I-TASSER results

I-TASSER results for job id Rv0925c

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

Input Sequence in FASTA format

>protein (245 residues)
MTTTSDQNAAAPPRFDGLRALFINATLKRSPELSHTDGLIERSSGIMREHGVQVDTLRAV
DHDIATGVWPDMTEHGWATDEWPALYRRVLDAHILVLCGPIWLGDNSSVMKRVIERLYAC
SSLLNEDGQYAYYGRAGGCLITGNEDGVKHCAMNVLYSLQHLGYTIPPQADAGWIGEAGP
GPSYLDPGSGGPENDFTNRNTTFMTFNLMHIAQMLRVAGGIPAYGNQRTKWDAGCRPDFA
NPDYR

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MTTTSDQNAAAPPRFDGLRALFINATLKRSPELSHTDGLIERSSGIMREHGVQVDTLRAVDHDIATGVWPDMTEHGWATDEWPALYRRVLDAHILVLCGPIWLGDNSSVMKRVIERLYACSSLLNEDGQYAYYGRAGGCLITGNEDGVKHCAMNVLYSLQHLGYTIPPQADAGWIGEAGPGPSYLDPGSGGPENDFTNRNTTFMTFNLMHIAQMLRVAGGIPAYGNQRTKWDAGCRPDFANPDYR
Prediction	CCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEHCCCCHHHHHHHHHHHHHHHCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCCC
Conf.Score	99887788888888778689999688999999998999999999999998996899997587678875678888887887899999999989989998477789984999999999855545445778754689879999995787789999999999998776775676655456778885555667777766899999999999999999999997899988877555555777888898889
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MTTTSDQNAAAPPRFDGLRALFINATLKRSPELSHTDGLIERSSGIMREHGVQVDTLRAVDHDIATGVWPDMTEHGWATDEWPALYRRVLDAHILVLCGPIWLGDNSSVMKRVIERLYACSSLLNEDGQYAYYGRAGGCLITGNEDGVKHCAMNVLYSLQHLGYTIPPQADAGWIGEAGPGPSYLDPGSGGPENDFTNRNTTFMTFNLMHIAQMLRVAGGIPAYGNQRTKWDAGCRPDFANPDYR
Prediction	76465554674555244010000000014545421023004201520573604112020362503200100246643550203301510350200000000111223220100000010222313544431034100000000134202300220131033301201131123223322333532456543564530350033003102300310375451244344474154345272743738
	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                 180                 200                 220                 240

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEEHCCCCHHHHHHHHHHHHHHHCCEHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCCCCCC
MTTTSDQNAAAPPRFDGLRALFINATLKRSPELSHTDGLIERSSGIMREHGVQVDTLRAVDHDIATGVWPDMTEHGWATDEWPALYRRVLDAHILVLCGPIWLGDNSSVMKRVIERLYACSSLLNEDGQYAYYGRAGGCLITGNEDGVKHCAMNVLYSLQHLGYTIPPQADAGWIGEAGPGPSYLDPGSGGPENDFTNRNTTFMTFNLMHIAQMLRVAGGIPAYGNQRTKWDAGCRPDFANPDYR

2vzfA

0.20

0.15

0.77

1.52

MUSTER

MT---------------YSIVAISGSPSRN---STTAKLAEYALAHVLARDSQGRHIHVIDLDPKALLRGDLS-----NAKLKEAVDATCNADGLIVATPIYKASYTGLLKAFLDIL----------PQFALAGKAALPLATGSPAHVLALDYGLRPVLHSMGVRHVVQSF------------FLVQSQFKLAVE--DDVASQLNNAIDHFRLSLSSEPSTRHLGHPRPSLDA-TR---------

1rliD

0.16

0.11

0.67

1.97

dPPAS

------------------KIAVINGGTRSG---GNTDVLAEKAVQ-----GFDAEHIYLQKYPIAQ------GGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPFKQQMSVKQAYVIAVGGDNPGLPLIQQFEHIFHFMGMSFK-----GYVLGEGNRPGDI------LRDHQALSAASRLLKR--------------------------------------

