I-TASSER results

I-TASSER results for job id Rv1081c

[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)
MTHTPIPRPDARYGRPRLSRRARRRVAIALGVLVAAAGIVIAVIGYQRISTSAVTGSLVG
YRLVDDETASVTISVTRSDPSRPVACIVRVRATNGSETGRRELLVPPSEATTVQVTTTVK
SSQPPVMADVYGCGTEVPSYLRLP

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTHTPIPRPDARYGRPRLSRRARRRVAIALGVLVAAAGIVIAVIGYQRISTSAVTGSLVGYRLVDDETASVTISVTRSDPSRPVACIVRVRATNGSETGRRELLVPPSEATTVQVTTTVKSSQPPVMADVYGCGTEVPSYLRLP
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEHCCCEEEEEEEEEHCCCCCCEEEEEEEHCCCCCEEEEEEEEHCCCCCCEEEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCC
Conf.Score	998875565557999999988775468889999999999999999986468887589999999589889999999958999777999999658898678999998899995899999998589976899976878887545799
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 \| \| \| \| \| \| \| MTHTPIPRPDARYGRPRLSRRARRRVAIALGVLVAAAGIVIAVIGYQRISTSAVTGSLVGYRLVDDETASVTISVTRSDPSRPVACIVRVRATNGSETGRRELLVPPSEATTVQVTTTVKSSQPPVMADVYGCGTEVPSYLRLP
Prediction	857565743773345645664442100001112223333322221124345561424323153246740403030316567440301020325643411333040445765335341404145433303034034413532758
	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

CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEHCCCEEEEEEEEEHCCCCCCEEEEEEEHCCCCCEEEEEEEEHCCCCCCEEEEEEEEHCCCCCEEEEEHCCCCCCCCCCCCC
MTHTPIPRPDARYGRPRLSRRARRRVAIALGVLVAAAGIVIAVIGYQRISTSAVTGSLVGYRLVDDETASVTISVTRSDPSRPVACIVRVRATNGSETGRRELLVPPSEATTVQVTTTVKSSQPPVMADVYGCGTEVPSYLRLP

2micA

0.15

0.04

0.28

1.47

dPPAS2

----------------MTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSSKQNKQ---------------------------------------------------------------------------------------

1s5lJ

0.18

0.05

0.26

1.39

dPPAS2

---------------SEGGRIPLWIVATVAGMGVIVIVGLFFYGAYAGLGSSL-------------------------------------------------------------------------------------------

1guiA

0.14

0.13

0.97

0.83

MUSTER

--SINNGTFDEPIVNDQANNPDEWFIWQAGDARVSDYGVRYAYITIADPGTDTWHQFNQWIGLYRGKTYTISFKAKA-DTPRPINVKILQNHDPWTNYFAQTVNLTA-DWQTFTFTYTHPDDADEVVQISFELGEGTATYFDSP

5bw0B

0.12

0.08

0.62

0.76

dPPAS

------------------------NASRLEDKTLAMWIADNRLNELQLEQTPPSSGRNQGELEFAGRRWEWRTQVDSTAEQDMRRVIVWVAAKPLGRG-------SIEERAAARLVGFLG------------------------

2jysA

0.17

0.09

0.53

0.86

wdPPAS

------------------------------------------------------------------QPLEAEIKGTK-DSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLANPSDVPWLMKKP

2vmfB

0.15

0.13

0.90

0.73

wMUSTER

QTLPQYASNGFNYPADNDHHEKHLSVFSRKAPYSYGWDWGIRMVT-RFYDIATISDYYVRQLSLTDERLSNELIVNQIVPQKPAEVRVNVSL-NGTTVTEVKQQVTQPGINHITLPAEVTNPVR-------------PNGWGTP

2jysA

0.17

0.09

0.53

0.81

wPPAS

------------------------------------------------------------------QPLEAEIKGTK-DSGATITCVPEAFLEDERPIQTMLIKTIHGEKQQDVYYLTFKVQGRKVEAEVLANPSDVPWLMKKP

2na8A

0.07

0.02

0.31

1.31

dPPAS2

-------------GKRSWDTESVLPMWVLALIVIFLTIAVLLALRFCGIYGYRLRRK---------------------------------------------------------------------------------------

3j4uH

0.11

0.09

0.82

0.80

PPAS

VTASAASTDVIDFGQANPN--------------------------TGMDDRSKMVITVDSADAAGAATVTFSVQDSADNATFADVAATGAIGKANLAAGQVVIPMPTKLRRYCRVYYTVATGPLKFSAQVVTGIQQNVAYPDSP

