I-TASSER results

I-TASSER results for job id Rv1724c

[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)
MVGNEENELQDLRNLRRPCFSRAEAPIGVYNGEQAIIVYDLRPVPHWPKYWIQALAKHFQ
RQLKPSPKIDISLLDDRIRFSVFVSTDVSAKDLCKLDDAVYNAVRNAGRAIENEQAALDH
KLAEVRKRRMDTWDESYFR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVGNEENELQDLRNLRRPCFSRAEAPIGVYNGEQAIIVYDLRPVPHWPKYWIQALAKHFQRQLKPSPKIDISLLDDRIRFSVFVSTDVSAKDLCKLDDAVYNAVRNAGRAIENEQAALDHKLAEVRKRRMDTWDESYFR
Prediction	CCCCHHHHHHHHHHHHHHHHCCCCCCCEHCCCCEEEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEHCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCC
Conf.Score	9886677899999875555545567755546875789986788998768999999999998678998755443355577889874677788888888999999999988988999999999999999864455556559
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 \| \| \| \| \| \| MVGNEENELQDLRNLRRPCFSRAEAPIGVYNGEQAIIVYDLRPVPHWPKYWIQALAKHFQRQLKPSPKIDISLLDDRIRFSVFVSTDVSAKDLCKLDDAVYNAVRNAGRAIENEQAALDHKLAEVRKRRMDTWDESYFR
Prediction	7445575425414514431254162302224453000112043334024200420153145524453514042135403111213341425311414520141045334316564342544135146542642465338
	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

CCCCHHHHHHHHHHHHHHHHCCCCCCCEHCCCCEEEEEEHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEHCCCEEEEEEEEHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCC
MVGNEENELQDLRNLRRPCFSRAEAPIGVYNGEQAIIVYDLRPVPHWPKYWIQALAKHFQRQLKPSPKIDISLLDDRIRFSVFVSTDVSAKDLCKLDDAVYNAVRNAGRAIENEQAALDHKLAEVRKRRMDTWDESYFR

5cwpA1

0.18

0.14

0.78

0.67

MUSTER

-MSSDEEEARELIERAKEAAERAQEAAERTGDPRV------------LARELKRLAQEAAEEVKRDPS----------------SSDV-NEALKLIVEAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEEVQRN

2fm1D2

0.17

0.12

0.67

0.56

dPPAS

----VDRLKEDHENARFLALKLKEIGYSVNDVKTNMVILRTDNLKVNAHGFIEALRNSG---------VLANAVDTEIRLVT--HKDVSRNDIEEALNIFEKLFRKFS-------------------------------

1ie0A

0.21

0.17

0.83

0.56

wdPPAS

SV--ESFEL-D---------NAVVAP-YVRTD-GVVNKFDIR-QPN-TIHTLEHLLAFTIRS-YDHFDIDISPMG-QTGYYLVVSGEPTSAEIVDLLEDTMKEAVEIGQALEGAKRLMRFWLSQDKEELLKVFG-----

5cwpA1

0.21

0.17

0.78

0.63

wMUSTER

--SSDEEEARELIERAKEAAERAQE-AAERTGDPRV-----RE----LARELKRLAQEAAEEVKRDPS----------------SSDV-NEALKLIVEAIEAAVRALEAAERTGDPEVRELARELVRLAVEAAEEVQ-R

2k0gA

0.16

0.12

0.78

0.52

wPPAS

--GSQGDFVRNWQLVAAPLFQKLGP-IRTVPAGAVIC--E--P------FFVVSVATPNPVELGPG---EMALISGEPR-TVSAATTV---SLLSLH-------SADFQMLCSSSPEIAEIFRKTALERRGAAASA---

2fm1D2

0.20

0.13

0.64

0.61

dPPAS2

-V---DRLKEDHENARFLALKLKEIGYSVNN----MVILRTDNLKVNAHGFIEALRNSG---------VLANAVDTEIRLVT--HKDVSRNDIEEALNIFEKLFRKFS-------------------------------

2vx8B

0.11

0.09

0.88

0.60

PPAS

-STPEVKPLKSLLGDSAPTLHLNKGMAILF-ARGTTILAKHAWCGG-----FLEVTEQILAKIPSENNKLTYICQDRIVYLCITDDDFERSAFSFLNEVKKRFQTTYGSRAQTALPAMNSEFSSVLAAQL---------

1dtyA1

0.17

0.16

0.94

0.64

Env-PPAS

M--TTDDLAFDERHIWHPYSMTPVYPVGCEDGRRLVDMSSWWAAIHGWQQQVADIEVQLREQLAPARDAEM-VADVRVLGAIGVVETTHPVNMAALQKFFVEQIRPFGKLIPQQLQRLTAAVNRAVQ------DETFFC

2gm2A

0.22

0.19

0.87

0.67

MUSTER

MPLNQE-HPDYTYALRA--ADGRHAKVNEQILQQSFILMPDELVEHWPVPSLGQLPAHMDAVLALNPAVILLGTGERQQF---------------PSTDVLAACLTRGIGLENAAAARTYNVLASEGRRVGGLEHHHHH