1rliD

0.15

0.10

0.67

2.58

wdPPAS

------------------KIAVINGGTRSGG---NTDVLAEKAVQ-----GFDAEHIYLQKYPIAQ------GGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPFKQQMSVKQAYVIAVGGDNPGLPLIQQFEHIFHFMGMSFKG-----YVLGEGNRPGDI------LRDHQALSAASRLLKR--------------------------------------

1rliD

0.17

0.11

0.67

1.90

wMUSTER

------------------KIAVINGGTRSG---GNTDVLAEKAVQ-----GFDAEHIYLQKYPIAQG------GFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLDPRFPDFKQQMSVKQAYVIAVGGDNPGLPLIQQFEHIFHFMGMSFK-----GYVLGEGNRPGDI------LRDHQALSAASRLLKR--------------------------------------

1rliD

0.16

0.11

0.67

2.87

wPPAS

------------------KIAVINGGTRSGG---NTDVLAEKAVQ-----GFDAEHIYLQKYPIAQGGFR------PVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPFKQQMSVKQAYVIAVGGDNPGLPLIQQFEHIFHFMGMSFKG-----YVLGEGNRPG------DILRDHQALSAASRLLKR--------------------------------------

1rliD

0.16

0.11

0.67

4.73

dPPAS2

------------------KIAVINGGTRSG---GNTDVLAEKAVQ-----GFDAEHIYLQKYPIAQ------GGFRPVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPFKQQMSVKQAYVIAVGGDNPGLPLIQQFEHIFHFMGMSFK-----GYVLGEGNRPGDI------LRDHQALSAASRLLKR--------------------------------------

1rliD

0.16

0.11

0.67

2.30

PPAS

------------------KIAVINGGTRSGG---NTDVLAEKAVQ-----GFDAEHIYLQKYPIAQGGFR------PVQDDYDSIIERILQCHILIFATPIYWFGMSGTLKLFIDRWSQTLRDPRFPFKQQMSVKQAYVIAVGGDNPGLPLIQQFEHIFHFMGMSFK-----GYVLGEGNRPGDILRD------HQALSAASRLLKR--------------------------------------

4ptyC

0.12

0.08

0.70

2.73

Env-PPAS

-----------------MRVITLAGSPRFP---SRSSSLLEYAREKLNGLDVEVYHWNLQNFAPEDLLYARFD-----SPALKTFTEQLQQADGLIVATPVYKAAYSGALKTLLDLL----------PERALQGKVVLPLATGGTVHLLAVDYALKPVLSALKAQEILHG------VFADDSQVIDYHHRPQFTPNLQTRLDTALETFWQALH--------------------------------

1sqsA

0.13

0.11

0.80

1.50

MUSTER

-----------------NKIFIYAGVRNHN---SKTLEYTKRLSSIISSRNVDISFRTPFNSELEISNSDSEEDRQSNADDGGVIKKELLESDIIIISSPVYLQNVSVDTKNFIERIGGWSHLFR------LAGKFVVTLDVAESNGSDNVSEYLRDIFSYGGQILHQVSIT----------------------NSLKDIAEAQLEATYKIEDVLEGKIKYKTTDYQERAYQTLENYDSEHFEKY

4ptyC

0.12

0.08

0.70

1.94

dPPAS

-----------------MRVITLAGSPRFP---SRSSSLLEYAREKLNGLDVEVYHWNLQNFAPEDLLYA-----RFDSPALKTFTEQLQQADGLIVATPVYKAAYSGALKTLLDLL----------PERALQGKVVLPLATGGTVAHLAVDYALKPVLSALKAQEILHG------VFADDSQVIDYHHRPQFTPNLQTRLDTALETFWQALH--------------------------------

