From DrugPedia: A Wikipedia for Drug discovery

Revision as of 06:00, 29 January 2010 (edit) Priyanka priyadarshini (Talk | contribs) (→MHC Class-II Binder) ← Previous diff		Current revision (18:14, 29 January 2010) (edit) (undo) Raghavagps (Talk | contribs)
(One intermediate revision not shown.)
Line 101:		Line 101:
	==NetMHC-II Analysis==		==NetMHC-II Analysis==
	Link to [http://www.cbs.dtu.dk/services/NetMHCII/ NetMHC-II]<br>		Link to [http://www.cbs.dtu.dk/services/NetMHCII/ NetMHC-II]<br>
-	Result Predicted by []	+	Result Predicted by [http://crdd.osdd.net/drugpedia/index.php/Image:Priyanka.txt]
		+
		+	[[Category:C2D]]
		+	[[Category:Mtb Immunotation]]

---

Current revision

Immunotation of Rv0667
Name
DNA-directed RNA polymerase subunit beta
Identifiers
Swiss Prot	P0A680
Genbank	NP_215181.1
PDB	?
Chemical data
Formula	[1]
Mol. wt.	129235.1
Pharmacokinetic data
Bioavailability	?
Solubility	?
Isoelectric-Point	4.67

Contents 1 General 1.1 Protein Sequence 2 Human Homologue Blast Result 3 Alergen Protein 4 Bacterial Toxin Prediction 5 Subcellular Location 6 Antigens 6.1 B cell Epitopes 6.1.1 BCEpred Analysis 6.1.2 ABCpred Analysis 6.1.3 IEDB Analysis 7 MHC Class-I Binder 7.1 nHLAPred Analysis 7.2 IEDB Analysis 8 MHC Class-II Binder 8.1 Propred Analysis 8.2 NetMHC-II Analysis

[edit] General

rpoB is a bacterial gene that codes for part of an enzyme which synthesises RNA. Specifically, rpoB is the β subunit of the bacterial RNA polymerase. It is the subunit which possesses the polymerase activity, that is, it catalyzes the synthesis of RNA. Some anti-bacterial drugs (most importantly, rifampicin) kill bacteria by targeting this enzyme.

rpoB is a highly conserved enzyme contained by many bacteria, including Mycobacterium tuberculosis. It is the target of the antibiotic, rifampicin. Mutations in this gene are the main mechanism of resistance to rifampicin.

A probe for rpoB can detect mutations in the gene that confer rifampicin resistance. For Mycobacterium tuberculosis, the resistance-mutations most commonly found are at codons 531, 526 and 516 (in decreasing order of frequency) in an area known as the "rifampicin resistance determining region". For Staphylococcus aureus, the most commonly identified mutation is at codon 481.Gene probes are commonly used to guide tuberculosis treatment when drug-resistant tuberculosis is suspected.

[edit] Protein Sequence

>Rv0667, TB.seq 759805:763320 MW:129220 LADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGL EEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTF IINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSE QIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGE PITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTT QDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPI ETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAG EVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEE SGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPW EGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKV TPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLA GRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEA QPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARST GPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLK ELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA

[edit] Human Homologue Blast Result

subject ids	% identity	% positives	alignment length	evalue
sp|Q9NW08	22	38	1235	3e-43
sp|P30876	29	43	455	1e-37
sp|Q9H9Y6	28	43	393	7e-31
sp|O14656	24	41	104	1.5
sp|O14657	25	40	126	2.6

[edit] Alergen Protein

Link to Algpred
Non Allergen Predicted by AlgPred Server

[edit] Bacterial Toxin Prediction

Link to btxpred
No Hit Fountd by btxpred server.

[edit] Subcellular Location

Link to TBpred
Cyoplasmic

[edit] Antigens

No Hit Found in AntigenDB
No. Hit Found in IEDB

[edit] B cell Epitopes

[edit] BCEpred Analysis

Link to Bcepred
Result Predicited by []

[edit] ABCpred Analysis

Link to ABCpred
Result Predicited by []

[edit] IEDB Analysis

Link to IEDB
Result Predicited by []

[edit] MHC Class-I Binder

[edit] nHLAPred Analysis

Link to nHLApred
Result Predicited by [2]

[edit] IEDB Analysis

Link to IEDB
Result Predicted by [3]

[edit] MHC Class-II Binder

[edit] Propred Analysis

Link to Propred
Result Predicted by [4]

[edit] NetMHC-II Analysis

Link to NetMHC-II
Result Predicted by [5]