I-TASSER results

I-TASSER results for job id Rv0121c

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

Input Sequence in FASTA format

>protein (144 residues)
MGEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEATGADVIYTAVDAKRKT
TQRLRRLANLEHNPRASVLVDSYADDWTQLWWVRADGVAAIHRDGEVMRAAYRLLRAKYA
QYQSVPLNGPVIAIAVQRWASWHA

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEATGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVDSYADDWTQLWWVRADGVAAIHRDGEVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWHA
Prediction	CCHHHHHHHHHCCCEEEEEEHCCCCCEEEEEEEEEEHCCEEEEEHCCCEEEEEHCCCCCCCCHHHHHHHHHHCCEEEEEEHCCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEHCCC
Conf.Score	988999999976986899996899986899899999899788985687788875677666655578999988996999996799988765799999999995898668999999999856667788998599999989985789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MGEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEATGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVDSYADDWTQLWWVRADGVAAIHRDGEVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWHA
Prediction	856740551156442020000346330100000001345432233444202232444454354143142146222000000346652441120203130323446652450042025214426734372000103043144358
	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

CCHHHHHHHHHCCCEEEEEEHCCCCCEEEEEEEEEEHCCEEEEEHCCCEEEEEHCCCCCCCCHHHHHHHHHHCCEEEEEEHCCCCCCCCEEEEEEEEEEEHCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEEEEEHCCC
MGEFDPKLRFAQSPVARLATSTPDGTPHLVPVVFALGARRPAEATGADVIYTAVDAKRKTTQRLRRLANLEHNPRASVLVDSYADDWTQLWWVRADGVAAIHRDGEVMRAAYRLLRAKYAQYQSVPLNGPVIAIAVQRWASWHA

4zkyA

0.59

0.57

0.97

3.36

MUSTER

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPH--VEGQPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.59

0.57

0.97

4.57

dPPAS

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPH--VEGQPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.59

0.57

0.97

5.01

wdPPAS

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPHVEG--QPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.59

0.57

0.97

4.13

wMUSTER

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPHVE--GQPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.58

0.56

0.97

5.13

wPPAS

F---DAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPHVEG--QPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.59

0.57

0.97

8.19

dPPAS2

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPH--VEGQPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.59

0.57

0.97

4.57

PPAS

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPH--VEGQPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

4zkyA

0.59

0.57

0.97

4.90

Env-PPAS

---FDAVTAFADAPAAVLSTLNADGAPHLVPVVFAVHVPH--VEGQPARIYTAVDAKRKTTRNLRRLANIDRDSRVSLLVDHYSDDWTQLWWVRADGVATTHHSGDEVATGYALLRAKYHQYERVSLDGPVISVEVSRWASWQA

5jabA

0.20

0.17

0.86

2.50

MUSTER

RLSDDALAFLSERHLAMLTTLRADNSPHVVAVGFTFDPK-------THIARVIT------TGGSQKAVNADRSGLAVLSQVDGA------RWLSLEGRAAVNSDIDAVRDAELRYAQRYRTPRPN-PRRVVIEVQIERVLGSAD

5jabA

0.19

0.17

0.86

3.31

dPPAS

RLSDDALAFLSERHLAMLTTLRADNSPHVVAVGFTFDPK-------THIARVITTGGS------QKAVNADRSGLAVLSQVDGA------RWLSLEGRAAVNSDIDAVRDAELRYAQRYRT-PRPNPRRVVIEVQIERVLGSAD

(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 1 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=1.28

Estimated TM-score = 0.89±0.07

Estimated RMSD = 2.2±1.7Å

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	4zkyA	0.924	1.32	0.597	0.965
2	5jabA	0.756	1.87	0.195	0.854
3	1rfeA	0.745	2.52	0.252	0.875
4	5bncA	0.741	2.34	0.244	0.882
5	3tgvA	0.736	2.57	0.147	0.889
6	2arzA1	0.732	2.45	0.183	0.875
7	3swjA2	0.732	2.55	0.124	0.889
8	4ybnA	0.725	2.57	0.165	0.875
9	1vl7A	0.725	2.18	0.139	0.847
10	1w3oA	0.724	2.94	0.180	0.882

