGYILAREPRDIKVGDIIRVLEGSLKFDF-------------SVTKSVWEKVKKSIEEVLDSITLADMLKDAEEAQM------------------AQGY

4hf0A

0.30

0.22

0.75

4.52

wPPAS

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4hf0A

0.30

0.22

0.75

10.22

dPPAS2

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4hf0A

0.30

0.22

0.75

3.86

PPAS

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4hf0A

0.30

0.22

0.75

5.42

Env-PPAS

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4hf0A

0.30

0.22

0.75

2.45

MUSTER

MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVD--------------AQGGDKALTHALWRDLSDRLTGFLNNITLGELVNNQ---------------------------

4cicA

0.33

0.27

0.83

5.82

dPPAS

LKVSTKGHYGVQAMFDLAQHFGEGPVSLKSIAERQGLSEPYLEQLIAVLRKAGLVKSVRGAQGGYILAREPRDIKVGDIIRVLEGSLKFD-------------FSVTKSVWEKVKKSIEEVLDSITLADMLKDAEEAQMAQGYMYYI--------------

(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=0.09

Estimated TM-score = 0.72±0.11

Estimated RMSD = 4.7±3.1Å

Download Model 2

C-score=-1.09

Download Model 3

C-score=-2.27

Download Model 4

C-score=-3.13

Download Model 5

C-score=-2.53

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	4cicA	0.757	2.11	0.306	0.826
2	4hf0A	0.685	1.47	0.300	0.745
3	3lwfA	0.678	3.03	0.233	0.820
4	3t8rA	0.664	2.07	0.287	0.752
5	1xd7A	0.613	1.83	0.164	0.683
6	3k69A	0.611	3.10	0.179	0.776
7	1ylfB	0.586	2.12	0.204	0.683
8	4i43B	0.507	5.13	0.052	0.888
9	4f91B	0.506	4.77	0.081	0.807
10	3mktA	0.505	4.45	0.049	0.783

(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	5	4hf2A	NUC	Rep, Mult	2,5,6,9,38,40,41,44,59,60,61
2	0.09	4	2xcrB	RXV	Rep, Mult	10,14,28,42
3	0.07	3	1xd70	III	Rep, Mult	7,11,12,15,36,103,104,106,107,110,111,113,114,117,118,121,125,130
4	0.05	2	3shfA	GBL	Rep, Mult	18,19,75,80,84
5	0.05	2	3e3gD	SO4	Rep, Mult	38,59
6	0.05	2	3foeA	QNA	Rep, Mult	11,35,37,38,41
7	0.02	1	2o01H	CLA	Rep, Mult	63,67
8	0.02	1	2iefB	NUC	Rep, Mult	60,61
9	0.02	1	1mbxA	YBT	Rep, Mult	1,8
10	0.02	1	2xcrS	RXV	Rep, Mult	10,14,17,30

	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	1qmhB	0.415	5.48	0.043	0.770	6.5.1.4	NA
2	0.060	2pffA	0.447	5.31	0.073	0.801	2.3.1.41,2.3.1.86	NA
3	0.060	3l9oA	0.430	5.17	0.025	0.764	3.6.4.13	71
4	0.060	2rgrA	0.488	4.93	0.069	0.783	5.99.1.3	NA
5	0.060	1y44A	0.438	4.59	0.094	0.727	3.1.26.11	43,49
6	0.060	2pflA	0.447	4.76	0.066	0.739	2.3.1.54	NA
7	0.060	3btaA	0.467	4.77	0.057	0.764	3.4.24.69	NA
8	0.060	3djlA	0.427	5.48	0.077	0.795	1.3.99.-	NA
9	0.060	2qyoA	0.466	4.49	0.078	0.708	2.1.1.46	NA
10	0.060	2r7oA	0.442	5.08	0.062	0.795	2.7.7.48	13,27,38
11	0.060	1dxlC	0.424	5.72	0.058	0.776	1.8.1.4	NA
12	0.060	3c46B	0.456	5.28	0.041	0.795	2.7.7.6	NA
13	0.060	2qaeA	0.427	5.45	0.068	0.752	1.8.1.4	NA
14	0.060	1fp2A	0.467	4.67	0.057	0.721	2.1.1.150	NA
15	0.060	1ub2A	0.437	5.41	0.055	0.820	1.11.1.7	12
16	0.060	2wl2B	0.493	4.98	0.069	0.789	5.99.1.3	NA
17	0.060	2vuaA	0.325	5.58	0.067	0.596	3.4.24.69	80,124,127
18	0.060	1h16A	0.450	4.62	0.066	0.733	2.3.1.54	NA
19	0.060	2hnhA	0.368	5.44	0.026	0.652	2.7.7.7	121