3l72R

0.10

1.00

0.76

Env-PPAS

FSAYRREDVMDATTSSQTSSEDRKYLVTATACVATAYAAKNVVTQFISSLSASADVLALSKIEIKLSDIPEGKNVAFKWRGKPLFVRHREAEVDVSKLRDPQHDLDRVKKPEWVILVGVCTIANSGDFGGYYCSGRIPYNLEVP

(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=-3.69

Estimated TM-score = 0.31±0.10

Estimated RMSD = 13.3±4.1Å

Download Model 2

C-score=-4.18

Download Model 3

C-score=-3.06

Download Model 4

C-score=-4.71

Download Model 5

C-score=-4.35

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	3p5pA	0.517	4.46	0.077	0.785
2	3saeA	0.512	4.48	0.083	0.799
3	1wygA	0.511	5.06	0.049	0.889
4	4okmA	0.506	4.54	0.059	0.792
5	1jroB	0.504	4.88	0.077	0.861
6	4ksiA	0.503	4.78	0.078	0.854
7	1hxgA	0.503	4.38	0.076	0.771
8	4av3A	0.502	4.38	0.056	0.819
9	1n63B	0.502	5.12	0.070	0.868
10	1ffvB	0.501	5.16	0.070	0.875

(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	4	4il9A	UNL	Rep, Mult	39,43,46
2	0.04	2	2ckjA	FES	Rep, Mult	93,94,95,97,119,120,121
3	0.04	2	3aefC	EPH	Rep, Mult	41,44,130
4	0.02	1	2is1B	NUC	Rep, Mult	13,14
5	0.02	1	3pddA	CA	Rep, Mult	79,81,83
6	0.02	1	2vvdA	CA	Rep, Mult	65,67
7	0.02	1	3mflB	DHY	Rep, Mult	9,13
8	0.02	1	4xk8L	CLA	Rep, Mult	46,50
9	0.02	1	3u14A	FRU	Rep, Mult	122,123
10	0.02	1	2hi8X	BR	Rep, Mult	41,62,63
11	0.02	1	2ff4B	III	Rep, Mult	100,121
12	0.02	1	5klgA	6UC	Rep, Mult	40,43
13	0.02	1	1wygA	CA	Rep, Mult	77,78,79,81,108,109
14	0.02	1	1fo4A	FES	Rep, Mult	75,86,87,89,101,102,103,116
15	0.02	1	2ckjC	FES	Rep, Mult	12,13,14,16,35,37,38
16	0.02	1	2h8pC	GOA	Rep, Mult	60,61
17	0.02	1	4fe1F	CLA	Rep, Mult	30,34
18	0.02	1	3eubS	FES	Rep, Mult	47,55,56,57,58,76
19	0.02	1	2x2vH	DPV	Rep, Mult	32,40
20	0.02	1	1lnyA	MG	Rep, Mult	79,99