(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=-0.59

Estimated TM-score = 0.64±0.13

Estimated RMSD = 7.0±4.1Å

Download Model 2

C-score=-1.66

Download Model 3

C-score=-1.02

Download Model 4

C-score=-1.73

Download Model 5

C-score=-3.57

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	1sqsA	0.685	2.94	0.137	0.804
2	2q62D	0.665	3.62	0.106	0.816
3	2fzvB	0.663	3.67	0.118	0.816
4	2vzfA	0.636	2.84	0.134	0.743
5	4ptyC	0.621	2.35	0.099	0.698
6	3s2yA	0.620	3.09	0.110	0.739
7	1f5nA	0.613	4.61	0.055	0.869
8	3svlA	0.611	2.96	0.136	0.722
9	1x77A	0.607	2.51	0.129	0.694
10	1d4aA	0.603	4.09	0.101	0.784

(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	0.39	15	4ptzC	FMN	Rep, Mult	26,28,34,35,36,100,101,102,103,104,142,143,144,145,147,179
2	0.08	3	1x77A	FMN	Rep, Mult	26,29,34,35,36,100,102,103
3	0.05	2	3o73A	O73	Rep, Mult	115,117,118,161
4	0.04	2	1kbqB	FAD	Rep, Mult	64,111,112,113
5	0.02	1	1gg5A	E09	Rep, Mult	58,59,98,99,108

	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	0.205	1t0iA	0.571	3.14	0.122	0.686	1.5.1.29	111
2	0.158	2z9dB	0.583	3.21	0.098	0.702	1.7.1.6	68
3	0.152	1b1cA	0.497	3.58	0.089	0.633	1.6.2.4	NA
4	0.146	2qx9B	0.589	3.93	0.098	0.747	1.10.99.2	111
5	0.066	1e0sA	0.466	3.32	0.052	0.580	3.6.1.47	NA
6	0.066	1aa9A	0.451	3.62	0.075	0.596	3.6.5.-	129
7	0.060	1d2eA	0.513	3.69	0.060	0.669	3.6.5.3	37
8	0.060	3dnyT	0.504	4.43	0.054	0.698	3.6.5.3	NA
9	0.060	1r64A	0.517	5.00	0.078	0.775	3.4.21.61	NA
10	0.060	1fuiA	0.524	3.83	0.068	0.694	5.3.1.25	NA
11	0.060	2elfA	0.509	3.69	0.097	0.653	3.6.1.48	38
12	0.060	1ygpA	0.524	5.23	0.069	0.800	2.4.1.1	NA
13	0.060	1p8jA	0.524	5.02	0.089	0.784	3.4.21.75	NA
14	0.060	1dxqA	0.603	3.94	0.097	0.775	1.6.5.2,1.6.99.2	NA
15	0.060	3ce6A	0.512	4.06	0.041	0.682	3.3.1.1	NA
16	0.060	3d64A	0.496	3.81	0.089	0.657	3.3.1.1	NA
17	0.060	1ha3B	0.530	4.42	0.056	0.735	3.1.5.1	37
18	0.060	3hr4A	0.506	3.30	0.094	0.625	1.14.13.39	26,39,143,173
19	0.060	3n58A	0.502	3.88	0.031	0.661	3.3.1.1	104,141
20	0.060	1aknA	0.508	5.15	0.057	0.796	3.1.1.13,3.1.1.3	NA
21	0.060	2hihA	0.508	5.15	0.061	0.771	3.1.1.3	NA
22	0.060	1gy8C	0.506	4.50	0.057	0.706	5.1.3.2	NA
23	0.060	1qr2A	0.587	4.04	0.098	0.751	1.10.99.2,1.6.99.2	NA
24	0.060	2rg1B	0.570	2.26	0.130	0.641	1.6.5.2	NA
25	0.060	2akaB	0.513	4.48	0.067	0.718	3.6.5.5	194

