I-TASSER results

I-TASSER results for job id Rv3162c

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

Input Sequence in FASTA format

>protein (145 residues)
MTSFAHPGTRGLSTVFGLMMVGSAAVGSHGLAVVVGLAAVIAVGVAAVFRLAATLAVVLS
VVMIVVSGPTHVLAALSGFCAAVYLVCRYGAGVVAGSWPTTVAAVGFTFAGLAATSFPLQ
VPWLPLAAPLAVLATYVLATRPFSR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTSFAHPGTRGLSTVFGLMMVGSAAVGSHGLAVVVGLAAVIAVGVAAVFRLAATLAVVLSVVMIVVSGPTHVLAALSGFCAAVYLVCRYGAGVVAGSWPTTVAAVGFTFAGLAATSFPLQVPWLPLAAPLAVLATYVLATRPFSR
Prediction	CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHEEEEEHCCCCC
Conf.Score	9988888887545788899999875567874589999999999999988888899999999988745996577898999999999986465544568863688899999999999864678855456655556655555445779
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTSFAHPGTRGLSTVFGLMMVGSAAVGSHGLAVVVGLAAVIAVGVAAVFRLAATLAVVLSVVMIVVSGPTHVLAALSGFCAAVYLVCRYGAGVVAGSWPTTVAAVGFTFAGLAATSFPLQVPWLPLAAPLAVLATYVLATRPFSR
Prediction	7443444344113200110001123343532100110111101221331432120003210100002534302110111010010002324334334332000122211102211333353331222333313102101322248
	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

CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHEEEEEHCCCCC
MTSFAHPGTRGLSTVFGLMMVGSAAVGSHGLAVVVGLAAVIAVGVAAVFRLAATLAVVLSVVMIVVSGPTHVLAALSGFCAAVYLVCRYGAGVVAGSWPTTVAAVGFTFAGLAATSFPLQVPWLPLAAPLAVLATYVLATRPFSR

5ezmA1

0.17

0.16

0.94

0.74

MUSTER

LFGLGEWQARLAVALSGLLGIGVSMMAAARAAAFTGLALLAAPMWSVAAHLDMTLAGVMSCVLAFMLAARRGWMVACWAAMGVAILTK---------GLVGIALPGLVLVVYTLVTRDWRRLHLALGVVVMLVITVPWFYLVSVR

4za6A2

0.10

0.09

0.91

0.62

dPPAS

-------------ATERTYRKAMSQASGQGPEYILDVFGRVMRSVESSTELRALTKREPMVFIKLAMMPGSIESISASITAEILQSQVDAGQLTITLSPQVLGEALVRICDVHLYAPLLGREKAEIETALDLIALLLGVTRNHHH

4jkzA2

0.10

0.08

0.79

0.61

wdPPAS

--RMPKTDD-------------VTA------DLASWAGTLAAALTT-----RRGHAMLKTLMAASLEHEDTAARLREGFSRPLIESVRDRLRDEDIDADHAQAAADALLGAVVNAVLSEGRSYSRQRAETSARII-VAGLRP---

3wajA

0.11

0.10

0.97

0.82

wMUSTER

FTYYPYGSYTHFGPFLVYLGSIAGI-SATSGAFIPAIGGVLAILPVYLLTREVKRAAVIAAFLIAIVDHHIWEAFWQVSALGTFLLAYNWKGHDLTARQMAYPVIAGITIGLYVLSWG---AGFIIAPIILAFMFFAFVLAGFVN

2qo3B3

0.23

0.17

0.75

0.84

wPPAS

--TTAHDGRPV------PLVVSA----RSTAALRAQAAQIAELLER----DLAGVGLGLATAAVVASTREEAVRGLREIAAGA----ATADAVVEGVTEV-LSAFLRSMATAHVS---VDIRWFAL--P-----TY-----PFQR

4zowA2

0.15

0.14

0.92

0.71

dPPAS2

ITGEQLS-----SYEYGLLQVPIFG------ALIAGNLLLARLTVRSLIIMGGWPIMIGLLVAAAATAYLWMTAGLSIYAFGIGLANAGLVRLTLFASDTVSAAMGMLQMLIFTVGIEIGNGLFNLFNLVNGILWLSLMVI-FLK

4zowA2

0.15

0.14

0.92

0.87

PPAS

ITGEQLS-----SYEYGLLQVPIFG------ALIAGNLLLARLTVRSLIIMGGWPIMIGLLVAAAATAYLWMTAGLSIYAFGIGLANAGLVRLTLFASDTVSAAMGMLQMLIFTVGIEIGNGLFNLFNLVNGILWLSLMVI-FLK

