I-TASSER results

I-TASSER results for job id Rv2256c

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

Input Sequence in FASTA format

>protein (177 residues)
MEPKEQQMRASNQFADVTSGVVYIHASPAAVCPHVEWALSSTLQAKANLVWTPQPALPPQ
LRAVTNWVGPVGTGARLANALRSWSVLRFEVTEDPSPGVDGQRFSHTPQLGLWSGAMSAN
GDIMVGEMRLRAMMAQGADTLAAELDSVLGTAWDQALEVYRDGGDAGEVTWLSRGVG

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MEPKEQQMRASNQFADVTSGVVYIHASPAAVCPHVEWALSSTLQAKANLVWTPQPALPPQLRAVTNWVGPVGTGARLANALRSWSVLRFEVTEDPSPGVDGQRFSHTPQLGLWSGAMSANGDIMVGEMRLRAMMAQGADTLAAELDSVLGTAWDQALEVYRDGGDAGEVTWLSRGVG
Prediction	CCCCCCCCCCCCCCCCCCCEEEEEHCCCCCHCHHHHHHHHHHHCCCCCCEEHCCCCCCCEEEEEEEEHCCCCCHHHHHHHHHHCCCEEEEEHCCCCCCCCCCEEEHCCCCCCEEEEHCCCCCEHCCHHHHHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCEEEEEHCCC
Conf.Score	985454446778776656669999859965566999999998688766678658888885788998875897489999999969876899976899998886578758887588875777877757899999999876899999999977765678777547899987577765469
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 \| \| \| \| \| \| \| \| MEPKEQQMRASNQFADVTSGVVYIHASPAAVCPHVEWALSSTLQAKANLVWTPQPALPPQLRAVTNWVGPVGTGARLANALRSWSVLRFEVTEDPSPGVDGQRFSHTPQLGLWSGAMSANGDIMVGEMRLRAMMAQGADTLAAELDSVLGTAWDQALEVYRDGGDAGEVTWLSRGVG
Prediction	864655525545534520210010011143012101100331244416061461424323220414141433202401410461550301113423642534311101331212032333141203352022005424640351035104530263042143147613032135448
	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                 160

                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCCEEEEEHCCCCCHCHHHHHHHHHHHCCCCCCEEHCCCCCCCEEEEEEEEHCCCCCHHHHHHHHHHCCCEEEEEHCCCCCCCCCCEEEHCCCCCCEEEEHCCCCCEHCCHHHHHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCEEEEEHCCC
MEPKEQQMRASNQFADVTSGVVYIHASPAAVCPHVEWALSSTLQAKANLVWTPQPALPPQLRAVTNWVGPVGTGARLANALRSWSVLRFEVTEDPSPGVDGQRFSHTPQLGLWSGAMSANGDIMVGEMRLRAMMAQGADTLAAELDSVLGTAWDQALEVYRDGGDAGEVTWLSRGVG

3tx8A2

0.12

0.07

0.55

1.03

dPPAS2

----------------------------------------------------------GNLRIKVTAHGVRAKLSPIISKVAAYKAAEVNID--------GLTYREGLNIVFCESGVANN---VIPDLAFRFAPNRDLNEAIEHVVETLEL----------DGQDGIEWAVEDGAGG

3oduA2

0.19

0.08

0.41

1.01

dPPAS2

-------------------------------------------------------------------------GSNIFEMLRIDEGLRLKIYKD-TEGYIGHLLTKSPSLNALDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILR------------------------------

1pn0C

0.13

0.12

0.90

0.60

MUSTER

-----------TKYSESYCDVLIVGAGPAGLMAARVLSEYVRQKPDLKIDKRSTKVYNG--QADGLQCRNLGLADKILSEANDMSTIALYNPDENGHIRRTDRIPDTPGISRYHQVVLHQGRI---ERRILDSIAEISDTRIKVERPLIPEKMEID-SSKAEDPEAYPVTMTLRYMS

2mj7A

0.10

0.07

0.76

0.88

dPPAS

MGHHHHHHSHMQELPDSGALMLVPNRQLTADYFEKTWLSL-----------------KVAHQQVLPWRGEF-HPDTLQMALQVVNIQTIAMSRAGSRPWKAYLSAQDDTGCLFLTELLLEPGSVKQNEARTETLNSFISVLETVIGTIEEIKS------------------------

2b7jB

0.23

0.18

0.79

0.68

wdPPAS

--PSYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNITLQLFITCDPASPAVLKE--SILGLTGTFDEVKNACKKY-RVYFSTPPNVKPGQDIFFYLMDPE-GQFVDALGRNYD-----------EKTGVDKIVEHVKSYVPEAWYSFL--------------------

