I-TASSER results

I-TASSER results for job id Rv2437

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

Input Sequence in FASTA format

>protein (139 residues)
MLQRTNVVQPLNTLRMVWIQVAGIIPATAGIAATVYAQLAMGDSWRIGVDEQENTTLVRT
GPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFILLVATLEVHVRRVEEPYLLRTHSAV
YRGYTASVGRFVPGVGLIR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLQRTNVVQPLNTLRMVWIQVAGIIPATAGIAATVYAQLAMGDSWRIGVDEQENTTLVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFILLVATLEVHVRRVEEPYLLRTHSAVYRGYTASVGRFVPGVGLIR
Prediction	CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCCCEEHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCHCCCCCCCC
Conf.Score	8764444346665665899999999999999999999999998778777777787687567633455979999999999999998559999999999999999999999999999979999999997796578788889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MLQRTNVVQPLNTLRMVWIQVAGIIPATAGIAATVYAQLAMGDSWRIGVDEQENTTLVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFILLVATLEVHVRRVEEPYLLRTHSAVYRGYTASVGRFVPGVGLIR
Prediction	4133333231233333332322133223313322320232034324341545664401132222321002022322333123133333312323323333333310430153027423753451274152444415648
	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

                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEHCCCCEEHCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCHCCCCCCCC
MLQRTNVVQPLNTLRMVWIQVAGIIPATAGIAATVYAQLAMGDSWRIGVDEQENTTLVRTGPFKWVRHPIYTAMMAFGLGLLLVTPNLVALAGFILLVATLEVHVRRVEEPYLLRTHSAVYRGYTASVGRFVPGVGLIR

4a2nB

0.21

0.20

0.96

2.40

MUSTER

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFPK-----

4a2nB

0.21

0.20

0.96

2.43

dPPAS

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFPK-----

4a2nB

0.21

0.20

0.96

4.73

wdPPAS

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFP-----K

4a2nB

0.21

0.20

0.96

3.28

wMUSTER

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFP-----K

4a2nB

0.21

0.20

0.96

4.92

wPPAS

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFP-----K

4a2nB

0.21

0.20

0.96

6.65

dPPAS2

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFPK-----

4a2nB

0.21

0.20

0.96

3.57

PPAS

TAVFSSYLDSFNINLPDSIRLFALIVTFLNIGLFTKIHKDLGNNWSAILEIKDGHKLVKEGIYKNIRHPMYAHLWLWVITQGIILSNWVVLIFGIVAWAILYFIRVPKEEELLIEEFGDEYIEYMGKTGRLFPK-----

4quvA2

0.19

0.17

0.88

3.15

Env-PPAS

--------------LPVWGIIAIVALNLAGYAIFRGANIQKHHFRAKYIKTKQGSLLLTSGWWGIARHMNYFGDLMIALSWCLPAAGSPIPYFHIVYFTILLLHREKRDDAMCLAKYGEDWLQYRKKVPRIVPKIY---

4quvA2

0.19

0.17

0.87

2.33

MUSTER

--------------LPVWGIIAIVALNLAGYAIFRGANIQKHHF-AKYIKTKQGSLLLTSGWWGIARHMNYFGDLMIALSWCLPAAGSPIPYFHIVYFTILLLHREKRDDAMCLAKYGEDWLQYRKKVPRIVPKI--Y-

4quvA2

0.20

0.17

0.88

2.09

dPPAS

--------------LPVWGIIAIVALNLAGYAIFRGANIQKHHFRRDPNRIKQGSLLLTSGWWGIARHMNYFGDLMIALSWCLPAAGSPIPYFHIVYFTILLLHREKRDDAMCLAKYGEDWLQYRKKVPRIVPKIY---

(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=1.22

Estimated TM-score = 0.88±0.07

Estimated RMSD = 2.3±1.8Å

Download Model 2

C-score=-1.13

Download Model 3

C-score=-4.42

Download Model 4

C-score=-3.08

Download Model 5

C-score=-5.00

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	4a2nB	0.940	0.71	0.209	0.964
2	4quvA	0.726	2.98	0.170	0.914
3	1syyA	0.575	4.07	0.055	0.878
4	4bmoA	0.571	4.03	0.079	0.871
5	4dr0A	0.571	4.06	0.048	0.878
6	3rkoN	0.562	4.44	0.100	0.914
7	2jcdA	0.561	4.54	0.073	0.928
8	1oquC	0.552	4.05	0.092	0.849
9	1t0sB	0.552	4.44	0.081	0.914
10	1mhyB	0.551	4.64	0.066	0.906

(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	3	4a2nB	SAH	Rep, Mult	41,45,46,49,50,51,55,57,58,63,68,69,70,71,109,113
2	0.11	2	1xvgB	BRJ	Rep, Mult	58,59,63,124,128
3	0.07	1	4a2nB	CDL	Rep, Mult	28,32,36,39
4	0.06	1	3rkoN	LFA	Rep, Mult	71,74,75,78,102
5	0.06	1	3rkoN	LFA	Rep, Mult	31,32,35,76,77,80
6	0.06	1	1mhy1	III	Rep, Mult	76,77,80,81,83,84,86,90,94,97