3kyzA

0.12

0.08

0.71

0.76

Env-PPAS

---------------------------YFLAPADRHYLADYARQAEDAWRREGAAGAERFRKELSAKEDT--WVA----------LVGPHLESLGSTPLSAEESSHLTFRKL---DWPSELPYVSIEFPGHPEQGRLVIQLPLLP

4wgvA

0.12

0.97

0.72

MUSTER

IDSNLQLSIAFVVNCLLLTLGAALFFGTKTNDLGGFYDLYHALKTEPVLATLGGVMSTLFAVALLAS---GQNSTITGTLAGQIVMEGFLRLSIPNWLITRSLAVIPVIICLIIFKGNSEKIELSIALPFSLIPLQLATSNK--K

4jkzA2

0.13

0.10

0.79

0.59

dPPAS

--------------------------RMPKTDDVTADLASWAGTLAAALTTRRGHAMLKTLMAASLEHEDTAARLREGFSRPLIESVRDRLRDEDIDADHAQAAADALLGAVVNAVLSEGRSYSRQRAETSARII-VAGLRP---

(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=-3.39

Estimated TM-score = 0.34±0.11

Estimated RMSD = 12.5±4.3Å

Download Model 2

C-score=-3.71

Download Model 3

C-score=-4.32

Download Model 4

C-score=-4.52

Download Model 5

C-score=-4.66

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	2w53A	0.682	3.10	0.109	0.917
2	3crjA	0.665	3.28	0.069	0.890
3	2zb9A	0.653	3.44	0.083	0.883
4	3angC	0.650	3.34	0.065	0.890
5	4gctA	0.650	3.62	0.082	0.890
6	2hyjA	0.649	3.30	0.083	0.890
7	4w97A	0.648	3.05	0.085	0.855
8	2pbxA	0.645	3.06	0.054	0.869
9	3lsjA	0.644	3.17	0.060	0.855
10	3ih4A	0.644	3.47	0.046	0.876

(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	0.08	5	3q0vA	LL4	Rep, Mult	22,33,37,38,41,80,86,87,90,106,109,136
2	0.06	4	3p9tA	TCL	Rep, Mult	15,18,41,61,62,79,80,83,87,105,106,109,113
3	0.06	4	3b6aC	ZCT	Rep, Mult	12,15,19,45,65,66,73,79,83,110,114
4	0.03	2	3htiA	MGR	Rep, Mult	7,11,12,15,45,58,61,62,79,110,113
5	0.03	2	2np5C	NDS	Rep, Mult	49,50,52,56
6	0.03	2	1jt0C	QNA	Rep, Mult	12,54,55,56,57,60,61
7	0.03	2	3q3sA	O8B	Rep, Mult	19,38,41,42,45,49,58,62,76,79,82,109,112,113,116,117,120,132
8	0.03	2	3angD	DCC	Rep, Mult	14,45,61,65,66,69,70,73,76,107,110,111,114
9	0.02	1	2wieC	CVM	Rep, Mult	76,81
10	0.02	1	3p9tA	TCL	Rep, Mult	11,15,18,47,55,58
11	0.02	1	3anpC	DCC	Rep, Mult	18,72,73,76,106,110,112,113
12	0.02	1	2qrjA	SO4	Rep, Mult	10,13,16
13	0.02	1	3rvzA	PX4	Rep, Mult	122,123
14	0.02	1	3k7tA	GP7	Rep, Mult	7,8
15	0.02	1	3locA	URA	Rep, Mult	117,120
16	0.02	1	2q69A	CA	Rep, Mult	70,72,78
17	0.02	1	2wse1	CLA	Rep, Mult	106,107,130