(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	0.46	0.654	1.81	0.27	0.72	4hf1A	GO:0003677 GO:0003690 GO:0003700 GO:0005506 GO:0005829 GO:0006351 GO:0006355 GO:0046872 GO:0051536 GO:0051537
1	0.44	0.690	1.64	0.29	0.76	4chuB	GO:0003677 GO:0003690 GO:0003700 GO:0005506 GO:0006351 GO:0006355 GO:0046872 GO:0051536 GO:0051537
2	0.38	0.691	2.36	0.25	0.79	2y75E	GO:0003677 GO:0006351 GO:0006355 GO:0042802
3	0.11	0.417	3.76	0.10	0.55	4b8xA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
4	0.06	0.389	5.10	0.08	0.68	4lk0D	GO:0003677 GO:0003899 GO:0006351 GO:0016740 GO:0016779
5	0.06	0.385	5.03	0.07	0.66	5ezkD	GO:0000428 GO:0003677 GO:0003899 GO:0005737 GO:0005829 GO:0006351 GO:0016020 GO:0016740 GO:0016779
6	0.06	0.416	3.48	0.09	0.53	4fhtB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0044212
7	0.06	0.420	2.87	0.14	0.50	3pqkB	GO:0003677 GO:0003700 GO:0006351 GO:0006355
8	0.06	0.358	5.61	0.05	0.68	5byhD	GO:0000428 GO:0003677 GO:0003899 GO:0005737 GO:0005829 GO:0006351 GO:0016020 GO:0016740 GO:0016779
9	0.06	0.388	4.76	0.04	0.63	5l3qB	GO:0000166 GO:0003924 GO:0005047 GO:0005525 GO:0005783 GO:0005785 GO:0005789 GO:0006613 GO:0006614 GO:0006810 GO:0006886 GO:0016020 GO:0016021 GO:0036498 GO:0044822 GO:0070062
10	0.06	0.401	2.65	0.16	0.47	4ooiB	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0009405
11	0.06	0.388	5.11	0.10	0.69	4xsxJ	GO:0003677 GO:0003899 GO:0006351 GO:0016740 GO:0016779
12	0.06	0.360	1.81	0.18	0.40	2jt1A	GO:0006355 GO:0009289
13	0.06	0.383	3.09	0.16	0.48	1j5yA	GO:0003677 GO:0006351 GO:0006355 GO:0036094 GO:0046872
14	0.06	0.283	5.93	0.06	0.58	3ewmA	GO:0004747 GO:0006014 GO:0016301 GO:0016310 GO:0016740 GO:0016773 GO:0046835
15	0.06	0.358	5.54	0.08	0.66	5iplD	GO:0000428 GO:0003677 GO:0003899 GO:0005737 GO:0005829 GO:0006351 GO:0016020 GO:0016740 GO:0016779
16	0.06	0.318	3.51	0.08	0.44	1xs9A	GO:0000987 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0019172 GO:0019243 GO:0043565 GO:0045892 GO:0045893 GO:0046677
17	0.06	0.319	5.53	0.02	0.59	1cnvA	GO:0004553 GO:0005975
18	0.06	0.303	4.82	0.05	0.50	3b38A	GO:0000785 GO:0001047 GO:0001933 GO:0001963 GO:0003690 GO:0003697 GO:0003713 GO:0003723 GO:0003729 GO:0005102 GO:0005507 GO:0005634 GO:0005737 GO:0005739 GO:0005747 GO:0005758 GO:0005759 GO:0005783 GO:0005829 GO:0005886 GO:0005913 GO:0006469 GO:0006508 GO:0006517 GO:0006914 GO:0006954 GO:0006979 GO:0007005 GO:0007265 GO:0007338 GO:0008134 GO:0008233 GO:0008344 GO:0010273 GO:0010628 GO:0010629 GO:0016020 GO:0016532 GO:0016605 GO:0016684 GO:0016787 GO:0018323 GO:0019172 GO:0019243 GO:0019249 GO:0019899 GO:0019900 GO:0019955 GO:0030424 GO:0031397 GO:0032091 GO:0032148 GO:0032435 GO:0032757 GO:0033138 GO:0033234 GO:0034599 GO:0034614 GO:0036470 GO:0036471 GO:0036478 GO:0042177 GO:0042493 GO:0042542 GO:0042743 GO:0042802 GO:0042803 GO:0043005 GO:0043066 GO:0043523 GO:0043524 GO:0044297 GO:0044388 GO:0044390 GO:0045121 GO:0045340 GO:0045560 GO:0045944 GO:0046295 GO:0046826 GO:0048471 GO:0050681 GO:0050727 GO:0050787 GO:0050821 GO:0051091 GO:0051444 GO:0051583 GO:0051881 GO:0051897 GO:0051899 GO:0051920 GO:0060081 GO:0060548 GO:0060765 GO:0070062 GO:0070301 GO:0070491 GO:0090073 GO:0097110 GO:0098609 GO:0098641 GO:0098793 GO:0098869 GO:1900182 GO:1901215 GO:1901671 GO:1901984 GO:1902177 GO:1902236 GO:1902903 GO:1902958 GO:1903073 GO:1903094 GO:1903122 GO:1903135 GO:1903136 GO:1903168 GO:1903178 GO:1903181 GO:1903190 GO:1903197 GO:1903200 GO:1903202 GO:1903204 GO:1903206 GO:1903208 GO:1903377 GO:1903384 GO:1903428 GO:1903599 GO:1990381 GO:1990422 GO:2000157 GO:2000277 GO:2000679 GO:2000825 GO:2001237 GO:2001268

Consensus prediction of GO terms

Molecular Function	GO:0003700	GO:0003690	GO:0051537	GO:0005506	GO:0042802
GO-Score	0.73	0.70	0.70	0.70	0.38
Biological Processes	GO:0006355
GO-Score	0.83
Cellular Component	GO:0005829
GO-Score	0.46

(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.