I-TASSER results

I-TASSER results for job id Rv1906c

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

Input Sequence in FASTA format

>protein (156 residues)
MRLKPAPSPAAAFAVAGLILAGWAGSVGLAGADPEPAPTPKTAIDSDGTYAVGIDIAPGT
YSSAGPVGDGTCYWKRMGNPDGALIDNALSKKPQVVTIEPTDKAFKTHGCQPWQNTGSEG
AAPAGVPGPEAGAQLQNQLGILNGLLGPTGGRVPQP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRLKPAPSPAAAFAVAGLILAGWAGSVGLAGADPEPAPTPKTAIDSDGTYAVGIDIAPGTYSSAGPVGDGTCYWKRMGNPDGALIDNALSKKPQVVTIEPTDKAFKTHGCQPWQNTGSEGAAPAGVPGPEAGAQLQNQLGILNGLLGPTGGRVPQP
Prediction	CCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCEEEHCCCCCCCCEEEEEHCCCCCCEEHCCCCCCCEEEEHCCCCEEEEHCCCCCCEHCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCC
Conf.Score	998877776544444455555445676677789889999888778996899767669958996789999876899867999976765788897799995786689968998857768899989899988887645554445667666788899999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MRLKPAPSPAAAFAVAGLILAGWAGSVGLAGADPEPAPTPKTAIDSDGTYAVGIDIAPGTYSSAGPVGDGTCYWKRMGNPDGALIDNALSKKPQVVTIEPTDKAFKTHGCQPWQNTGSEGAAPAGVPGPEAGAQLQNQLGILNGLLGPTGGRVPQP
Prediction	753454634303313321311122233334434364464465414451203024403213040536576330102235447330222434633330304444440416614404424564546452444454241323233132334465564468
	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

CCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCEEEHCCCCCCCCEEEEEHCCCCCCEEHCCCCCCCEEEEHCCCCEEEEHCCCCCCEHCCCCCCCCCCCCCCCCCCCEEEHCCCCCCCCCCCCCCCCCC
MRLKPAPSPAAAFAVAGLILAGWAGSVGLAGADPEPAPTPKTAIDSDGTYAVGIDIAPGTYSSAGPVGDGTCYWKRMGNPDGALIDNALSKKPQVVTIEPTDKAFKTHGCQPWQNTGSEGAAPAGVPGPEAGAQLQNQLGILNGLLGPTGGRVPQP

5fzpA1

0.15

0.12

0.82

1.35

dPPAS2

------DSTSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDTPNLLATHNDSTDAGCTWTKVATL---------GSGSTWLTAATGGRAFAWEKNGGVTKLSSPSADIGISANPARPSVMYLGLEEVQ-------------

5ay6A2

0.13

0.12

0.94

1.12

dPPAS2

ANLRSEQPYDPSTWSMSDYAKDNSKGVKPDFEVQIPLSDSKGGGPGPNQWYAELRAKPGD--LANNGNGQISTGIIEFTTDGKLKNTGSLFGTT----SPTAITIKSSG----YIAPTVTPPAVQPPTPPGIDEQEVQIDLASAAGGLTQYNSQSV

5fzpA1

0.12

0.11

0.87

0.91

MUSTER

STSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTALDTPNLLATHND---ELQRST----DAGCTWTKVATLGSGSTWLTAATGGRAFAWEKNGGYLARVDGRTVTKLSSPSADIGISAIPARPSVMYLGLEEVQ-------------

5fzpA1

0.12

0.11

0.88

0.96

dPPAS

------DSTSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDTPNLLATHNDSTDAGCTWTKVATLGSGSTWLTAATGGRAFAWEKNGGYLARVDGRTVTKLSSPSADIGISANPARPSVMYLGLEEVQ-------------

5fzpA1

0.11

0.10

0.87

0.76

wdPPAS

STSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHLDTPNTLLATHN---ELQRST----DAGCTWTKVATLGSGSTWLTAATGGRAFAWEKNGGYLARVDGRTVTKLSSPSADIG-AFNPARPSVMYLGLEEVQ-------------

5fzpA1

0.13

0.12

0.87

0.95

wMUSTER

TSGWRAPSCTKVTGDGAV-TFTTDDGATLAPTTGTLQSVSYTHLDTPNLLATHND---ELQRST----DAGCTWTKVATLGSGSTWLTAATGGRAFAWEKNGGYLARVDGRTVTKLSSPSADIGISANPARPSVMYLGLEEVQ-------------

