I-TASSER results

I-TASSER results for job id Rv2061c

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

Input Sequence in FASTA format

>protein (134 residues)
MTPTFSDLAEAQYLLLTTFTKDGRPKPVPIWAALDTDRGDRLLVITEKKSWKVKRIRNTP
RVTLATCTLRGRPTSEAVEATAAILDESQTGAVYDAIVKRYGIQGKLFTFVSKLRGGMRN
NIGLELKVAESETG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTPTFSDLAEAQYLLLTTFTKDGRPKPVPIWAALDTDRGDRLLVITEKKSWKVKRIRNTPRVTLATCTLRGRPTSEAVEATAAILDESQTGAVYDAIVKRYGIQGKLFTFVSKLRGGMRNNIGLELKVAESETG
Prediction	CCCHHHHHHCCCEEEEEEHCCCCCCEEEEEEEEHCCCCCCEEEEEHCCCCHHHHHHHHCCCEEEEHCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCEEEEEEEHCCCCCC
Conf.Score	98588987568789999988999855666999985899989999978986678888779958999857999975789999999968976599999999997766654444566557788879999996899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MTPTFSDLAEAQYLLLTTFTKDGRPKPVPIWAALDTDRGDRLLVITEKKSWKVKRIRNTPRVTLATCTLRGRPTSEAVEATAAILDESQTGAVYDAIVKRYGIQGKLFTFVSKLRGGMRNNIGLELKVAESETG
Prediction	64632550465410100022464432300000021464422000003653321331363340201011454524223040303224675144015201631434230342044144456420000031475678
	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

CCCHHHHHHCCCEEEEEEHCCCCCCEEEEEEEEHCCCCCCEEEEEHCCCCHHHHHHHHCCCEEEEHCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCEEEEEEEHCCCCCC
MTPTFSDLAEAQYLLLTTFTKDGRPKPVPIWAALDTDRGDRLLVITEKKSWKVKRIRNTPRVTLATCTLRGRPTSEAVEATAAILDESQTGAVYDAIVKRYGIQGKLFTFVSKLRGGMRNNIGLELKVAESETG

3f7eA

0.20

0.19

0.92

2.64

MUSTER

VAGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLT------EPPADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

3.91

dPPAS

PEGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLTEPP------ADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

3.99

wdPPAS

VPEYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLTEPP------ADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

3.25

wMUSTER

VPGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLT------EPPADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

3.97

wPPAS

VAGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLTEP------PADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

6.61

dPPAS2

PEGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLTEPP------ADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

3.54

PPAS

VAGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLT------EPPADKADRVIIVVRPTAFSKQ

3f7eA

0.20

0.19

0.92

3.70

Env-PPAS

VAGYESLLERPLYGHLATVRPDGTPQVNA-WFAWD---GEVLRFTHTTKRQKYRNIKANPAVASVI-DPDNPYRYLEVRGLVEDIVPDPTGAFYLKLNDRYDGPLTEP------PADKADRVIIVVRPTAFSKQ

1y30A

0.16

0.97

2.53

MUSTER

VFDLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPR-KLLIQVSIAEPRAKTRNLRRDPRASILVDADDG-WSYAVAEGTAQLTPPAATVEALIALYRNIAGEHDWDDYRQAMVT--DRRVLLTLPISHVPPG

1y30A

0.16

0.98

3.69

dPPAS

DDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPR-KLLIQVSIAEPRAKTRNLRRDPRASILVDADDG-WSYAVAEGTAQLTPPAATVEALIALYRNIAGEHSDWDDYRQAMV-TDRRVLLTLPISHVPPG

(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 3 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=0.77

Estimated TM-score = 0.82±0.09

Estimated RMSD = 3.0±2.2Å

Download Model 2

C-score=-2.79

Download Model 3

C-score=-2.04

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	3f7eA	0.821	1.65	0.211	0.918
2	1y30A	0.788	2.62	0.154	0.963
3	3dnhA1	0.773	2.23	0.089	0.918
4	5jabA	0.764	2.00	0.167	0.895
5	3swjA2	0.757	2.55	0.103	0.940
6	4zkyA	0.753	2.74	0.169	0.925
7	2arzA	0.747	2.50	0.169	0.918
8	2iabA	0.746	2.22	0.218	0.881
9	1vl7A	0.746	2.28	0.131	0.910
10	2re7A	0.742	2.37	0.150	0.895

(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	0.50	28	2hq9A	FAD	Rep, Mult	26,28,29,30,31,45,46,50,51,52
2	0.03	2	2iab0	III	Rep, Mult	13,15,17,18,19,20,21,23,24,25,26,27,29,59,61,63,64,65,72,75,77,134
3	0.03	2	5jabB	6J4	Rep, Mult	71,73,75,130,132
4	0.02	2	2ou5A	FMN	Rep, Mult	31,44,46,124,126
5	0.02	2	3gasA	UUU	Rep, Mult	46,47,49,50,52,114,118,121
6	0.02	2	3hy8A	PO4	Rep, Mult	33,34,43,45
7	0.01	1	2asfA	CIT	Rep, Mult	46,47,50,51,52
8	0.01	1	1vl70	III	Rep, Mult	11,12,13,15,17,19,23,24,25,26,27,29,31,47,50,61,63,65,69,73,75,111
9	0.01	1	2i02A	FMN	Rep, Mult	13,28,29,30,31,45,46,50,51,52,101,102

