I-TASSER results

I-TASSER results for job id Rv0695

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

Input Sequence in FASTA format

>protein (251 residues)
MNSSYHRRVPVVGELGSATSSQLPSTSPSIVIPLGSTEQHGPHLPLDTDTRIATAVARTV
TARLHAEDLPIAQEEWLMAPAIAYGASGEHQRFAGTISIGTEALTMLLVEYGRSAACWAR
RLVFVNGHGGNVGALTRAVGLLRAEGRDAGWCPCTCPGGDPHAGHTETSVLLHLSPADVR
TERWRAGNRAPLPVLLPSMRRGGVAAVSETGVLGDPTTATAAEGRRIFAAMVDDCVRRVA
RWMPQPDGMLT

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MNSSYHRRVPVVGELGSATSSQLPSTSPSIVIPLGSTEQHGPHLPLDTDTRIATAVARTVTARLHAEDLPIAQEEWLMAPAIAYGASGEHQRFAGTISIGTEALTMLLVEYGRSAACWARRLVFVNGHGGNVGALTRAVGLLRAEGRDAGWCPCTCPGGDPHAGHTETSVLLHLSPADVRTERWRAGNRAPLPVLLPSMRRGGVAAVSETGVLGDPTTATAAEGRRIFAAMVDDCVRRVARWMPQPDGMLT
Prediction	CCCCCCCCCHHHHHCCHHHHHHHHHCCCEEEEHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCCCEHCCCCCCCCCCEEHCCHHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCHHHHHHHHHHCHHHCCHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Conf.Score	98766676546877888999999876999999767777889988874689999999999999968766666788789968865555766688997688699999999999999999969889999789865899999999999984645888755788888888899999998787767846546788877654455545677777479987788556999999999999999999999999986789999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MNSSYHRRVPVVGELGSATSSQLPSTSPSIVIPLGSTEQHGPHLPLDTDTRIATAVARTVTARLHAEDLPIAQEEWLMAPAIAYGASGEHQRFAGTISIGTEALTMLLVEYGRSAACWARRLVFVNGHGGNVGALTRAVGLLRAEGRDAGWCPCTCPGGDPHAGHTETSVLLHLSPADVRTERWRAGNRAPLPVLLPSMRRGGVAAVSETGVLGDPTTATAAEGRRIFAAMVDDCVRRVARWMPQPDGMLT
Prediction	75432533132034012520550277330000000022231210000000000130042006404654254442200000000002032124100002043500130032003002420210000000100230033004202440200000001153232000110001001011120336315546446244214313423033124210002035023510330042005200500450176374417
	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                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCHHHHHCCHHHHHHHHHCCCEEEEHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCCCEHCCCCCCCCCCEEHCCHHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCHHHHHHHHHHHHHHHCCEEEEEHCCCCCCCCCCHHHHHHHHHHCHHHCCHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
MNSSYHRRVPVVGELGSATSSQLPSTSPSIVIPLGSTEQHGPHLPLDTDTRIATAVARTVTARLHAEDLPIAQEEWLMAPAIAYGASGEHQRFAGTISIGTEALTMLLVEYGRSAACWARRLVFVNGHGGNVGALTRAVGLLRAEGRDAGWCPCTCPGGDPHAGHTETSVLLHLSPADVRTERWRAGNRAPLPVLLPSMRRGGVAAVSETGVLGDPTTATAAEGRRIFAAMVDDCVRRVARWMPQPDGMLT

3no4A

0.22

0.20

0.92

2.34

MUSTER

IHHHHHYFQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAK-FSKFYFINGHGGNIATLKAAFSETYAHLEDVQCQVANWFCEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIY----SAADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3no4A

0.22

0.20

0.92

4.31

dPPAS

-DKIHHHHQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAFSKFYFINGHGGNIATLKAAFSETYAHLEVQCQVANWFCQEGSHATPSEVALTQYVYPEAIK----QAPLSPEVASGHRIYSAADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3no4A

0.23

0.21

0.91

4.51

wdPPAS

-DKIHHHHQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAK-FSKFYFINGHGGNIATLKAAFSETYAHLEDANWFCGSGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASG----HRIYSAADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3no4A

0.23

0.21

0.92

2.80

wMUSTER

IHHHHHYFQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAK-FSKFYFINGHGGNIATLKAAFSETYAHLEVANWFCGSVYQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIY----SAADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3no4A

0.23

0.21

0.91

4.15

wPPAS

-DKIHHHHQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAK-FSKFYFINGHGGNIATLKAAFSETYAHLEDANWFCGSGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASG----HRIYSAADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3no4A

0.22

0.20

0.92

12.05

dPPAS2

-DKIHHHHQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAKAFSKFYFINGHGGNIATLKAAFSETYAHLEDVQCQVANWFCEGSHATPSEVALTQYVYPEAIKQAPLSPEVASGHRIYS----AADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3no4A

