I-TASSER results

I-TASSER results for job id Rv0080

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

Input Sequence in FASTA format

>protein (152 residues)
MSPGSRRASPQSAREVVELDRDEAMRLLASVDHGRVVFTRAALPAIRPVNHLVVDGRVIG
RTRLTAKVSVAVRSSADAGVVVAYEADDLDPRRRTGWSVVVTGLATEVSDPEQVARYQRL
LHPWVNMAMDTVVAIEPEIVTGIRIVADSRTP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSPGSRRASPQSAREVVELDRDEAMRLLASVDHGRVVFTRAALPAIRPVNHLVVDGRVIGRTRLTAKVSVAVRSSADAGVVVAYEADDLDPRRRTGWSVVVTGLATEVSDPEQVARYQRLLHPWVNMAMDTVVAIEPEIVTGIRIVADSRTP
Prediction	CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEHCCCEEEEEEEEEEEHCCEEEEEHCCCCCHHHHHHHCCCCCCEEEEEHCCCCCCCCCEEEEEEEEEEEEHCCHHHHHHHHHCCCCCCCCCCCEEEEEEEEEEEEEEHCCCCCCC
Conf.Score	99999998888776654599999999998699579999859978999978999899999995899878999986877786799998577787776568999999999589999999998576678888857999997799867875799999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MSPGSRRASPQSAREVVELDRDEAMRLLASVDHGRVVFTRAALPAIRPVNHLVVDGRVIGRTRLTAKVSVAVRSSADAGVVVAYEADDLDPRRRTGWSVVVTGLATEVSDPEQVARYQRLLHPWVNMAMDTVVAIEPEIVTGIRIVADSRTP
Prediction	75347544465565435514461034006724101000136530100001002344200000155332341244355432200010142367442100000203043054652243046205423535431000030440122303465778
	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

                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEHCCCEEEEEEEEEEEHCCEEEEEHCCCCCHHHHHHHCCCCCCEEEEEHCCCCCCCCCEEEEEEEEEEEEHCCHHHHHHHHHCCCCCCCCCCCEEEEEEEEEEEEEEHCCCCCCC
MSPGSRRASPQSAREVVELDRDEAMRLLASVDHGRVVFTRAALPAIRPVNHLVVDGRVIGRTRLTAKVSVAVRSSADAGVVVAYEADDLDPRRRTGWSVVVTGLATEVSDPEQVARYQRLLHPWVNMAMDTVVAIEPEIVTGIRIVADSRTP

3u0iA

0.14

0.12

0.82

2.79

MUSTER

--------------LITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTTD-GQKTNAMRKND----AICILFDQIESQT-KWRTVLVQGRYREIAREDEEEAIVRIM-ANEPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.14

0.12

0.82

4.82

dPPAS

--------------LITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTTD-GQKTNAMRKND----AICILFDQIESQT-KWRTVLVQGRYREIAREDEEEAIVRIMA-NEPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.14

0.12

0.82

4.48

wdPPAS

--------------LITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTTD-GQKTNAMRKND----AICILFDQIESQ-TKWRTVLVQGRYREIAREDEEEAIVRIMAN-EPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.15

0.12

0.82

3.47

wMUSTER

---------------ITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTT-DGQKTNAMRKND----AICILFDQIESQ-TKWRTVLVQGRYREIAREDEEEAIVRIM-ANEPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.14

0.12

0.82

4.27

wPPAS

L--------------ITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTTD-GQKTNAMRKND----AICILFDQIESQ-TKWRTVLVQGRYREIAREDEEEAIVRIM-ANEPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.14

0.12

0.82

7.68

dPPAS2

--------------LITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTTD-GQKTNAMRKND----AICILFDQIESQT-KWRTVLVQGRYREIAREDEEEAIVRIMA-NEPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.14

0.12

0.82

3.87

PPAS

--------------LITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTT-DGQKTNAMRKND----AICILFDQIESQTK-WRTVLVQGRYREIAREDEEEAIVRIM-ANEPTWKPVFFRVDIEKLSGHQAE------

