I-TASSER results

I-TASSER results for job id Rv1728c

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

Input Sequence in FASTA format

>protein (256 residues)
MSVNGLPGAHNAGLQPIDSKGCHTRRTRHTKVLFVSKGVLANGRGRWLAIAASLVVSAAI
LYAQGAEHTCCRETPAAIPTGPDSAPANAPRIASPTEADLLAASAPVAAQQFQFALPAGV
ASEEGLQVKTIWVARAVSVLFPQITNIFGYRQDPLKWHPNGLAIDVMIPNHHSDEGIQLG
NQVAGLALANAKRWGVLHVIWRQGYYPGIGAPSWTADYGSETLNHYDHVHIATDGGGYPT
GRETYYVGSMSPTPPE

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MSVNGLPGAHNAGLQPIDSKGCHTRRTRHTKVLFVSKGVLANGRGRWLAIAASLVVSAAILYAQGAEHTCCRETPAAIPTGPDSAPANAPRIASPTEADLLAASAPVAAQQFQFALPAGVASEEGLQVKTIWVARAVSVLFPQITNIFGYRQDPLKWHPNGLAIDVMIPNHHSDEGIQLGNQVAGLALANAKRWGVLHVIWRQGYYPGIGAPSWTADYGSETLNHYDHVHIATDGGGYPTGRETYYVGSMSPTPPE
Prediction	CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHHHCCCCCCCCCCCEEHCCCCCCCCCCCHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEHCCEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCC
Conf.Score	9878888777777776667888655555533444443446777765444344445565444455788877777777888888888888888888877777888888888878888888888888877779999999999889865777768999888889868999968999967899999999999999999899789987866588889888899999888888768898668888988876556888998999
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 220 240 \| \| \| \| \| \| \| \| \| \| \| \| MSVNGLPGAHNAGLQPIDSKGCHTRRTRHTKVLFVSKGVLANGRGRWLAIAASLVVSAAILYAQGAEHTCCRETPAAIPTGPDSAPANAPRIASPTEADLLAASAPVAAQQFQFALPAGVASEEGLQVKTIWVARAVSVLFPQITNIFGYRQDPLKWHPNGLAIDVMIPNHHSDEGIQLGNQVAGLALANAKRWGVLHVIWRQGYYPGIGAPSWTADYGSETLNHYDHVHIATDGGGYPTGRETYYVGSMSPTPPE
Prediction	7625424233512043146541444435423012103222354332012101321332021314456453456444543544553436454444445463344433344453433125434457414422330141027424423200000334462113010000000324445035103300310351076150310002220132433452252212333302000000132432154654143356554368
	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

CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEHHHCCCCCCCCCCCEEHCCCCCCCCCCCHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEEHCCCCCCCCCCCCEEEEEHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEHCCEEHCCCCCCCCCCCCCCCCCCCCCEEEEEHCCCCCCCCCCCCCCCCCCCCCCC
MSVNGLPGAHNAGLQPIDSKGCHTRRTRHTKVLFVSKGVLANGRGRWLAIAASLVVSAAILYAQGAEHTCCRETPAAIPTGPDSAPANAPRIASPTEADLLAASAPVAAQQFQFALPAGVASEEGLQVKTIWVARAVSVLFPQITNIFGYRQDPLKWHPNGLAIDVMIPNHHSDEGIQLGNQVAGLALANAKRWGVLHVIWRQGYYPGIGAPSWTADYGSETLNHYDHVHIATDGGGYPTGRETYYVGSMSPTPPE

4bedB

0.11

0.99

0.79

MUSTER

FAGFLLHGIRTSADVQFQICKTSEDCHHGGQIFVLGTKEMAWAYNRLFKYDITHALHDAHITPEDVFHPSEPFFIKVSVTAVNGTVLPASILHAPTIIYEPGLDHHEDHHSSSMAGHGVRKEINTLTAEVDNLKDAMRAVMADHGAIAAFGNPPMCPMPDGKNYSCCTHGMATHWHRLYTKQMEDALTAHGARVGLPYWDGTT---AFTALPTFVTDEEDNPFHHGHIDYLGVDTTRSPRDKLFNDPERGSESFFY

5gaoE

0.15

0.14

0.94

1.03

dPPAS

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-------AAAAAAAAAAAAAAAAA--------AAAAAAAAAAAAAAAAAAAAAAARA

1lbuA2

0.21

0.09

0.45

1.08

wdPPAS

----------------------------------------------------------------------------------------------PVNFTYAELNRCNSDWSGGKVSAATARA---NALVTMWKLQAMRHAMGDITVNGGFRSASNSRHMYGHAADLGAGSQG-------FCALAQAARN----HGFTEIL-----------------PG--YPGHNDHTHVAGGDGSAPSCGI-------------

