I-TASSER results

I-TASSER results for job id Rv0492A

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

Input Sequence in FASTA format

>protein (109 residues)
MSFLLDPPLLFVCGVLIERRLPVDRRDAAEAAALGVFFGASFGLYHNVPGLGMLWRPFRA
QNGRDFMWNSGVFSVDVARAEWPLHAMAAAIFATYPFFIKLGRRLGRRI

Predicted Secondary Structure

Sequence	20 40 60 80 100 \| \| \| \| \| MSFLLDPPLLFVCGVLIERRLPVDRRDAAEAAALGVFFGASFGLYHNVPGLGMLWRPFRAQNGRDFMWNSGVFSVDVARAEWPLHAMAAAIFATYPFFIKLGRRLGRRI
Prediction	CCCCCCHHHHHHHCCEEEHCCCCHHHHHHHHHHHHHHHHEEHCCHCCCCCCCHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
Conf.Score	9866787888765734554699658999999999987644554344798874455565545797467764576655444677457888889999999999999987659
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 \| \| \| \| \| MSFLLDPPLLFVCGVLIERRLPVDRRDAAEAAALGVFFGASFGLYHNVPGLGMLWRPFRAQNGRDFMWNSGVFSVDVARAEWPLHAMAAAIFATYPFFIKLGRRLGRRI
Prediction	6424242321211033255425664630130123223332312123634233111210426533412143211414465353423210123233333112104434657
	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

                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCHHHHHHHCCEEEHCCCCHHHHHHHHHHHHHHHHEEHCCHCCCCCCCHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
MSFLLDPPLLFVCGVLIERRLPVDRRDAAEAAALGVFFGASFGLYHNVPGLGMLWRPFRAQNGRDFMWNSGVFSVDVARAEWPLHAMAAAIFATYPFFIKLGRRLGRRI

5a43A

0.15

0.14

0.94

0.79

MUSTER

KSLFA-CTLRWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTLAYFLRQPHLDPFWKLI--TTG--LC--GGLFSVEVFALNYIWALTSVLVHVIGSLITALGFFIITIL

4b4oA1

0.06

0.88

0.61

dPPAS

-------------RVLVGGGTGFIGTALTQLLNARGHEVTLVSRKPGPGRITWDELAASGLPSCDAAVNLAGENILNPLRRWNETFQKEVLGSRLETTQLLAKAITKAP

1u7nA1

0.26

0.22

0.86

0.60

wdPPAS

KGFDLD------LGA----NADNKPEHLVQYAVLGSFYA-RVGLLNNGTGTKKAFELLAADETINFVGNVGVADVD----GFTGNAVLKSIEGTANSLLKTAILSGALL

5a43A

0.15

0.14

0.94

0.80

wMUSTER

KSLFA-CTLRWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTLAYFLRQPHLDPFWKLI--TTG--LC--GGLFSVEVFALNYIWALTSVLVHVIGSLITALGFFIITIL