3u0iA

0.14

0.12

0.82

4.49

Env-PPAS

--------------LITEMSDYDIREMIQHKHVGRLGYVVDDRPIIVPMTFRFSGGSFYSFTTD-GQKTNAMRKND----AICILFDQIESQTK-WRTVLVQGRYREIAREDEEEAIVRIM-ANEPTWKPVFFRVDIEKLSGHQAE------

3fkhD

0.32

0.28

0.86

2.64

MUSTER

-----------GDNPVNILNEQEALERLQSVSLGRVVVRRSD-EDIFPVNFIVDKGAIYIRTAEGNKLFSNLNH------DVLFEADEVKD--GKAWSVVVRATAEIVRKLDEIAYADTLLKPWIPTLKYNYVRIVPNEITGREFTLGEE--

3fkhD

0.32

0.28

0.86

4.56

dPPAS

-----------GDNPVNILNEQEALERLQSVSLGRVVVRRSD-EDIFPVNFIVDKGAIYIRTAEGNKLFSNLNH------DVLFEADEVKD--GKAWSVVVRATAEIVRKLDEIAYADTLLKPWIPTLKYNYVRIVPNEITGREFTLGEE--

(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 = 0.70±0.12

Estimated RMSD = 5.0±3.2Å

Download Model 2

C-score=-1.46

Download Model 3

C-score=-2.04

Download Model 4

C-score=-0.32

Download Model 5

C-score=-0.89

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	3u0iA	0.760	1.57	0.144	0.803
2	4ybnA	0.746	3.05	0.120	0.934
3	1w3oA	0.718	3.07	0.156	0.882
4	3cp3A	0.711	1.75	0.308	0.789
5	2hq9B	0.709	2.21	0.202	0.816
6	1rfeA	0.709	3.05	0.157	0.882
7	3fkhD	0.708	2.28	0.305	0.829
8	2arzA1	0.701	2.74	0.106	0.836
9	4zkyA	0.700	1.93	0.150	0.789
10	2fg9A	0.695	3.15	0.121	0.849

(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	0.35	21	2ptfA	FMN	Rep, Mult	45,47,48,49,50,61,62,63,66,67,68
2	0.17	7	2fg9A	FAD	Rep, Mult	16,87,96,97,98,99,100,102,141,142,143,145
3	0.03	2	1xxo0	III	Rep, Mult	33,35,39,40,42,43,44,45,46,47,48,49,81,85,96,98,102,103,141
4	0.03	2	2vpaA	PYR	Rep, Mult	50,61
5	0.02	1	1w3rA	2MN	Rep, Mult	47,48
6	0.01	1	3hy8A	PO4	Rep, Mult	53,54,59,61,113,117
7	0.01	1	2i51A	FMN	Rep, Mult	52,59,61,137
8	0.01	1	3fkhC	CA	Rep, Mult	17,18

	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	0.129	1ty9B	0.627	3.28	0.096	0.796	1.4.-.-	44,49
2	0.066	1nrgA	0.624	3.09	0.094	0.789	1.4.3.5	144
3	0.060	2puxB	0.464	4.15	0.074	0.684	3.4.21.5	NA
4	0.060	2zwlH	0.489	3.94	0.090	0.691	3.4.21.21	NA
5	0.060	1eawA	0.461	4.24	0.050	0.684	3.4.21.109,3.4.21.-	NA
6	0.060	2qy0C	0.242	4.39	0.045	0.388	3.4.21.41,3.4.21.42	62
7	0.060	2iphA	0.467	3.82	0.091	0.678	3.4.22.66	40
8	0.060	1c5mD	0.481	3.95	0.107	0.684	3.4.21.6	NA
9	0.060	1dleA	0.449	4.33	0.050	0.671	3.4.21.47	NA
10	0.060	1autC	0.480	4.01	0.083	0.691	3.4.21.69	NA
11	0.060	1jnwA	0.614	3.26	0.138	0.783	1.4.3.5	NA
12	0.060	2ok5A	0.469	3.97	0.047	0.678	3.4.21.47	51
13	0.060	3h09B	0.472	3.96	0.077	0.697	3.4.21.72	NA
14	0.060	2gv6A	0.464	4.25	0.042	0.684	3.4.21.109	NA
15	0.060	1rtkA	0.306	5.72	0.035	0.592	3.4.21.47	76,79,106
16	0.060	1z8gA	0.473	4.39	0.075	0.704	3.4.21.106	NA
17	0.060	3dfjA	0.455	4.26	0.050	0.678	3.4.21.-	NA
18	0.060	1ci0A	0.615	3.25	0.102	0.796	1.4.3.5	144
19	0.060	1ekbB	0.463	4.19	0.052	0.678	3.4.21.9	NA
20	0.060	1bbrE	0.330	3.55	0.033	0.467	3.4.21.5	NA
21	0.060	1zjkA	0.476	4.15	0.082	0.697	3.4.21.104	22,98