(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	0.38	23	1wv4A	FMN	Rep, Mult	30,31,32,33,35,53,54,64,65,66,129
2	0.08	6	4ybnB	FAD	Rep, Mult	81,90,92,93,94,96,140,142
3	0.05	4	1ty9A	FMN	Rep, Mult	19,77,96,138
4	0.04	3	2i02A	FMN	Rep, Mult	15,30,31,32,33,44,45,64,65,66,119,120
5	0.03	2	2aq6A	PLP	Rep, Mult	30,31,58,65,66,129
6	0.02	2	2iab0	III	Rep, Mult	15,17,19,20,21,22,23,25,26,27,28,29,31,73,75,77,78,79,92,94,142
7	0.01	1	3gasB	UUU	Rep, Mult	54,55,57,66,125,126,127,129
8	0.01	1	1vl70	III	Rep, Mult	13,14,15,17,19,21,25,27,28,29,31,33,55,64,75,77,79,92,119
9	0.01	1	1g76A	PLP	Rep, Mult	33,35,111,116,129

	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	0.067	1wv4A	0.660	2.26	0.145	0.764	1.4.3.5	NA
2	0.060	2iphA	0.472	3.75	0.095	0.681	3.4.22.66	99
3	0.060	1esbA	0.453	3.96	0.057	0.660	3.4.21.36	NA
4	0.060	1dleA	0.440	4.38	0.052	0.681	3.4.21.47	NA
5	0.060	1mskA	0.492	4.65	0.094	0.806	2.1.1.13	72
6	0.060	3cb0A	0.526	2.64	0.073	0.646	1.14.13.3	50,131
7	0.060	1autC	0.461	3.74	0.064	0.660	3.4.21.69	73
8	0.060	1ty9B	0.669	2.76	0.169	0.819	1.4.-.-	19,27,32,77,142
9	0.060	1fuiA	0.492	4.33	0.063	0.764	5.3.1.25	NA
10	0.060	1eawA	0.453	4.33	0.019	0.701	3.4.21.109,3.4.21.-	NA
11	0.060	1o5fH	0.455	4.23	0.028	0.694	3.4.21.106	NA
12	0.060	1nrgA	0.664	2.64	0.178	0.812	1.4.3.5	NA
13	0.060	1zjkA	0.468	4.17	0.045	0.708	3.4.21.104	NA
14	0.060	1ci0A	0.657	2.92	0.118	0.826	1.4.3.5	NA
15	0.060	1pfxC	0.471	3.97	0.019	0.681	3.4.21.22	NA
16	0.060	1yc0A	0.457	4.14	0.049	0.688	3.4.21.-	NA
17	0.060	2o2kB	0.469	4.58	0.119	0.785	2.1.1.13	NA
18	0.060	1o6eB	0.478	4.25	0.119	0.764	3.4.21.97	NA
19	0.060	1bruP	0.454	4.06	0.056	0.667	3.4.21.71	NA
20	0.060	2oq5A	0.468	4.02	0.067	0.674	3.4.21.-	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	0.56	0.924	1.32	0.60	0.97	4zkyA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
1	0.41	0.757	2.32	0.25	0.88	1rfeA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
2	0.37	0.709	2.83	0.21	0.88	4qvbB	GO:0004733 GO:0010181 GO:0016491 GO:0030170 GO:0042803 GO:0042816 GO:0042823 GO:0055114
3	0.37	0.716	1.95	0.20	0.82	5escA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
4	0.33	0.733	1.88	0.15	0.82	3u5wA	GO:0010181 GO:0016491 GO:0055114
5	0.33	0.723	2.04	0.25	0.83	3cp3A	GO:0010181 GO:0016491 GO:0055114
6	0.32	0.745	1.83	0.20	0.84	2asfA	GO:0004733 GO:0005576 GO:0005618 GO:0010181 GO:0016491 GO:0042823 GO:0055114
7	0.29	0.684	2.61	0.17	0.83	3fkhD	GO:0010181 GO:0016491 GO:0055114
8	0.29	0.736	2.57	0.15	0.89	3tgvA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
9	0.28	0.741	2.34	0.24	0.88	5bncA	GO:0010181 GO:0016491 GO:0055114
10	0.28	0.679	2.03	0.13	0.78	2htdB	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