1mliA

0.29

0.19

0.66

0.65

wPPAS

MLFHVKPV-----------DMDPAKATADEKEL-------AQRLQREGTWRH-LWRI----AGH----NYSVFDVPSVEA---LH-----TLMQLPLYM-LCRHSDDR-

5awwG

0.20

0.13

0.64

0.83

dPPAS2

-------------------------MDLLYTLVILFYLGVAGL---------LVYLVLVQQGAGDLMGGSALFSARGVTGGYRLTVILGVVFAALALVIGLWPR-----

2ahzA

0.18

0.16

0.85

0.81

PPAS

LSFLLTLKRMLRA---CLRAWKDKEFQVLFVLTILTLISGTIF-YSTVEG----LRPIDA-----FSVVTGNF-SPQTDFG--KIFTILYIFIGIGLVFGFIHKLAVNV

1ze1A3

0.20

0.17

0.89

0.74

Env-PPAS

MRLGLITETFDITGEVVEERCNVTEEEIREAIFS--F----VGEYDQVPPAERLYKLARELPPKRKIFKIWDVNIEGRDVSFRVEVSPG----TY--IRSLCMDIGYKL

5a40A

0.15

0.96

0.78

MUSTER

LTYALNFIAIGIGATVLGLKLNGAGWGTLTANLVGGYLIG-VALIASHPEWPAWIRLAAV-TG--FLFSAETVDMLCRGVYATAAAYAGASLAGSLAMTGLGLATVRLL

2ahzA

0.10

0.09

0.90

0.60

dPPAS

LSFLLTLKRMLRA---CLRAWKDKEFQVLFVLTILTLISGTIFYSTGLRPIDALYFSVVTLT--------TVGDGNFSPQTDFKIFTILYIFIGIGLVFGFIHKLAVNV

(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=-3.16

Estimated TM-score = 0.36±0.12

Estimated RMSD = 11.2±4.6Å

Download Model 2

C-score=-3.97

Download Model 3

C-score=-4.07

Download Model 4

C-score=-3.80

Download Model 5

C-score=-4.58

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	5a43A	0.600	4.00	0.086	0.945
2	5a40A	0.595	3.94	0.154	0.927
3	2pywA2	0.572	3.68	0.069	0.890
4	3k07A	0.566	3.46	0.065	0.844
5	4czbA2	0.565	4.32	0.029	0.945
6	3cxnB	0.563	4.07	0.056	0.945
7	4zyoA	0.560	3.39	0.055	0.817
8	3bqkA1	0.555	2.88	0.079	0.771
9	2pulA	0.551	3.99	0.080	0.890
10	4cz8A2	0.548	4.42	0.086	0.936

(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	0.09	5	4n7tA	AZI	Rep, Mult	33,36,91,92,95
2	0.06	3	3to3B	MG	Rep, Mult	61,62,65
3	0.06	3	3q3mF	Z82	Rep, Mult	32,75,85,88,92
4	0.04	2	1gdlA	NO	Rep, Mult	85,89
5	0.04	2	4tt0B	IOD	Rep, Mult	103,104,107
6	0.04	2	1biqB	UUU	Rep, Mult	10,14,17,31
7	0.04	2	3cehB	PO4	Rep, Mult	3,56,103,104
8	0.04	2	3dntB	MG	Rep, Mult	47,65
9	0.02	1	1xjgB	DTP	Rep, Mult	41,99,100
10	0.02	1	1hjsA	EPE	Rep, Mult	55,57,64
11	0.02	1	1jgtB	MG	Rep, Mult	6,76
12	0.02	1	1ethA	CA	Rep, Mult	22,25,27,30
13	0.02	1	1av8B	FEO	Rep, Mult	35,55,59
14	0.02	1	5ddlB	5AU	Rep, Mult	96,100