2b7jB

0.22

0.19

0.85

0.67

wMUSTER

GGPMYGNEFTEKNLLGKFSIIYFGFSNCPDICPDELDKLGLWLNYGITLFITCDPASPAVLKE--SILGLTGTFDEVKNACKKY-RVYFSTPPNVKPGQDIFFYLMDPE-GQFVDALGRNYD-----------EKTGVDKIVEHVKSYVPA------EQRAKQKEA----WYSFL--

2m47A

0.22

0.16

0.75

0.60

wPPAS

M-PKSLTFE----------DSINIA-AP----INQVYALVS----ITRTEW-----SPVCEKCWWD--EGPVVGAHFTGRNVTWE-TRSEVIVEPN-VTDGNIYSMEPEEG-ESWEFTPKG--KFGD-KSIEEIEKRRLAAITGIPETLVA--QRILEVELEHHHH------HH---

2mk4A

0.19

0.09

0.47

1.01

dPPAS2

KVPQQTLMQGAASPELTVSGTLLVEAD-----DASAKALATRHG----LNFKQSSGGIALLEA------KPGTLNAIATKLKSEGNVQIELSGAEQQPK------------------------------------------------------------------------------

4byzA

0.15

0.14

0.94

0.67

PPAS

YTMSAQVIQIGRQR---VGG-LFWQSLSR---RNELRAEAVELAKKLKFDLMVLRIDRGVAAAGYANTGFAPGGAMVSRAIALEGAFYNGRRQPAPN-LPDGRWAY---FAVRDHAFMPNGDWVGSREEALERLHTDYAWGGPELERQGFQNFQPRLDDLRGGRPRTERWWALRPVE

1al3A1

0.07

0.06

0.76

0.62

Env-PPAS

--------------TWPDKGSLYVATTHTQARYALPGVIKGFIE-----------RYPR---VSLHMH--QGSPTQIAEAVSK-GNADFAIATEALH--LYDDLVMLPCYHTTKIGFRR--STFLRSYMYDFIQRFAPHLTRDVVDTAVALRSNEDIEAM-FKDIKLPEK-------

(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=-3.95

Estimated TM-score = 0.29±0.09

Estimated RMSD = 14.5±3.7Å

Download Model 2

C-score=-4.89

Download Model 3

C-score=-4.87

Download Model 4

C-score=-5.00

Download Model 5

C-score=-4.89

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	2b7jB	0.611	3.65	0.088	0.825
2	2k6vA	0.543	3.78	0.127	0.746
3	2hrnA	0.540	3.82	0.043	0.763
4	3me7A	0.539	3.76	0.126	0.729
5	2rliA	0.532	4.12	0.108	0.774
6	4bpyA	0.524	3.67	0.071	0.706
7	2v2gA	0.514	4.01	0.038	0.729
8	4hdeA	0.511	3.76	0.071	0.712
9	2cvbA	0.510	3.69	0.127	0.706
10	3u5rE	0.510	3.81	0.109	0.718

(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	0.10	5	2hrfA	CU1	Rep, Mult	27,31,32,104
2	0.08	4	2xkpA	AKG	Rep, Mult	141,144
3	0.06	3	1fbmA	RTL	Rep, Mult	134,141,144
4	0.04	2	1dxoA	DQN	Rep, Mult	84,111
5	0.02	1	3zcbB	ATP	Rep, Mult	149,150
6	0.02	1	2wgrA	POP	Rep, Mult	86,87,105,116,117,118,119
7	0.02	1	3nkqA	NKQ	Rep, Mult	34,37
8	0.02	1	4aahC	CA	Rep, Mult	36,121,154
9	0.02	1	1v72A	ZN	Rep, Mult	158,162
10	0.02	1	2hrnA	CU1	Rep, Mult	32,36,106
11	0.02	1	3lsmA	SO3	Rep, Mult	174,177
12	0.02	1	3nz4A	TCA	Rep, Mult	54,62
13	0.02	1	3n92A	BGC	Rep, Mult	84,85,97,98
14	0.02	1	3se1A	MG	Rep, Mult	143,146
15	0.02	1	1kb0A	CA	Rep, Mult	36,120,154,163