2vx8B

0.10

0.09

0.90

0.53

dPPAS

-STPEVKPLKSLLGDSAPTLHLNKGMAILFAARGTTILAKHAWCGGN----FLEVTEQILAKIPSENNKLTYICQDRIVYLCITDDDFERSAFSFLNEVKKRFQTTYGSRAQTALPAMNSEFSSVLAAQL---------

(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=-3.74

Estimated TM-score = 0.31±0.10

Estimated RMSD = 13.3±4.1Å

Download Model 2

C-score=-4.22

Download Model 3

C-score=-4.56

Download Model 4

C-score=-4.54

Download Model 5

C-score=-4.96

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	4obuE	0.589	2.83	0.048	0.755
2	3bcbA	0.579	3.03	0.038	0.763
3	3nuiA	0.563	2.86	0.078	0.741
4	4lglA2	0.563	3.69	0.079	0.813
5	4ppmA	0.559	3.11	0.065	0.770
6	5g4iA2	0.556	3.10	0.058	0.741
7	3i5tA	0.555	3.06	0.077	0.748
8	3hmuA2	0.551	3.16	0.070	0.755
9	2b0tA	0.547	3.79	0.077	0.799
10	2okjB	0.546	3.12	0.109	0.727

(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	3	2drdA	MIY	Rep, Mult	20,27,29,36
2	0.06	2	3i5aA	C2E	Rep, Mult	21,22,26
3	0.06	2	1b5dA	DCM	Rep, Mult	128,129
4	0.06	2	1q0kA	THJ	Rep, Mult	98,129,132
5	0.03	1	3pgyA	GLY	Rep, Mult	109,114,115,116
6	0.03	1	4edgA	MN	Rep, Mult	75,92
7	0.03	1	2qx0A	MG	Rep, Mult	75,76
8	0.03	1	2x5fA	PO4	Rep, Mult	4,8,89,90
9	0.03	1	3q8nD	SSN	Rep, Mult	27,28,102,104
10	0.03	1	1ex8A	MG	Rep, Mult	61,70
11	0.03	1	1w6rA	MG	Rep, Mult	75,134
12	0.03	1	2j3dA	MG	Rep, Mult	75,131,134
13	0.03	1	3hl2D	SEP	Rep, Mult	84,85,86