(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	0.32	0.600	2.85	0.12	0.69	1ydgE	GO:0000166 GO:0003955 GO:0010181 GO:0016491 GO:0045892 GO:0055114
1	0.25	0.665	3.62	0.11	0.82	2q62D	GO:0000166 GO:0010038 GO:0010181 GO:0016491 GO:0051289 GO:0052873 GO:0055114
2	0.25	0.577	2.62	0.16	0.66	2arkA	GO:0009055 GO:0010181 GO:0055114
3	0.24	0.696	2.93	0.14	0.82	1sqsA	GO:0016491 GO:0055114
4	0.24	0.663	3.67	0.12	0.82	2fzvB	GO:0000166 GO:0010181 GO:0016491 GO:0050446 GO:0051289 GO:0052873 GO:0055114
5	0.24	0.573	2.27	0.13	0.64	2rg1A	GO:0000166 GO:0003955 GO:0005829 GO:0006979 GO:0010181 GO:0016020 GO:0016491 GO:0042802 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
6	0.24	0.585	2.26	0.15	0.65	1rliD	GO:0016491 GO:0055114
7	0.22	0.606	2.94	0.10	0.71	4c76A	GO:0016491 GO:0052873 GO:0055114
8	0.22	0.593	2.96	0.11	0.71	3k1yA	GO:0016491 GO:0055114
9	0.22	0.595	2.81	0.13	0.69	4lafA	GO:0003955 GO:0010181 GO:0016491 GO:0019439 GO:0045892 GO:0046196 GO:0050660 GO:0050661 GO:0051287 GO:0055114
10	0.22	0.633	2.74	0.14	0.73	4ltdA	GO:0000166 GO:0008752 GO:0016491 GO:0046306 GO:0055114
11	0.20	0.617	3.02	0.11	0.73	4h6pA	GO:0000166 GO:0016491 GO:0055114
12	0.20	0.589	2.61	0.12	0.67	3b6iA	GO:0000166 GO:0003955 GO:0005829 GO:0006979 GO:0010181 GO:0016020 GO:0016491 GO:0042802 GO:0045892 GO:0050660 GO:0050661 GO:0051287 GO:0055114
13	0.19	0.617	2.91	0.14	0.73	3svlB	GO:0003955 GO:0005829 GO:0006805 GO:0010181 GO:0016491 GO:0055114
14	0.19	0.498	2.12	0.11	0.56	2faxA	GO:0009055 GO:0010181 GO:0055114
15	0.19	0.570	3.33	0.10	0.70	3w78A	GO:0000166 GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
16	0.19	0.588	2.99	0.15	0.69	3gfrD	GO:0016491 GO:0042802 GO:0055114
17	0.19	0.620	2.31	0.10	0.70	4ptyD	GO:0006974 GO:0008752 GO:0009970 GO:0016491 GO:0046306 GO:0051289 GO:0052873 GO:0055114
18	0.18	0.608	2.49	0.12	0.69	1rttA	GO:0000166 GO:0010181 GO:0016491 GO:0042802 GO:0042803 GO:0052873 GO:0055114
19	0.16	0.498	2.01	0.11	0.55	2fz5A	GO:0009055 GO:0010181 GO:0055114
20	0.15	0.566	3.55	0.12	0.70	4f8yA	GO:0000166 GO:0003955 GO:0016491 GO:0055114
21	0.15	0.590	3.12	0.10	0.71	1t5bA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
22	0.15	0.579	3.28	0.15	0.70	3r6wA	GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016661 GO:0055114
23	0.14	0.592	3.32	0.10	0.72	1tikA	GO:0005829 GO:0006979 GO:0008752 GO:0009055 GO:0010181 GO:0016491 GO:0016652 GO:0016655 GO:0016661 GO:0050446 GO:0055114
24	0.14	0.493	3.18	0.14	0.60	3hlyC	GO:0010181 GO:0016491 GO:0055114

Consensus prediction of GO terms

Molecular Function	GO:0010181	GO:0046857	GO:0052873	GO:0003955
GO-Score	0.71	0.49	0.43	0.32
Biological Processes	GO:0055114	GO:0010035	GO:0051289	GO:0045892
GO-Score	0.78	0.50	0.43	0.32
Cellular Component
GO-Score

(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.