	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	2i3yA	0.463	4.61	0.104	0.723	1.11.1.9	NA
2	0.060	2zidA	0.487	4.89	0.046	0.802	3.2.1.70	51
3	0.060	2wgrA	0.486	3.88	0.082	0.678	1.11.1.9	NA
4	0.060	2ze0A	0.487	4.82	0.066	0.802	3.2.1.20	NA
5	0.060	1ygpA	0.486	5.09	0.051	0.774	2.4.1.1	35
6	0.060	2z9sJ	0.497	4.20	0.061	0.723	1.11.1.15	31,33,104,120,125
7	0.060	1prxA	0.508	4.35	0.044	0.751	1.11.1.7,1.11.1.15	NA
8	0.060	2azdB	0.482	4.97	0.064	0.768	2.4.1.1	NA
9	0.060	3a5wB	0.491	4.34	0.052	0.729	1.11.1.15	31
10	0.060	1zjaA	0.490	4.80	0.048	0.802	5.4.99.11	NA
11	0.060	1e1yA	0.488	4.79	0.063	0.780	2.4.1.1	NA
12	0.060	2c4mC	0.480	5.04	0.057	0.768	2.4.1.1	NA
13	0.060	3cynC	0.493	4.41	0.082	0.751	1.11.1.9	NA
14	0.060	1ea9C	0.482	4.80	0.049	0.791	3.2.1.54	NA
15	0.060	2wkgA	0.478	4.74	0.066	0.774	3.2.1.54	NA
16	0.060	1qmvA	0.492	4.30	0.068	0.723	1.11.1.15	31
17	0.060	2f8aA	0.478	4.38	0.067	0.718	1.11.1.9	NA
18	0.060	1zyeK	0.491	3.94	0.079	0.701	1.11.1.15	33,118,126
19	0.060	2d0gA	0.483	4.95	0.040	0.797	3.2.1.135	42

(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	0.12	0.502	3.98	0.10	0.72	1we0A	GO:0006979 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
1	0.08	0.437	4.28	0.06	0.66	1on4A	GO:0005886 GO:0016020 GO:0046872
2	0.07	0.611	3.65	0.09	0.82	2b7jB	GO:0005507 GO:0005739 GO:0005743 GO:0006461 GO:0006825 GO:0006878 GO:0008379 GO:0008535 GO:0016020 GO:0016021 GO:0046872 GO:0051775 GO:0098869
3	0.07	0.554	3.61	0.05	0.75	2gqkA	GO:0005507 GO:0005739 GO:0005743 GO:0006091 GO:0006825 GO:0006878 GO:0008535 GO:0030016 GO:0046872 GO:0072492
4	0.07	0.539	3.76	0.13	0.73	3me7A	GO:0016020 GO:0016021
5	0.07	0.532	4.12	0.11	0.77	2rliA	GO:0001654 GO:0001701 GO:0003012 GO:0005507 GO:0005654 GO:0005739 GO:0005743 GO:0005759 GO:0006825 GO:0006878 GO:0008535 GO:0014823 GO:0022904 GO:0030016 GO:0046872 GO:0055070 GO:0055114
6	0.07	0.533	3.67	0.06	0.73	4hdeA	GO:0005524
7	0.07	0.543	3.78	0.13	0.75	2k6vA
8	0.07	0.508	3.59	0.07	0.68	2l5oA	GO:0016491 GO:0055114
9	0.07	0.515	3.69	0.13	0.71	2ywoA	GO:0016209 GO:0016491 GO:0016853 GO:0055114 GO:0098869
10	0.07	0.498	4.10	0.09	0.72	3ztlB	GO:0004601 GO:0016209 GO:0016491 GO:0051920 GO:0055114 GO:0098869
11	0.07	0.477	3.65	0.09	0.65	3ia1A	GO:0016209 GO:0016491 GO:0016853 GO:0055114 GO:0098869
12	0.07	0.478	3.70	0.08	0.67	3kcmD	GO:0005623 GO:0016209 GO:0016491 GO:0045454 GO:0055114 GO:0098869
13	0.07	0.502	3.95	0.06	0.73	4txoD	GO:0016020 GO:0016021
14	0.07	0.477	4.12	0.09	0.69	3ixrA	GO:0016209 GO:0016491 GO:0055114 GO:0098869
15	0.07	0.469	3.73	0.09	0.65	3hdcA	GO:0005623 GO:0016209 GO:0016491 GO:0045454 GO:0055114 GO:0098869
16	0.07	0.467	3.87	0.07	0.64	1o73A	GO:0005623 GO:0045454 GO:0055114
17	0.06	0.405	4.80	0.08	0.65	3tztA	GO:0016740 GO:0016757
18	0.06	0.362	4.91	0.04	0.59	1nl3A	GO:0000166 GO:0005524 GO:0005576 GO:0005618 GO:0005737 GO:0005829 GO:0005886 GO:0005887 GO:0006605 GO:0006810 GO:0006886 GO:0015031 GO:0015462 GO:0016020 GO:0016887 GO:0017038 GO:0031522 GO:0040007 GO:0043952 GO:0052059 GO:0065002

Consensus prediction of GO terms

Molecular Function	GO:0043169
GO-Score	0.40
Biological Processes	GO:1990748
GO-Score	0.35
Cellular Component	GO:0005743	GO:0016021	GO:0005886	GO:0030016	GO:0072492
GO-Score	0.13	0.13	0.08	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.