4xupA1

0.11

0.09

0.84

0.75

wPPAS

---------ASAAKAGDILLEGTTGGVKVDVTAEQAYQGKQRTEAWNGSLSLTDVVHKNVVEI--------SGYVKLVAGSAPVERRDGNGDTQYDQVNAA--EQVTDQK--WVKLQGQYSYEQGSSSTDAKAAYLLD-EF---QIRLVKAAPENP

1mv3A

0.15

0.12

0.84

1.10

dPPAS2

IRVNHEPEPAGGATPGATLPKSPSQLRKGPPVPPPPKHTPSKEVKQ---------EQILSLFEDTFVPEIS-----VTTPSQPAEASEVAGGTQPAAGAQEPGE-----------TAASEAASSSLPAVVVETFPATVNGTVEGGSGAGRLDLPPG

5fzpA1

0.15

0.12

0.82

0.94

PPAS

------DSTSGWRAPSCTKVTGDGAVTFTTDDGATLAPTTGTLQSVSYTHGLVALDTPNLLATHNDSTDAGCTWTKVATL---------GSGSTWLTAATGGRAFAWEKNGGVTKLSSPSADIGISANPARPSVMYLGLEEVQ-------------

2as5F

0.17

0.09

0.53

0.60

Env-PPAS

-------IVRPPFTYATLIRQAI-------------MESSDRQLTLNEIYSWFTRTFA-YFRRNAAT------WK-------NAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRR---------------------------------------

(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=-2.43

Estimated TM-score = 0.43±0.14

Estimated RMSD = 10.3±4.6Å

Download Model 2

C-score=-3.41

Download Model 3

C-score=-3.75

Download Model 4

C-score=-4.52

Download Model 5

C-score=-4.81

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	5fzpA	0.785	2.03	0.102	0.878
2	5aydA	0.556	4.14	0.044	0.840
3	3vgzA	0.554	4.51	0.073	0.859
4	1yifA	0.553	4.28	0.040	0.846
5	2dsoC	0.551	3.68	0.061	0.782
6	1yi7A	0.550	4.31	0.040	0.827
7	5hrmA	0.549	4.47	0.026	0.853
8	2oitA	0.549	4.45	0.073	0.833
9	4yy8A	0.548	4.75	0.075	0.885
10	3qz4A	0.548	4.37	0.059	0.846

(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	0.25	14	4ah5B	FUC	Rep, Mult	50,61,74,77,93,95,108,113
2	0.04	2	1ptsB	III	Rep, Mult	61,63
3	0.04	2	1urkA	FUC	Rep, Mult	48,59,60
4	0.04	2	2bf6A	CA	Rep, Mult	69,70,113
5	0.04	2	1v2iA	CA	Rep, Mult	55,58,59,60,80
6	0.02	1	3hdbA	CA	Rep, Mult	99,102
7	0.02	1	3fbyA	CA	Rep, Mult	45,47,50,55
8	0.02	1	2ivzA	CA	Rep, Mult	55,56
9	0.02	1	2dg1A	CA	Rep, Mult	62,63,64,69,71,72,73
10	0.02	1	2xzjA	NA	Rep, Mult	102,104,117,118,119,120