1zlgA

0.12

0.11

0.90

0.75

wMUSTER

GIQTQLPFQRRRPTRPLEVGAPFYQDGQLQVKVYWKKTEDPTVNRRWFPEACAHNRTTGSEASSGMTHENYIILQPIRPKSHSKAEAVFFTTPPCSALKGKSHKPIGCLGEAGHVLSKVLAKPENLSASF------IVQDVNITGHFSKMAKANLYQPMTGFQVTWAEVTTESRQNS-----------------LPNSIISQSQILPSDHYVLTVPNLRPST--LY-RLEVVLTPGGEPATIKTFRTPELPPSSAH

1lbuA2

0.25

0.09

0.38

0.96

wPPAS

--------------------------------------------------------------------------------------------------------------------PVNSDWSGGKVLVTMWKLQAMRHAMGDITVNGGFRSASNSRHMYGHAADLGAGSQG-------FCALAQAARN----HGFTEIL-----------------PG--YPGHNDHTHVAGGDGSAPSCGI-------------

5gaoE

0.17

0.13

0.78

2.16

dPPAS2

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA--------------------------------AAAAAAAAAAAAAAAAAAAA-----------------AAAAAAAAAAAAAA--------AAAAAAAAAAAAAAAAAAAAAAARA

5gaoE

0.14

0.99

1.24

PPAS

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA--AAAAAAAAAAAAAAAAAARAA-AAAAAAAAAAAAAAAAAAAAAAAAAAAA

5hsxA

0.11

0.99

0.80

Env-PPAS

IEVTPLSAHIGAEIHGVDLTQKLEARQIAEIRAALLKWRVVFFREQFLTHEQHVAFSAQFGELTLGVFGHVEGHPEVYSISKYQTLQRPWTGWHTDVTAAVNPPWASILRGVTIPPYGGDTQWTNLVAAYQKLSAPLRSFVDGLRGIHRFTPRILVVHPETGERALYVSPSFLKSSPRESQVLLELLWEHVTRPEFTVRFWQAAFWDNRATALAPTDIFD--LDFDRQLYRTTLVGDVPVGPDGTQSVAIEGSPV-

3vtaA

0.08

0.07

0.95

0.78

MUSTER

LSVGG-ANPRHYFVDAI-AIGSFHAVERGILTSNSAGNGGPNFFTTASLSPWLLSVAASTMDRKFVTQVQIGNGQSFQGVSINTFDNQYYPLVSGRDIPNTGFDKSTSRFCTDKSVNPNLLKGKIVVCEASFGPHEFFKSLDGAAGVLMTSNTRDYADSYPLPSSVLD--------PNDLLATLRYIYS---IRSPGATIFKSTTILNASAPVVVSRGPNRATKDVIKPDISGPGVEWPSVAPVGGIRRNTLNIIS

2rrlA

0.09

0.05

0.63

0.90

dPPAS

-----------------------------------------------------------HMASDDRATGPALTPLVVAAAATSAKVEVDSPPAPVTHGAAMPTLSSATAQPLPVASAPVLSAPLGSHEWQQTFSQQVMLFTRQGQQSAQLRLHPEELGQDNQAQLQMV--SPHSHVRAALEAALPMLRTQLAESGIQLGQS--SISSESFAGQQQSSSQQQSSR--------------------------------

(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=-3.16

Estimated TM-score = 0.36±0.12

Estimated RMSD = 13.4±4.1Å

Download Model 2

C-score=-4.72

Download Model 3

C-score=-4.25

Download Model 4

C-score=-4.97

Download Model 5

C-score=-4.92

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	4bedB	0.947	1.40	0.107	0.988
2	4bedA	0.547	4.28	0.069	0.684
3	1lnlA	0.495	2.23	0.107	0.547
4	4m5dA	0.485	5.52	0.063	0.781
5	1js8A1	0.477	2.17	0.120	0.519
6	2y9wA	0.466	3.13	0.097	0.555
7	3l6wA	0.464	2.52	0.119	0.523
8	3w6qA	0.463	3.38	0.063	0.562
9	4ouaB	0.450	3.32	0.062	0.539
10	3hlkB	0.446	5.37	0.070	0.695

(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	0.16	8	1lbuA	ZN	Rep, Mult	158,165,230
2	0.08	4	4q54x	CLA	Rep, Mult	176,177,180,183
3	0.04	2	3qj1A	PEG	Rep, Mult	181,184
4	0.04	2	1oczB	HEA	Rep, Mult	147,186
5	0.04	2	2y9xA	0TR	Rep, Mult	133,136,137,184,187
6	0.02	1	3nq1A	KOJ	Rep, Mult	216,219,224,226
7	0.02	1	1h18B	DTL	Rep, Mult	125,129,133
8	0.02	1	1iw7P	MG	Rep, Mult	174,178
9	0.02	1	3od4A	ZN	Rep, Mult	225,227
10	0.02	1	2y4sA	CA	Rep, Mult	134,137,222,223
11	0.02	1	2a0iA	MG	Rep, Mult	225,228,230
12	0.02	1	4z10D	RCO	Rep, Mult	138,141,219,220,222