	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	2qb0B	0.352	4.56	0.058	0.561	3.2.1.17	NA
2	0.060	1mhsA	0.489	4.72	0.023	0.827	3.6.3.6	NA
3	0.060	2rccA	0.544	4.13	0.050	0.842	1.17.4.1	NA
4	0.060	1jqoA	0.529	4.45	0.082	0.827	4.1.1.31	NA
5	0.060	2qcxB	0.479	4.54	0.061	0.784	3.5.99.2	36
6	0.060	2w90B	0.491	5.02	0.030	0.813	1.1.1.44	NA
7	0.060	3ee4A	0.542	4.23	0.045	0.849	1.17.4.1	NA
8	0.060	3fwnA	0.401	4.96	0.051	0.669	1.1.1.44	NA
9	0.060	1qd1B	0.322	5.50	0.038	0.626	2.1.2.5,4.3.1.4	NA
10	0.060	1mhyD	0.539	4.74	0.052	0.906	1.14.13.25	NA
11	0.060	1mhyB	0.551	4.64	0.066	0.906	1.14.13.25	NA
12	0.060	1ezfB	0.500	4.02	0.056	0.755	2.5.1.21	104
13	0.060	2p4qA	0.496	4.92	0.060	0.827	1.1.1.44	NA
14	0.060	2vuxB	0.502	4.55	0.055	0.842	1.17.4.1	NA
15	0.060	1fziA	0.422	5.10	0.039	0.791	1.14.13.25	NA
16	0.060	2epoB	0.489	4.44	0.074	0.799	3.2.1.52	50,51
17	0.060	3djlA	0.479	4.91	0.070	0.820	1.3.99.-	NA
18	0.060	2jg0A	0.488	4.37	0.046	0.791	3.2.1.28	50,112
19	0.060	2epoA	0.491	4.27	0.113	0.791	3.2.1.52	50,51

(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	0.43	0.940	0.71	0.21	0.96	4a2nB	GO:0004671 GO:0006481 GO:0016020 GO:0016021
1	0.26	0.726	2.98	0.17	0.91	4quvA	GO:0000166 GO:0006696 GO:0016020 GO:0016021 GO:0016126 GO:0016491 GO:0016628 GO:0050613 GO:0050661 GO:0055114
2	0.07	0.572	4.00	0.09	0.87	4bmqA	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016020 GO:0016021 GO:0016491 GO:0046872 GO:0055114
3	0.07	0.575	4.09	0.04	0.87	4m1hB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
4	0.07	0.531	4.53	0.03	0.88	1smsA	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0051188 GO:0055114
5	0.07	0.557	4.22	0.05	0.86	2rccA	GO:0004748 GO:0006260 GO:0009186 GO:0016491 GO:0046872 GO:0055114
6	0.07	0.545	4.14	0.05	0.84	1h0nA	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009262 GO:0009263 GO:0016491 GO:0046872 GO:0051259 GO:0051290 GO:0055114
7	0.07	0.542	4.20	0.07	0.86	2bq1I	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
8	0.07	0.547	4.12	0.05	0.85	4n83A	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
9	0.07	0.519	4.14	0.02	0.83	2o1zA	GO:0009186 GO:0016491 GO:0046872 GO:0055114
10	0.07	0.568	4.12	0.05	0.88	4dr0B	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
11	0.07	0.521	4.60	0.07	0.89	4djnA	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
12	0.07	0.502	4.55	0.06	0.84	2vuxB	GO:0001822 GO:0003014 GO:0004748 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005971 GO:0006260 GO:0006264 GO:0006281 GO:0006974 GO:0006979 GO:0009186 GO:0009200 GO:0009263 GO:0014075 GO:0015949 GO:0016491 GO:0046872 GO:0055114 GO:0070062 GO:1902254
13	0.06	0.527	4.63	0.05	0.89	1jk0A	GO:0004748 GO:0005634 GO:0005737 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
14	0.06	0.552	4.05	0.09	0.85	1oquC	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
15	0.06	0.546	4.24	0.04	0.86	4ac8A	GO:0004748 GO:0005506 GO:0005829 GO:0005971 GO:0009186 GO:0009263 GO:0016491 GO:0030145 GO:0046872 GO:0055114
16	0.06	0.545	4.16	0.06	0.86	1uzrB	GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0040007 GO:0046872 GO:0055114
17	0.06	0.561	4.54	0.07	0.93	2jcdA	GO:0046872
18	0.06	0.387	4.19	0.05	0.55	5ijxA	GO:0000166 GO:0003723 GO:0004812 GO:0004831 GO:0005524 GO:0005737 GO:0006412 GO:0006418 GO:0006437 GO:0016874

Consensus prediction of GO terms

Molecular Function	GO:0036094	GO:0016628	GO:1901265	GO:0050662	GO:0004671	GO:0061731
GO-Score	0.52	0.52	0.52	0.52	0.43	0.37
Biological Processes	GO:0016129	GO:0044108	GO:0008204	GO:0097384	GO:1902653	GO:0006481	GO:0055114	GO:0009132	GO:0006259	GO:0009165	GO:0034645	GO:1901137	GO:0009262
GO-Score	0.52	0.52	0.52	0.52	0.52	0.43	0.40	0.37	0.37	0.37	0.37	0.37	0.37
Cellular Component	GO:0016021	GO:1990204	GO:0044445
GO-Score	0.61	0.37	0.37

(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.