0.23

0.21

0.91

3.41

PPAS

-DKIHHHHQGLLHLSTWQEVEAYLQQSKGIIFPIGSTEQHGPTGLIGTDAICAEAIAAGVGDATG----------AIVGPTINVG-ALHHTAFPGTISLRPSTLIQVVRDYVTCLAK-FSKFYFINGHGGNIATLKAAFSETYAHLEDANWFCGSGDQEGSHATPSEVALTQYVYPEAIKQAPLSPEVASG----HRIYSAADFRVRYPDGRGSNPGLATPEHGKQFYDLAVKELSNGYLEFVNAD-----

3lubA

0.22

0.20

0.91

5.01

Env-PPAS

------NKEVDLSVSCLGKVKEL--KYDVIILPWGATEPHNLHLPYLTDCILPHDIAVEAAELALSR------SGVRCVPPVPFGAHPGQRELPFCIHTRYATQQAILEDIVSSLHVQFRKLLILSGHGGNNFK---GIRDLAFEYPDFLIAAANEAEIDDHAGESETSVHYH--PELVNLAEAGDGESKPFAIASVAWVPRHWDKATVDSGVGNPKKATAEKGERYVKPIVEKLAGLFEEAQHDLYE---

1q3kA

0.29

0.26

0.90

2.29

MUSTER

------SKSVFVGELTWKEYEARVAAGDVLMLPVGALEQHGHHMCMNVDVLLPTAVCQRVAERIG----------ALVLPGLQYGYKSQQKHFPGTTSLDGATLTGTVQDIIRELAR-VRRLVLMNGHYENVEGIDLALRELRYAGIHLSYWDFVLGWDIEHGGVFETSLMLALYPDLVDLERVVDHPPATFPPY--DVFPVDPARTPAPGTLSSAKTASREKGELILEVCVQGIADAIGQEF--PP---T

1q3kA

0.28

0.25

0.91

4.19

dPPAS

------SKSVFVGELTWKEYEARVAAGCVLMLPVGALEQHGHHMCMNVDVLLPTAVCQRVAERIG----------ALVLPGLQYGYKSQQKSFPGTTSLDGATLTGTVQDIIRELARHVRRLVLMNGHYENVEGIDLALRELRYAGIHDFKVVVLLGWDIEHGGVFETSLMLALYPDLVDLERVVDHPPATFPPYD--VFPVDPARTPAPGTLSSAKTASREKGELILEVCVQGIADAIGQEFPPT-----

(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=1.05

Estimated TM-score = 0.86±0.07

Estimated RMSD = 3.7±2.5Å

Download Model 2

C-score=0.65

Download Model 3

C-score=-1.35

Download Model 4

C-score=0.58

Download Model 5

C-score=-0.86

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	3no4A	0.884	1.45	0.212	0.920
2	1q3kA	0.821	2.11	0.261	0.896
3	3lubA	0.782	2.73	0.231	0.896
4	3f98A	0.530	4.38	0.048	0.717
5	3o8lA	0.528	4.66	0.057	0.737
6	1wpxA	0.525	4.75	0.057	0.761
7	2y6uA	0.525	4.76	0.036	0.741
8	2q0xA	0.523	4.60	0.059	0.709
9	2e4xB	0.521	4.25	0.060	0.705
10	3o8oB	0.519	4.99	0.066	0.753

(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	0.54	17	3a6eA	MN	Rep, Mult	38,49,128,130
2	0.28	7	3lubA	ZN	Rep, Mult	40,49,167
3	0.15	8	3a6jB	CRN	Rep, Mult	40,49,128,129,161,162,167
4	0.03	2	3o8lA	ATP	Rep, Mult	34,35,84,105,127,130,131,133,134
5	0.01	1	3etgE	GWD	Rep, Mult	102,106,109,145