	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	1ezfB	0.494	4.29	0.044	0.771	2.5.1.21	82
2	0.060	1bk4A	0.478	4.57	0.057	0.764	3.1.3.11	NA
3	0.060	3bpsA	0.401	4.89	0.083	0.708	3.4.21.-	NA
4	0.060	2oa6D	0.474	4.17	0.042	0.715	4.2.3.9	NA
5	0.060	1r58A	0.481	5.15	0.043	0.826	3.4.11.18	NA
6	0.060	3fmrB	0.491	4.69	0.090	0.799	3.4.11.18	96
7	0.060	3kb9A	0.484	4.81	0.037	0.778	4.2.3.37	NA
8	0.060	2j5cB	0.488	4.69	0.100	0.785	4.2.3.-	NA
9	0.060	1ftaA	0.486	4.77	0.073	0.799	3.1.3.11	NA
10	0.060	3h8eA	0.477	4.91	0.065	0.792	3.4.11.1	35
11	0.060	1z11A	0.479	4.23	0.034	0.722	1.14.14.1	NA
12	0.060	3b9jC	0.511	4.96	0.070	0.889	1.17.3.2,1.17.1.4	NA
13	0.060	1spiA	0.471	4.66	0.062	0.771	3.1.3.11	NA
14	0.060	1fsaA	0.482	4.72	0.076	0.792	3.1.3.11	NA
15	0.060	1t3qB	0.498	4.86	0.056	0.861	1.3.99.17	NA
16	0.060	3g4dA	0.497	4.46	0.042	0.771	4.2.3.13	NA
17	0.060	3b9jJ	0.363	5.20	0.044	0.674	1.17.1.4,1.17.3.2	84
18	0.060	1ffuB	0.510	5.16	0.085	0.875	1.2.99.2	NA
19	0.060	2hb6B	0.493	4.66	0.079	0.826	3.4.11.1	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	0.497	4.46	0.04	0.77	3g4dA	GO:0000287 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872 GO:0047461
1	0.07	0.499	4.91	0.07	0.82	3s9vB	GO:0000287 GO:0003824 GO:0008152 GO:0009507 GO:0009536 GO:0010333 GO:0016829 GO:0016853 GO:0046872 GO:0050554 GO:0050559
2	0.07	0.490	4.61	0.05	0.78	2ongA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
3	0.07	0.495	4.50	0.06	0.77	3pybB	GO:0000287 GO:0008152 GO:0009507 GO:0009536 GO:0009686 GO:0009740 GO:0009905 GO:0010333 GO:0016829 GO:0016853
4	0.07	0.492	4.30	0.08	0.76	4gaxA	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0034006 GO:0046872
5	0.07	0.499	4.42	0.04	0.77	5c05B	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
6	0.07	0.488	4.69	0.10	0.78	2j5cB	GO:0000287 GO:0008152 GO:0010333 GO:0016829 GO:0046872
7	0.07	0.501	4.40	0.06	0.77	5dhiA	GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016114 GO:0016829 GO:0046872
8	0.06	0.398	5.25	0.03	0.74	1vkhA	GO:0004061 GO:0006569 GO:0008152 GO:0009435 GO:0016787 GO:0019441 GO:0030307 GO:0034354
9	0.06	0.382	4.96	0.10	0.67	4rifB	GO:0016740
10	0.06	0.358	4.37	0.03	0.54	2p0uA	GO:0003824 GO:0008152 GO:0009058 GO:0016740 GO:0016746 GO:0016747
11	0.06	0.354	4.72	0.07	0.57	3on7B	GO:0016491 GO:0046872 GO:0051213 GO:0055114
12	0.06	0.321	4.89	0.07	0.52	4gc3A	GO:0000105 GO:0003677 GO:0003824 GO:0003887 GO:0004401 GO:0006260 GO:0008652 GO:0016311 GO:0016787 GO:0071897
13	0.06	0.369	4.34	0.07	0.58	1r5aA	GO:0016740 GO:0046872
14	0.06	0.512	4.48	0.08	0.80	3saeA	GO:0000287 GO:0005737 GO:0008152 GO:0010333 GO:0016829 GO:0046872 GO:0052681
15	0.06	0.361	4.31	0.01	0.56	2ab6A	GO:0004364 GO:0005102 GO:0005737 GO:0005829 GO:0006749 GO:0008152 GO:0010880 GO:0010881 GO:0014809 GO:0016529 GO:0016740 GO:0018916 GO:0019899 GO:0042178 GO:0042803 GO:0043295 GO:0055119 GO:0060315 GO:0060316 GO:0070062 GO:0070458 GO:0071313 GO:1901687
16	0.06	0.370	4.76	0.04	0.65	1y4uB	GO:0000166 GO:0005524 GO:0005737 GO:0005829 GO:0005886 GO:0006457 GO:0006950 GO:0006974 GO:0009408 GO:0016020 GO:0016887 GO:0042623 GO:0042802 GO:0051082
17	0.06	0.360	4.69	0.04	0.60	4v06A	GO:0004497 GO:0004510 GO:0005506 GO:0005829 GO:0007623 GO:0008152 GO:0009072 GO:0014823 GO:0016491 GO:0016597 GO:0016714 GO:0031667 GO:0042427 GO:0043005 GO:0043627 GO:0046219 GO:0046872 GO:0051384 GO:0051592 GO:0055114 GO:0071285
18	0.06	0.448	4.46	0.04	0.72	3t3zA	GO:0000139 GO:0004497 GO:0005506 GO:0005739 GO:0005783 GO:0005789 GO:0006641 GO:0006805 GO:0008202 GO:0008392 GO:0008395 GO:0010193 GO:0010243 GO:0016020 GO:0016098 GO:0016491 GO:0016705 GO:0016709 GO:0016712 GO:0017144 GO:0018885 GO:0018910 GO:0019373 GO:0019825 GO:0019899 GO:0020037 GO:0031090 GO:0031227 GO:0042197 GO:0042493 GO:0043231 GO:0045471 GO:0046483 GO:0046872 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0016838	GO:0046872
GO-Score	0.58	0.58
Biological Processes	GO:0009686	GO:0009740
GO-Score	0.07	0.07
Cellular Component	GO:0009507
GO-Score	0.13

(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.