	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	2fhbA	0.506	3.39	0.122	0.752	3.2.1.41	NA
2	0.060	1gytA	0.506	3.98	0.065	0.817	3.4.11.1	103
3	0.060	2ckpA	0.515	3.78	0.055	0.835	2.7.1.32	NA
4	0.060	1ffuB	0.402	4.28	0.011	0.670	1.2.99.2	NA
5	0.060	3f2sA	0.511	3.78	0.055	0.835	2.7.1.32	NA
6	0.060	1wgzA	0.504	4.62	0.046	0.908	3.4.24.66	95
7	0.060	3npkA	0.524	4.25	0.038	0.917	2.5.1.10	10
8	0.060	2f8zF	0.523	4.26	0.057	0.908	2.5.1.10,2.5.1.1	34,57
9	0.060	2dh4A	0.510	4.64	0.038	0.927	2.5.1.29	NA
10	0.060	2vuaA	0.336	4.73	0.041	0.651	3.4.24.69	NA
11	0.060	2ckpB	0.496	4.19	0.041	0.844	2.7.1.32	NA
12	0.060	3ckeD	0.492	4.60	0.077	0.881	4.2.3.9	NA
13	0.060	1dgpA	0.501	4.29	0.074	0.853	4.2.3.9,4.1.99.7	NA
14	0.060	3ffzA	0.500	3.82	0.039	0.798	3.4.24.69	NA
15	0.060	2h8oA	0.533	4.34	0.047	0.945	2.5.1.10	NA
16	0.060	1wmwA	0.532	4.32	0.048	0.917	2.5.1.-	NA
17	0.060	2j1pB	0.525	4.50	0.037	0.917	2.5.1.1,2.5.1.10,2.5.1.29	NA
18	0.060	2fp0B	0.497	4.00	0.065	0.826	3.2.1.143	NA
19	0.060	3ihyC	0.500	4.08	0.074	0.844	2.7.1.137	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	0.13	0.595	3.94	0.15	0.93	5a40A	GO:0005886 GO:0005887 GO:0006810 GO:0015103 GO:0015698 GO:0016020 GO:0016021 GO:0034220
1	0.07	0.619	3.71	0.09	0.94	5a43B	GO:0005886 GO:0005887 GO:0006810 GO:0015103 GO:0015698 GO:0016020 GO:0016021 GO:0034220
2	0.07	0.566	3.29	0.05	0.81	4k0eB	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
3	0.07	0.546	3.62	0.02	0.84	4mt1A	GO:0005215 GO:0006810 GO:0016020 GO:0016021
4	0.07	0.484	4.25	0.11	0.85	4k0eA	GO:0005215 GO:0006810 GO:0006812 GO:0008324 GO:0016020 GO:0016021 GO:0098655
5	0.07	0.494	4.19	0.03	0.84	2ig7B	GO:0000166 GO:0004103 GO:0004305 GO:0005524 GO:0005829 GO:0006629 GO:0006646 GO:0006656 GO:0006657 GO:0008654 GO:0016301 GO:0016310 GO:0016740 GO:0046474
6	0.07	0.534	4.08	0.06	0.88	3sf5C	GO:0005737 GO:0006807 GO:0009405 GO:0016151
7	0.07	0.496	4.19	0.04	0.84	2ckpB	GO:0000166 GO:0004103 GO:0004104 GO:0004305 GO:0004871 GO:0005524 GO:0005737 GO:0005829 GO:0006580 GO:0006629 GO:0006646 GO:0006656 GO:0006657 GO:0006869 GO:0007165 GO:0008144 GO:0008654 GO:0009636 GO:0016301 GO:0016310 GO:0016740 GO:0019695 GO:0033265 GO:0042803 GO:1904681
8	0.07	0.501	3.73	0.06	0.83	3nogA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
9	0.07	0.407	3.74	0.07	0.62	3d9bA	GO:0005215 GO:0005886 GO:0005887 GO:0006810 GO:0006855 GO:0015238 GO:0015307 GO:0016020 GO:0016021 GO:0042493 GO:0042802 GO:0046618
10	0.07	0.442	3.82	0.05	0.69	3u0oB	GO:0000166 GO:0000287 GO:0004756 GO:0005524 GO:0005829 GO:0016260 GO:0016301 GO:0016310 GO:0016740 GO:0070329
11	0.06	0.413	4.30	0.02	0.69	4iboD	GO:0016491 GO:0055114
12	0.06	0.551	3.99	0.08	0.89	2pulA	GO:0000166 GO:0005524 GO:0008652 GO:0009086 GO:0016301 GO:0016310 GO:0016740 GO:0019284 GO:0019509 GO:0046522
13	0.06	0.390	3.98	0.04	0.63	2r8bA	GO:0016787
14	0.06	0.552	4.15	0.07	0.91	4cz8A	GO:0006810 GO:0006812 GO:0015299 GO:0016020 GO:0016021 GO:0055085 GO:1902600
15	0.06	0.484	4.76	0.06	0.93	2pywA	GO:0000166 GO:0005524 GO:0005829 GO:0008652 GO:0009086 GO:0016301 GO:0016310 GO:0016740 GO:0019509 GO:0042802 GO:0046522 GO:0071281 GO:0071369 GO:0071732
16	0.06	0.469	4.43	0.06	0.84	2v50D	GO:0005215 GO:0005886 GO:0006810 GO:0006855 GO:0015238 GO:0016020 GO:0016021 GO:0046677
17	0.06	0.401	4.13	0.07	0.65	3ts9A	GO:0000166 GO:0002376 GO:0003677 GO:0003723 GO:0003725 GO:0003727 GO:0004386 GO:0005524 GO:0005634 GO:0005737 GO:0008270 GO:0009615 GO:0016787 GO:0016817 GO:0016925 GO:0032727 GO:0032728 GO:0039530 GO:0043021 GO:0045087 GO:0046872 GO:0051607
18	0.06	0.416	3.94	0.07	0.69	4czbB	GO:0005886 GO:0006810 GO:0006811 GO:0006812 GO:0006814 GO:0015297 GO:0015299 GO:0016020 GO:0016021 GO:0042802 GO:0055085 GO:1902600

Consensus prediction of GO terms

Molecular Function	GO:0008509
GO-Score	0.39
Biological Processes	GO:0006820	GO:0055085
GO-Score	0.39	0.39
Cellular Component	GO:0031226	GO:0016021
GO-Score	0.39	0.34

(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.