	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	2oa6D	0.476	5.03	0.054	0.848	4.2.3.9	NA
2	0.060	1kizA	0.498	4.65	0.055	0.855	4.2.3.6	114
3	0.060	2h1nA	0.497	5.01	0.050	0.862	3.4.24.-	113
4	0.060	1dgpA	0.475	5.11	0.054	0.848	4.2.3.9,4.1.99.7	NA
5	0.060	1j36A	0.519	4.42	0.071	0.828	3.4.15.1	NA
6	0.060	1pgjA	0.515	4.07	0.080	0.779	1.1.1.44	NA
7	0.060	2qm6C	0.523	4.88	0.088	0.890	2.3.2.2	47
8	0.060	1n1zA	0.537	4.47	0.083	0.903	5.5.1.8	49
9	0.060	2i2xA	0.521	4.27	0.071	0.814	2.1.1.90	83
10	0.060	1jk0A	0.477	4.63	0.048	0.800	1.17.4.1	NA
11	0.060	2j5cB	0.513	4.47	0.043	0.841	4.2.3.-	107
12	0.060	2fhcA	0.448	5.31	0.082	0.841	3.2.1.41	76,105,108
13	0.060	3ckeD	0.465	4.11	0.039	0.690	4.2.3.9	NA
14	0.060	3fwnA	0.486	4.23	0.116	0.759	1.1.1.44	NA
15	0.060	1u8vA	0.487	3.95	0.025	0.752	5.3.3.3	NA
16	0.060	1a5tA	0.512	3.95	0.085	0.759	2.7.7.7	110
17	0.060	2iz1B	0.521	3.48	0.074	0.738	1.1.1.44	NA
18	0.060	3ffzA	0.505	4.56	0.045	0.841	3.4.24.69	NA
19	0.060	1cb5A	0.479	3.87	0.059	0.717	3.4.22.40	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	0.25	0.599	3.63	0.11	0.88	3bhqA	GO:0003677 GO:0006351 GO:0006355
1	0.24	0.638	3.73	0.11	0.92	2np5A	GO:0003677 GO:0006351 GO:0006355
2	0.23	0.688	3.32	0.11	0.94	3p9tA	GO:0003677 GO:0006351 GO:0006355
3	0.22	0.634	3.13	0.09	0.85	2np3B	GO:0003677 GO:0006351 GO:0006355
4	0.22	0.652	3.00	0.07	0.88	2hytA	GO:0003677 GO:0006351 GO:0006355
5	0.21	0.630	3.25	0.03	0.86	4ichA	GO:0003677 GO:0006351 GO:0006355
6	0.21	0.681	3.24	0.06	0.92	3crjA	GO:0003677
7	0.20	0.654	3.72	0.07	0.94	5h9tH	GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0051051
8	0.20	0.626	3.36	0.04	0.89	4pxiB	GO:0003677 GO:0006351 GO:0006355
9	0.19	0.665	2.92	0.06	0.87	3f0cA	GO:0003677 GO:0006351 GO:0006355
10	0.18	0.638	2.98	0.06	0.84	3whcA	GO:0003677 GO:0005737 GO:0006351 GO:0006355 GO:0006629 GO:0006631 GO:0016042
11	0.18	0.648	3.53	0.04	0.89	4gclB	GO:0003677 GO:0005737 GO:0007049 GO:0009295 GO:0010974 GO:0043565 GO:0043590 GO:0051301 GO:0051302
12	0.17	0.627	3.26	0.06	0.84	2oerB	GO:0003677 GO:0006351 GO:0006355
13	0.16	0.637	3.72	0.07	0.91	3bcgA	GO:0003677 GO:0003700 GO:0006351 GO:0006355 GO:0008144 GO:0042493 GO:0043565 GO:0045892
14	0.15	0.654	3.57	0.07	0.92	3c07A	GO:0003677 GO:0006351 GO:0006355
15	0.14	0.580	3.45	0.09	0.82	3t6nA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
16	0.13	0.667	3.41	0.05	0.90	2id6A	GO:0003677 GO:0006351 GO:0006355
17	0.12	0.655	3.05	0.07	0.86	2g3bA	GO:0003677 GO:0006351 GO:0006355
18	0.10	0.621	3.47	0.11	0.89	3htaA	GO:0003677 GO:0006351 GO:0006355
19	0.10	0.615	3.35	0.08	0.84	3vprA	GO:0003677 GO:0006351 GO:0006355 GO:0042802
20	0.09	0.630	3.49	0.06	0.87	2g7sA	GO:0003677 GO:0006351 GO:0006355
21	0.09	0.639	3.49	0.09	0.88	2nx4A	GO:0003677 GO:0006351 GO:0006355
22	0.09	0.639	3.47	0.07	0.90	3eupA	GO:0003677 GO:0006351 GO:0006355
23	0.08	0.644	3.49	0.10	0.92	3qbmA	GO:0003677 GO:0003700 GO:0006351 GO:0006355
24	0.08	0.624	3.34	0.07	0.87	5f1jA	GO:0003677 GO:0006351 GO:0006355

Consensus prediction of GO terms

Molecular Function	GO:0003677
GO-Score	0.73
Biological Processes	GO:0006355
GO-Score	0.73
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.