(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	0.42	0.711	1.75	0.31	0.79	3cp3A	GO:0010181 GO:0016491 GO:0055114
1	0.37	0.717	2.31	0.30	0.84	3fkhD	GO:0010181 GO:0016491 GO:0055114
2	0.31	0.719	3.19	0.16	0.89	2x1kA	GO:0010181 GO:0016491 GO:0055114
3	0.30	0.767	1.21	0.16	0.80	3u5wA	GO:0010181 GO:0016491 GO:0055114
4	0.28	0.630	2.63	0.16	0.75	2htdB	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
5	0.27	0.637	2.30	0.13	0.75	5escA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
6	0.26	0.730	2.91	0.17	0.89	1rfeA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
7	0.23	0.731	3.14	0.11	0.89	2fg9A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
8	0.23	0.723	2.30	0.20	0.84	2hq9B	GO:0000166 GO:0010181 GO:0016491 GO:0055114
9	0.23	0.674	2.57	0.12	0.80	2htiA	GO:0000166 GO:0010181 GO:0016491 GO:0055114
10	0.22	0.649	2.91	0.13	0.80	4qvbB	GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
11	0.22	0.746	3.05	0.12	0.93	4ybnA	GO:0010181 GO:0016491 GO:0055114
12	0.22	0.670	2.61	0.06	0.82	3tgvA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
13	0.22	0.677	2.91	0.12	0.84	5bncA	GO:0010181 GO:0016491 GO:0055114
14	0.21	0.711	2.63	0.11	0.86	2furA	GO:0010181 GO:0016491 GO:0055114
15	0.20	0.680	2.83	0.10	0.83	3dnhA	GO:0010181 GO:0016491 GO:0055114
16	0.20	0.625	2.86	0.12	0.76	1wv4A	GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
17	0.19	0.668	2.06	0.12	0.76	2hq7B	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
18	0.18	0.629	3.19	0.10	0.76	2ou5A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
19	0.17	0.636	3.19	0.14	0.80	1jnwA	GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
20	0.17	0.660	2.22	0.12	0.76	3ec6A	GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
21	0.16	0.617	2.97	0.12	0.74	3f7eA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
22	0.08	0.524	2.29	0.17	0.61	3r5lA	GO:0005618 GO:0005886 GO:0010181 GO:0016020 GO:0016491 GO:0055114 GO:0070967
23	0.06	0.307	5.64	0.05	0.59	1ay0A	GO:0003824 GO:0004802 GO:0005737 GO:0006098 GO:0008152 GO:0016740 GO:0046872
24	0.06	0.307	3.99	0.05	0.45	1a9nB	GO:0000166 GO:0000398 GO:0002230 GO:0003676 GO:0003723 GO:0005634 GO:0005654 GO:0005681 GO:0005686 GO:0005730 GO:0006397 GO:0008380 GO:0030529 GO:0035614 GO:0071013 GO:0098792

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0016641
GO-Score	0.87	0.55
Biological Processes	GO:0055114	GO:1901576	GO:0009108	GO:0042822
GO-Score	0.87	0.55	0.55	0.55
Cellular Component
GO-Score

(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.