	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	3a2bA	0.528	2.49	0.056	0.640	2.3.1.50	NA
2	0.060	1x0mA	0.501	3.10	0.032	0.676	2.6.1.7	43
3	0.060	2z9xB	0.525	3.60	0.088	0.755	2.6.1.30	NA
4	0.060	1wstA	0.516	2.93	0.021	0.676	2.6.1.-	95
5	0.060	2cinA	0.527	2.76	0.116	0.683	2.6.1.36	NA
6	0.060	2a7vA	0.538	4.22	0.063	0.856	2.1.2.1	NA
7	0.060	2jisB	0.538	3.02	0.081	0.712	4.1.1.29	NA
8	0.060	3e77A	0.524	3.49	0.087	0.741	2.6.1.52	NA
9	0.060	1kkjA	0.526	4.08	0.061	0.827	2.1.2.1	NA
10	0.060	1n8pC	0.358	5.38	0.096	0.683	4.4.1.1	NA
11	0.060	1ax4A	0.522	3.19	0.074	0.727	4.1.99.1	97,127
12	0.060	2vmzA	0.523	4.09	0.069	0.835	2.1.2.1	25,52
13	0.060	2c7tA	0.517	3.60	0.125	0.748	2.6.1.-	NA
14	0.060	3i5tA	0.555	3.06	0.077	0.748	2.6.1.-	NA
15	0.060	1c7gA	0.520	3.46	0.079	0.755	4.1.99.2	NA
16	0.060	1szkC	0.526	3.53	0.105	0.755	2.6.1.19,2.6.1.22	9,79
17	0.060	3h7fB	0.538	3.72	0.104	0.813	2.1.2.1	NA
18	0.060	2okjB	0.546	3.12	0.109	0.727	4.1.1.15	NA
19	0.060	1sf2A	0.529	3.32	0.105	0.748	2.6.1.19,2.6.1.22	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	0.07	0.554	2.76	0.06	0.73	3rchA	GO:0003824 GO:0004058 GO:0005737 GO:0005829 GO:0006520 GO:0007623 GO:0008021 GO:0009636 GO:0010259 GO:0015842 GO:0016597 GO:0016829 GO:0016831 GO:0019752 GO:0019899 GO:0019904 GO:0030170 GO:0030424 GO:0033076 GO:0035690 GO:0036468 GO:0042416 GO:0042423 GO:0042427 GO:0043025 GO:0046219 GO:0046684 GO:0052314 GO:0070062 GO:0071312 GO:0071363
1	0.07	0.586	2.80	0.05	0.75	4obvA	GO:0003824 GO:0006520 GO:0016829 GO:0016831 GO:0019752 GO:0030170
2	0.07	0.527	3.04	0.08	0.72	3k40A	GO:0003824 GO:0004058 GO:0006520 GO:0006584 GO:0006585 GO:0006587 GO:0007611 GO:0007615 GO:0007616 GO:0007619 GO:0008062 GO:0009611 GO:0016829 GO:0016831 GO:0019752 GO:0030170 GO:0035220 GO:0040007 GO:0040040 GO:0042423 GO:0043052 GO:0048066 GO:0048082 GO:0048085
3	0.07	0.517	3.60	0.04	0.76	3nnkA	GO:0003824 GO:0008483 GO:0016740
4	0.07	0.541	2.92	0.12	0.70	2okkA	GO:0000139 GO:0003824 GO:0004351 GO:0005737 GO:0005794 GO:0005829 GO:0005886 GO:0006540 GO:0007268 GO:0007269 GO:0016020 GO:0016023 GO:0016595 GO:0016829 GO:0016831 GO:0019752 GO:0030054 GO:0030170 GO:0030424 GO:0030672 GO:0031225 GO:0031410 GO:0042136 GO:0042493 GO:0042734 GO:0045202 GO:0046982 GO:0048471 GO:0060077 GO:0061202
5	0.07	0.550	3.12	0.05	0.73	4zdoB	GO:0000049 GO:0001514 GO:0003723 GO:0003824 GO:0005634 GO:0005737 GO:0005829 GO:0006412 GO:0016259 GO:0016740 GO:0016785 GO:0097056 GO:0098621
6	0.07	0.521	3.20	0.05	0.73	2qmaA	GO:0003824 GO:0008483 GO:0009058 GO:0016831 GO:0019752 GO:0030170
7	0.07	0.518	3.30	0.11	0.73	4w1yB	GO:0003824 GO:0005737 GO:0005829 GO:0006520 GO:0006568 GO:0006569 GO:0009034 GO:0009072 GO:0016020 GO:0016829 GO:0016830 GO:0030170 GO:0030955 GO:0042802 GO:0060187 GO:0080146
8	0.07	0.538	3.02	0.08	0.71	2jisB	GO:0003824 GO:0004782 GO:0016829 GO:0016831 GO:0019752 GO:0030170 GO:0042412
9	0.07	0.530	3.09	0.06	0.73	4rizC	GO:0003824 GO:0016829 GO:0016831 GO:0019752 GO:0030170
10	0.07	0.546	3.12	0.11	0.73	2okjB	GO:0003824 GO:0004351 GO:0005622 GO:0005886 GO:0006538 GO:0006540 GO:0007268 GO:0007269 GO:0009449 GO:0012506 GO:0016595 GO:0016829 GO:0016831 GO:0018352 GO:0019752 GO:0030170 GO:0042136 GO:0042493 GO:0046982 GO:0047485 GO:0048786 GO:0061202
11	0.07	0.496	3.61	0.07	0.73	3fz6E	GO:0003824 GO:0004351 GO:0005737 GO:0005829 GO:0006536 GO:0016020 GO:0016829 GO:0016831 GO:0019752 GO:0030170 GO:0051454
12	0.07	0.460	3.40	0.04	0.65	2z67A	GO:0000049 GO:0003723 GO:0003824 GO:0006412 GO:0016740 GO:0016785 GO:0097056
13	0.07	0.511	3.39	0.03	0.73	2ch1A	GO:0003824 GO:0004760 GO:0005777 GO:0008453 GO:0019265
14	0.07	0.496	3.31	0.13	0.70	4up2D	GO:0003824 GO:0006520 GO:0006568 GO:0006569 GO:0009034 GO:0009072 GO:0016829 GO:0016830
15	0.07	0.503	2.95	0.11	0.68	2fm1D	GO:0003824 GO:0004793 GO:0005829 GO:0006520 GO:0006545 GO:0006567 GO:0008732 GO:0016829 GO:0046872
16	0.07	0.508	3.42	0.08	0.74	2c44C	GO:0003824 GO:0005737 GO:0005829 GO:0006520 GO:0006568 GO:0006569 GO:0009034 GO:0009072 GO:0016020 GO:0016829 GO:0016830 GO:0030170 GO:0030955 GO:0042802 GO:0060187 GO:0080146
17	0.07	0.479	3.71	0.08	0.70	2e7iA	GO:0003824 GO:0006412 GO:0016740 GO:0043766 GO:0071952
18	0.07	0.479	3.44	0.09	0.70	3if2A	GO:0003824 GO:0008483 GO:0009058 GO:0016740 GO:0030170

Consensus prediction of GO terms

Molecular Function	GO:0043168	GO:0016830	GO:0048037
GO-Score	0.48	0.48	0.48
Biological Processes	GO:0043436	GO:1901564	GO:0044238
GO-Score	0.48	0.37	0.32
Cellular Component	GO:0005829	GO:0030424	GO:0042734	GO:0031225	GO:0048471	GO:0061202	GO:0070062	GO:0030054	GO:0043025	GO:0000139	GO:0060077	GO:0030672
GO-Score	0.13	0.13	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07	0.07

(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.