	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	0.137	1ty9B	0.723	2.64	0.131	0.910	1.4.-.-	25
2	0.067	1ci0A	0.700	2.92	0.107	0.910	1.4.3.5	NA
3	0.067	1nrgA	0.723	2.63	0.172	0.910	1.4.3.5	NA
4	0.067	1wv4A	0.662	2.45	0.179	0.791	1.4.3.5	NA
5	0.060	1zjkA	0.490	3.53	0.051	0.716	3.4.21.104	NA
6	0.060	1ekbB	0.483	3.92	0.021	0.716	3.4.21.9	NA
7	0.060	3dfjA	0.477	3.36	0.055	0.672	3.4.21.-	7
8	0.060	2qy0C	0.239	5.05	0.082	0.448	3.4.21.41,3.4.21.42	46,56
9	0.060	2oq5A	0.497	3.40	0.063	0.694	3.4.21.-	NA
10	0.060	3h09B	0.488	3.82	0.051	0.716	3.4.21.72	81
11	0.060	1p57A	0.367	3.71	0.053	0.545	3.4.21.106	80,81
12	0.060	2zwlH	0.510	3.29	0.073	0.702	3.4.21.21	NA
13	0.060	2w1jB	0.478	4.43	0.008	0.769	2.3.2.12	95
14	0.060	1fizA	0.511	3.49	0.072	0.724	3.4.21.10	NA
15	0.060	2a2jA	0.718	2.77	0.124	0.903	1.4.3.5	NA
16	0.060	1bdaA	0.480	4.68	0.085	0.754	3.4.21.68	NA
17	0.060	2iphA	0.496	3.07	0.084	0.664	3.4.22.66	56,82
18	0.060	1ca0C	0.369	3.84	0.050	0.552	3.4.21.1	NA
19	0.060	8gchF	0.420	4.11	0.104	0.642	3.4.21.1	46,122
20	0.060	3beuA	0.488	3.50	0.041	0.694	3.4.21.4	NA
21	0.060	1gpzA	0.479	3.69	0.063	0.702	3.4.21.41	NA
22	0.060	1o5fH	0.477	4.04	0.041	0.716	3.4.21.106	NA
23	0.060	1kdqB	0.239	4.52	0.087	0.418	3.4.21.1	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	0.38	0.835	1.64	0.21	0.93	3f7eA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
1	0.36	0.802	2.52	0.15	0.97	4qvbB	GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
2	0.31	0.693	2.78	0.16	0.86	5escA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
3	0.30	0.735	2.63	0.16	0.90	2i02A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
4	0.29	0.742	2.62	0.18	0.91	1rfeA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
5	0.29	0.758	2.08	0.17	0.88	2fhqA	GO:0010181 GO:0016491 GO:0055114
6	0.29	0.750	2.54	0.15	0.91	2re7A	GO:0010181 GO:0016491 GO:0055114
7	0.28	0.726	2.44	0.11	0.87	3db0B	GO:0010181 GO:0016491 GO:0055114
8	0.28	0.706	2.65	0.15	0.86	2htiA	GO:0000166 GO:0010181 GO:0016491 GO:0055114
9	0.26	0.723	2.68	0.11	0.93	3tgvA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
10	0.25	0.668	2.53	0.18	0.82	2htdB	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
11	0.24	0.700	3.08	0.12	0.92	3dmbA	GO:0010181 GO:0016491 GO:0055114
12	0.24	0.742	2.49	0.13	0.90	5bncA	GO:0010181 GO:0016491 GO:0055114
13	0.23	0.719	2.75	0.10	0.92	2hq7B	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
14	0.23	0.780	2.23	0.09	0.93	3dnhA	GO:0010181 GO:0016491 GO:0055114
15	0.22	0.734	2.90	0.11	0.92	1xhnA	GO:0003714 GO:0005576 GO:0005615 GO:0005667 GO:0006355 GO:0006357 GO:0007275 GO:0008134 GO:0008283 GO:0010181 GO:0016491 GO:0040008 GO:0055114 GO:0070062 GO:1903507
16	0.21	0.746	2.28	0.13	0.91	1vl7A	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
17	0.20	0.747	2.50	0.17	0.92	2arzA	GO:0010181 GO:0016491 GO:0055114
18	0.20	0.662	2.45	0.18	0.79	1wv4A	GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
19	0.19	0.727	2.71	0.16	0.91	1jnwA	GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
20	0.14	0.757	2.55	0.10	0.94	3swjA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
21	0.13	0.727	2.47	0.16	0.87	3ec6A	GO:0000166 GO:0003677 GO:0010181 GO:0016491 GO:0055114
22	0.13	0.749	2.60	0.08	0.94	3gasA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0046872 GO:0055114
23	0.08	0.728	2.98	0.15	0.93	2fg9A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
24	0.07	0.682	3.05	0.15	0.89	2qeaA	GO:0010181 GO:0016491 GO:0046872 GO:0055114
25	0.06	0.355	4.88	0.04	0.66	3jxgC	GO:0004721 GO:0004725 GO:0006470 GO:0010633 GO:0016020 GO:0016021 GO:0016311 GO:0016787 GO:0016791 GO:0035335 GO:0042802 GO:0070062 GO:1901998
26	0.06	0.368	3.95	0.04	0.56	3vmnA	GO:0005576 GO:0005618 GO:0008152 GO:0016787 GO:0016798 GO:0033904
27	0.06	0.361	4.80	0.02	0.67	4coqB	GO:0004089 GO:0006730 GO:0008270 GO:0016829 GO:0046872
28	0.06	0.285	5.74	0.02	0.59	2pp0A	GO:0003824 GO:0008152 GO:0008867 GO:0009063 GO:0016829 GO:0046392 GO:0046872 GO:1903663 GO:1990594

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0004733	GO:0042803	GO:0030170
GO-Score	0.86	0.81	0.36	0.36
Biological Processes	GO:0055114	GO:0042823	GO:0042816
GO-Score	0.86	0.81	0.36
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.