	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	3la4A	0.401	6.21	0.033	0.707	3.5.1.5	NA
2	0.060	1rtkA	0.338	6.51	0.028	0.625	3.4.21.47	187
3	0.060	1bt1A	0.420	3.30	0.046	0.508	1.10.3.1	NA
4	0.060	3k2iA	0.415	5.69	0.062	0.688	3.1.2.2	NA
5	0.060	2ok5A	0.380	6.02	0.040	0.652	3.4.21.47	NA
6	0.060	1g8kE	0.399	6.06	0.078	0.703	1.20.98.1	178
7	0.060	1qf6A	0.386	6.05	0.032	0.672	6.1.1.3	NA
8	0.060	2vuaA	0.334	6.17	0.041	0.590	3.4.24.69	175,179
9	0.060	1h16A	0.417	5.91	0.056	0.699	2.3.1.54	NA
10	0.060	3komA	0.400	5.89	0.048	0.668	2.2.1.1	187
11	0.060	1d8yA	0.403	5.75	0.048	0.672	2.7.7.7	127
12	0.060	3btaA	0.405	6.23	0.012	0.711	3.4.24.69	NA
13	0.060	2pflA	0.406	5.71	0.024	0.668	2.3.1.54	NA
14	0.060	2bhrA	0.282	6.16	0.082	0.488	3.4.21.91	NA
15	0.060	1g0dA	0.390	6.29	0.052	0.707	2.3.2.13	NA
16	0.060	2p3xA	0.420	3.40	0.029	0.512	1.10.3.1	127
17	0.060	1rs0A	0.340	6.56	0.038	0.629	3.4.21.47	191
18	0.060	2r8oB	0.405	5.69	0.048	0.656	2.2.1.1	NA
19	0.060	1hbmB	0.386	6.14	0.045	0.672	2.8.4.1	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	0.495	2.23	0.11	0.55	1lnlA	GO:0005344 GO:0005576 GO:0005615 GO:0006810 GO:0008152 GO:0015671 GO:0016491 GO:0046872 GO:0055114
1	0.07	0.480	2.09	0.13	0.53	3qjoA	GO:0008152 GO:0016491 GO:0046872 GO:0055114
2	0.07	0.477	2.17	0.12	0.52	1js8A	GO:0005344 GO:0006810 GO:0008152 GO:0015671 GO:0016491 GO:0046872 GO:0055114
3	0.06	0.421	4.03	0.07	0.54	4hd4A	GO:0008152 GO:0016491 GO:0046872 GO:0055114
4	0.06	0.398	4.05	0.07	0.51	3awtA	GO:0008152 GO:0016491 GO:0046872 GO:0055114
5	0.06	0.450	3.32	0.06	0.54	4ouaB	GO:0004503 GO:0008152 GO:0016491 GO:0046872 GO:0055114
6	0.06	0.291	6.38	0.07	0.52	4fuqC	GO:0000166 GO:0003824 GO:0005524 GO:0008152 GO:0016874
7	0.06	0.412	3.59	0.04	0.51	4j3rA	GO:0004097 GO:0008152 GO:0016491 GO:0046872 GO:0055114
8	0.06	0.422	3.39	0.03	0.52	4z11A	GO:0004097 GO:0008152 GO:0016491 GO:0046148 GO:0046872 GO:0055114
9	0.06	0.284	6.72	0.04	0.53	4ntcA	GO:0000166 GO:0016491 GO:0055114
10	0.06	0.271	5.90	0.06	0.45	3r25B	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0046872
11	0.06	0.272	5.91	0.05	0.45	4girB	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0046872
12	0.06	0.281	6.50	0.05	0.49	4hnlA	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0046872
13	0.06	0.236	6.25	0.03	0.43	3p71T	GO:0003880 GO:0005829 GO:0006464 GO:0006479 GO:0006481 GO:0008168 GO:0008276 GO:0008757 GO:0010906 GO:0016740 GO:0018423 GO:0031333 GO:0032259 GO:0042981 GO:0090266
14	0.06	0.420	3.40	0.03	0.51	2p3xA	GO:0004097 GO:0008152 GO:0009507 GO:0009536 GO:0009543 GO:0009579 GO:0016491 GO:0046148 GO:0046872 GO:0055114
15	0.06	0.420	3.30	0.05	0.51	1bt1A	GO:0004097 GO:0008152 GO:0009507 GO:0009536 GO:0009543 GO:0009579 GO:0016491 GO:0046872 GO:0055114
16	0.06	0.272	5.97	0.06	0.45	3dfhA	GO:0000287 GO:0003824 GO:0008152 GO:0009063 GO:0046872
17	0.06	0.468	3.32	0.07	0.57	3w6wA	GO:0004503 GO:0005634 GO:0008152 GO:0016491 GO:0046872 GO:0055114
18	0.06	0.282	5.59	0.04	0.46	3bp5B	GO:0005886 GO:0016020 GO:0016021 GO:0032689 GO:0032693 GO:0042102 GO:0042130 GO:0046007 GO:0070062

Consensus prediction of GO terms

Molecular Function	GO:0043169	GO:0003824
GO-Score	0.57	0.40
Biological Processes	GO:0044710
GO-Score	0.57
Cellular Component	GO:0005615
GO-Score	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.