	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	1gz3A	0.523	5.05	0.083	0.765	1.1.1.38	NA
2	0.060	1vjpA	0.511	4.21	0.082	0.681	5.5.1.4	54,216,230
3	0.060	2c1cA	0.504	4.52	0.090	0.709	3.4.17.2	206
4	0.060	1hlgA	0.510	4.94	0.057	0.741	3.1.1.3	NA
5	0.060	1cpyA	0.528	4.80	0.056	0.765	3.4.16.5	NA
6	0.060	1ac5A	0.505	5.02	0.048	0.757	3.4.16.6	NA
7	0.060	1uwyA	0.506	4.50	0.043	0.713	3.4.17.12	163,213
8	0.060	2dvmA	0.501	4.52	0.066	0.693	1.1.1.38	NA
9	0.060	1jqgA	0.515	4.66	0.101	0.733	3.4.17.1	NA
10	0.060	1obrA	0.512	4.36	0.027	0.709	3.4.17.18	NA
11	0.060	1cpbA	0.160	4.09	0.054	0.211	3.4.17.2	NA
12	0.060	1q3kA	0.821	2.11	0.261	0.896	3.5.2.10	NA
13	0.060	2fj0A	0.507	5.49	0.061	0.789	3.1.1.1	NA
14	0.060	2f48B	0.508	5.05	0.060	0.741	2.7.1.90	NA
15	0.060	1zg7A	0.504	4.29	0.039	0.685	3.4.17.2	NA
16	0.060	1k8qA	0.510	5.10	0.049	0.765	3.1.1.3	234
17	0.060	1pytA	0.180	4.53	0.085	0.259	3.4.17.1	NA
18	0.060	1hlgB	0.507	5.14	0.057	0.765	3.1.1.3	103
19	0.060	1thgA	0.511	4.88	0.074	0.741	3.1.1.3	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	0.57	0.890	1.35	0.21	0.92	3no4A
1	0.54	0.787	2.65	0.23	0.90	3lubF	GO:0046872
2	0.40	0.821	2.13	0.27	0.90	3a6kA	GO:0006601 GO:0006602 GO:0008270 GO:0016787 GO:0030145 GO:0046872 GO:0047789
3	0.07	0.518	5.39	0.06	0.78	3etdA	GO:0000166 GO:0004352 GO:0004353 GO:0005524 GO:0005525 GO:0005739 GO:0005743 GO:0005759 GO:0006520 GO:0006538 GO:0006541 GO:0016491 GO:0055114 GO:0072350
4	0.07	0.530	4.38	0.05	0.72	3f98A	GO:0003847 GO:0005543 GO:0005576 GO:0005615 GO:0005737 GO:0006629 GO:0016042 GO:0016787 GO:0016788 GO:0034362 GO:0034374 GO:0034440 GO:0034441 GO:0047499 GO:0050729 GO:0090026
5	0.07	0.479	5.16	0.04	0.70	4hxgF	GO:0006508 GO:0008236 GO:0046872
6	0.07	0.418	4.95	0.08	0.61	4wfiA	GO:0003847 GO:0016042 GO:0046872
7	0.07	0.440	4.72	0.07	0.61	3visA	GO:0003847 GO:0015996 GO:0016042 GO:0046872 GO:0047746
8	0.07	0.421	5.06	0.08	0.61	4eb0A	GO:0003847 GO:0016042 GO:0016787 GO:0050525
9	0.07	0.427	5.06	0.06	0.61	4cg3A	GO:0003847 GO:0015996 GO:0016042 GO:0016787 GO:0047746 GO:0050525
10	0.07	0.445	4.71	0.09	0.64	2rh4B	GO:0016491 GO:0017000 GO:0055114
11	0.06	0.403	4.47	0.05	0.54	3bdvA	GO:0016787 GO:0046872
12	0.06	0.347	5.85	0.05	0.57	5awoA	GO:0003824 GO:0004553 GO:0005975 GO:0030246
13	0.06	0.345	5.43	0.04	0.53	4rxlA	GO:0015412 GO:0015689 GO:0030288
14	0.06	0.358	4.23	0.04	0.49	2r3bB	GO:0000166 GO:0005524 GO:0016829 GO:0046496 GO:0052855
15	0.06	0.397	5.80	0.07	0.65	1edqA	GO:0004553 GO:0004568 GO:0005975 GO:0006032 GO:0008152 GO:0016787 GO:0016798
16	0.06	0.341	5.47	0.05	0.54	4cbhD	GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004175 GO:0004197 GO:0004252 GO:0004386 GO:0005216 GO:0005524 GO:0006508 GO:0006810 GO:0006811 GO:0008026 GO:0008233 GO:0008234 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019062 GO:0019079 GO:0019082 GO:0030430 GO:0030683 GO:0033644 GO:0033897 GO:0034220 GO:0039503 GO:0039520 GO:0039548 GO:0039654 GO:0039663 GO:0039694 GO:0039707 GO:0042025 GO:0044228 GO:0044385 GO:0046718 GO:0051259 GO:0055036 GO:0070008 GO:0090502 GO:1903608 GO:1990219
17	0.06	0.334	5.04	0.03	0.49	3d6kC	GO:0003824
18	0.06	0.320	5.55	0.04	0.52	2f2gA	GO:0009228 GO:0009229 GO:0016787 GO:0050334

Consensus prediction of GO terms

Molecular Function	GO:0047789	GO:0030145	GO:0008270
GO-Score	0.40	0.40	0.40
Biological Processes	GO:0006601	GO:0006602
GO-Score	0.40	0.40
Cellular Component	GO:0005759	GO:0005743	GO:0034362
GO-Score	0.07	0.07	0.07

(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.