	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	1yifA	0.553	4.28	0.040	0.846	3.2.1.37	44,74
2	0.060	1euuA	0.520	4.22	0.047	0.788	3.2.1.18	44,61,78,107,109
3	0.060	2f10A	0.528	3.97	0.046	0.769	3.2.1.18	NA
4	0.060	1eusA	0.523	4.35	0.054	0.814	3.2.1.18	NA
5	0.060	2htrA	0.518	4.06	0.083	0.763	3.2.1.18	NA
6	0.060	1vcuB	0.527	4.46	0.075	0.827	3.2.1.18	NA
7	0.060	1k3iA	0.519	4.11	0.074	0.756	1.1.3.9	NA
8	0.060	2vskC	0.519	3.67	0.061	0.731	3.2.1.18	50
9	0.060	1v04A	0.524	3.70	0.022	0.744	3.1.1.2,3.1.8.1	NA
10	0.060	1aomB	0.528	4.03	0.086	0.769	1.7.99.1,1.7.2.1	NA
11	0.060	1w18B	0.524	3.53	0.054	0.731	2.4.1.10	NA
12	0.060	1sliA	0.517	4.20	0.053	0.795	4.2.2.15,3.2.1.18	NA
13	0.060	1k32A	0.525	4.25	0.055	0.808	3.4.21.-	NA
14	0.060	1jofA	0.523	4.60	0.052	0.827	5.5.1.5	NA
15	0.060	1a4gA	0.522	3.83	0.042	0.750	3.2.1.18	NA
16	0.060	1st8A	0.523	4.80	0.019	0.859	3.2.1.80	NA
17	0.060	3beqB	0.521	4.02	0.054	0.763	3.2.1.18	55
18	0.060	1qksB	0.526	4.06	0.086	0.769	1.7.2.1	43,86,125
19	0.060	1kitA	0.519	4.38	0.041	0.782	3.2.1.18	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	0.10	0.554	4.23	0.09	0.83	1l0qA	GO:0016020 GO:0016021
1	0.07	0.556	4.14	0.04	0.84	5aydA	GO:0005975 GO:0016740 GO:0016757 GO:0071555
2	0.07	0.552	4.12	0.05	0.84	3qz4A	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0045493
3	0.07	0.530	4.46	0.04	0.81	1jjuB
4	0.07	0.553	4.10	0.05	0.84	1vkdA	GO:0016787
5	0.07	0.542	4.21	0.04	0.82	3r4yA	GO:0004553 GO:0005975 GO:0016787
6	0.07	0.527	4.50	0.05	0.81	3s2kB	GO:0001843 GO:0001933 GO:0003344 GO:0005041 GO:0005102 GO:0005109 GO:0005576 GO:0005769 GO:0005783 GO:0005794 GO:0005829 GO:0005886 GO:0005901 GO:0006355 GO:0006469 GO:0006897 GO:0007204 GO:0007268 GO:0007275 GO:0009880 GO:0009986 GO:0014029 GO:0014033 GO:0016020 GO:0016021 GO:0016055 GO:0016337 GO:0017147 GO:0019210 GO:0019534 GO:0021587 GO:0021794 GO:0021987 GO:0030917 GO:0031410 GO:0031901 GO:0034185 GO:0034392 GO:0035261 GO:0042475 GO:0042802 GO:0042803 GO:0042813 GO:0043025 GO:0043235 GO:0043434 GO:0044332 GO:0044335 GO:0044340 GO:0045202 GO:0045787 GO:0045893 GO:0045944 GO:0051091 GO:0060021 GO:0060026 GO:0060059 GO:0060070 GO:0060325 GO:0060535 GO:0071397 GO:0071542 GO:0071901 GO:0071936 GO:0072659 GO:0090009 GO:0090090 GO:0090118 GO:0090244 GO:0090245 GO:0090263 GO:1901998 GO:1904886 GO:1904928 GO:1904948 GO:1904953 GO:1990851 GO:1990909 GO:2000055
7	0.07	0.553	4.28	0.04	0.85	1yifA	GO:0000272 GO:0004553 GO:0005886 GO:0005975 GO:0008152 GO:0009044 GO:0016020 GO:0016787 GO:0016798 GO:0045493
8	0.07	0.551	4.39	0.03	0.85	1y7bA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
9	0.07	0.520	4.36	0.04	0.81	3p2nA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0033954 GO:0102253 GO:0102254 GO:0102256
10	0.07	0.527	4.32	0.06	0.82	3vsfC	GO:0000272 GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0030246
11	0.07	0.520	4.07	0.10	0.76	3dr2A	GO:0004341 GO:0016787 GO:0046872
12	0.07	0.538	4.25	0.05	0.81	3nqhA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798
13	0.07	0.518	4.10	0.07	0.77	1gjqA	GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
14	0.07	0.528	4.03	0.09	0.77	1aomB	GO:0009055 GO:0016491 GO:0020037 GO:0042597 GO:0046872 GO:0050418 GO:0050421 GO:0055114
15	0.07	0.509	4.85	0.06	0.84	5ay9A	GO:0005975 GO:0016740 GO:0016757 GO:0016758 GO:0071555
16	0.07	0.531	4.26	0.05	0.81	4u6bA	GO:0004553 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0046872
17	0.07	0.503	4.73	0.04	0.83	3wasA	GO:0005975 GO:0016740 GO:0016757 GO:0016758 GO:0071555
18	0.07	0.515	4.28	0.08	0.78	3bwsA

Consensus prediction of GO terms

Molecular Function	GO:0016757	GO:0004553
GO-Score	0.07	0.07
Biological Processes	GO:0045493	GO:0071555
GO-Score	0.07	0.07
Cellular Component	GO:0016021
GO-Score	0.10

(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.