11	0.26	0.708	2.26	0.19	0.82	4n7rC	GO:0006783 GO:0009507 GO:0009534 GO:0009536 GO:0009570 GO:0009767 GO:0009791 GO:0010181 GO:0015995 GO:0016491 GO:0033014 GO:0043234 GO:0043495 GO:0055114 GO:0070455
12	0.25	0.685	2.78	0.17	0.84	3f7eA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
13	0.25	0.721	2.69	0.19	0.86	2hq9B	GO:0000166 GO:0010181 GO:0016491 GO:0055114
14	0.25	0.719	2.51	0.17	0.87	3dnhA	GO:0010181 GO:0016491 GO:0055114
15	0.24	0.729	2.51	0.17	0.88	2arzA	GO:0010181 GO:0016491 GO:0055114
16	0.23	0.671	2.68	0.18	0.82	1t9mA	GO:0000166 GO:0002047 GO:0004733 GO:0008615 GO:0010181 GO:0016491 GO:0016638 GO:0042823 GO:0055114
17	0.22	0.709	2.78	0.17	0.84	2htiA	GO:0000166 GO:0010181 GO:0016491 GO:0055114
18	0.20	0.725	2.18	0.14	0.85	1vl7A	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
19	0.19	0.699	2.44	0.08	0.84	2hq7B	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
20	0.18	0.660	2.26	0.14	0.76	1wv4A	GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
21	0.17	0.677	2.63	0.14	0.82	1jnwA	GO:0004733 GO:0005829 GO:0008615 GO:0009443 GO:0010181 GO:0016491 GO:0016638 GO:0042816 GO:0055114
22	0.16	0.658	2.69	0.15	0.78	2ou5A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
23	0.13	0.731	2.51	0.12	0.89	3swjA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0055114
24	0.10	0.757	2.62	0.15	0.90	2fg9A	GO:0000166 GO:0010181 GO:0016491 GO:0055114
25	0.10	0.716	2.65	0.16	0.89	3gasA	GO:0004733 GO:0010181 GO:0016491 GO:0042823 GO:0046872 GO:0055114
26	0.10	0.669	2.74	0.17	0.82	4hmtB	GO:0002047 GO:0004733 GO:0008615 GO:0009405 GO:0010181 GO:0016491 GO:0016638 GO:0017000 GO:0042823 GO:0055114
27	0.06	0.331	5.32	0.06	0.62	4k0vA	GO:0000165 GO:0000166 GO:0001525 GO:0001666 GO:0001725 GO:0001934 GO:0001935 GO:0001938 GO:0001958 GO:0002040 GO:0004672 GO:0004713 GO:0004714 GO:0004872 GO:0005088 GO:0005524 GO:0005576 GO:0005737 GO:0005856 GO:0005884 GO:0005886 GO:0005887 GO:0005902 GO:0005911 GO:0005925 GO:0006468 GO:0007165 GO:0007169 GO:0007267 GO:0007507 GO:0009925 GO:0009986 GO:0010033 GO:0010595 GO:0014068 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016323 GO:0016324 GO:0016525 GO:0016740 GO:0018108 GO:0019838 GO:0030054 GO:0031100 GO:0032878 GO:0034446 GO:0035556 GO:0043066 GO:0043114 GO:0043434 GO:0043547 GO:0043552 GO:0043627 GO:0045121 GO:0045766 GO:0046777 GO:0048014 GO:0050728 GO:0050900 GO:0051259 GO:0051591 GO:0051894 GO:0051897 GO:0060216 GO:0060347 GO:0070374 GO:1902533 GO:2000251 GO:2000351 GO:2000352
28	0.06	0.365	5.89	0.06	0.76	1w18B	GO:0005576 GO:0009758 GO:0016740 GO:0016757 GO:0050053

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0004733	GO:0030170	GO:0042803
GO-Score	0.93	0.90	0.37	0.37
Biological Processes	GO:0055114	GO:0042823	GO:0042816
GO-Score	0.93	0.90	0.37
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.