TB Genome Annotation Portal

Rv1661 (pks7)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: polyketide synthase 7
  • REFSEQ: polyketide synthase pks7
  • PATRIC: Probable polyketide synthase pks7
  • TUBERCULIST: Probable polyketide synthase Pks7
  • NCBI: Probable polyketide synthase Pks7
  • updated information (H37Rv4):
    • gene name: pks7
    • function:
    • reference:
• Coordinates in H37Rv: 1875304 - 1881684
• Gene length: 6381 bp (with stop codon), 2126 aa (without stop codon)
• Operon:


• Trans-membrane region:
  
• Role: I.I - Polyketide and non-ribosomal peptide synthesis
• GO terms:
  • GO:0071770 - DIM/DIP cell wall layer assembly (Uniprot)
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0031177 - phosphopantetheine binding (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • 2 SMMALONYLCOA[c] + 3 MALCOA[c] + PHPAA_COA[c] -> 5 CO2[c] + 5 COA[c] + PHENOLPHTHIODIOLONE[A][c]
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  2HG4	56%	Saccharopolyspora erythraea	Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS.
  6C9U	55%	Saccharopolyspora erythraea	Crystal structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase in complex with antibody fragment (Fab)
  2QO3	55%	Saccharopolyspora erythraea	Crystal Structure of [KS3][AT3] didomain from module 3 of 6-deoxyerthronolide B synthase
  6H0J	54%	Mycobacterium ulcerans (strain Agy99)	A1-type ACP domain from module 5 of MLSA1
  6OBV	52%	Actinomadura vulgaris	Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases
  5HVC	52%	Mycobacterium ulcerans	Solution structure of the apo state of the acyl carrier protein from the MLSA2 subunit of the mycolactone polyketide synthase
  5HV8	52%	Mycobacterium ulcerans	Solution structure of an octanoyl- loaded acyl carrier protein domain from module MLSA2 of the mycolactone polyketide synthase.
  6H0Q	50%	Mycobacterium ulcerans (strain Agy99)	B1-type ACP domain from module 7 of MLSB
  6IYR	49%	Streptomyces albus subsp. albus	Crystal Structure of the acyltransferase domain from module 8 of the salinomycin polyketide synthase
  3SLK	49%	Saccharopolyspora spinosa	Structure of ketoreductase and enoylreductase didomain from modular polyketide synthase

• Links to additional information on pks7:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.572 (from Jeremy Rock's lab)
  • Photo of spot titer

Amino Acid Sequence

MNSTPEDLVKALRRSLKQNERLKRENRDLLARTTEPVAVVGMGCRYPGGVDSPETLWELVAHGRDAVSEFPADRGWDVAGLFDPDPDAVGKSYTRCGGFL
TDVAGFDAEFFGIAPSEALAMDPQQRLLLEVSWEALERAGIDPITLRGSQTGVFAGVFHGSYGGQGRVPGDLERYGLRGSTLSVASGRVAYVLGLQGPAV
SVDTACSSSLVALHLAVQSLRLGECDLALVGGVTVMATPAMFIEFSRQRALSADGRCKAYAGAADGTAFAEGAGVLVLARLADARRLGHPVLALVRGSAV
NQDGASNGLATPNGPAQQRVITAALASARLGVADVDVVEGHGTGTTLGDPIEAQAILATYGQRPADRPLWLGSIKSNIGHTSAAAGVAGVIKMVQAMRHG
VLPKTLHVDVPTPHVDWSAGAVSLLTEPRPWHVPGRPRRAGVSSFGISGTNAHVILEEAPAVEPVGAAHGNDPVAVPWVLSARSAQALTNQARRLLAWVG
ADENVRPLDVGWSLVNTRSLFDHRAVVVGADRTQLMEGLTGLAAGVPGADVVAGRAQTVGKTAFVFPGQGAQWLGMGAQLCATAPVFAEHIHRCERALRE
HVEWSLLDVLRGAPGAPGLDRVDVVQPALWAVMVSLAELWRSVGVVPDAVIGHSQGEIAAAYVAGALSLRDAAAVVALRSRLLVRLGGAGGMVSLACGQP
QAEKLASQWGDRLNIAAVNGVSSVVLAGETDAVTELMQRCEAEGIRARRIDVDYASHSAQVDAIREELIAALRGIEPRTSTVAFFSTVTGELMDTAGVNA
EYWYRSIRQPVQFERAVRNAFDGGYRVFVESSPHPVLIAGIEETLVDCDRGATGEPIVIPTLGRDDGGVGRFWLSAGQAHVAGVGVDWRAAFADLGGRRV
ELPTYAFARQRFWLDGLGAVGGDLGGVGLVGAEHGLLAAVVQRPDSGGVVLTGRISVVAAPWLADHAVGPVVLFPGTGFVELALRAGDEVGCSVLQELTL
QAPLVLPADGVRVQVVVGGVEQSGTRNVWVYSAAGQADSSPGWTLHAQGVLGVGSVQPAAELSVWPPVGARAMDVADGYQVLAARGYGYGPAFRGLQALW
RRGAEVFADVTLPEGVPIRGFGIHPAVLDAALHAWGIVEGEQQTMLPFSWQGVCLHASGAARVRVRLAPVGRGAVSVELADPQGLPVLSVRQLMVRPVSA
AALSRSTAGDRGLLEMIWTPVPLEGGDIGDDAVVWELPPHAGAQAGGDVLAAVYRGVHEVLEVLQSWLASDATGLGVVVTRGAVGPVDDDVTDLAGAAVW
GLVRSAQAEHPGRVVLVDTDGSVAVEDAVGFGARSGEPQLVVRRGRVYAARLAPVAAGLTLPSASAGGWRLVAGGGGTLADVVVAPVAPVELATGQVRVA
VGAVGVNFRDVLVALGMYPGGGELGVDGAGVVVEVGPGVTGLAVGDRVMGLLGLVGSEAVVDARLVTMVPAGWSLVEAAAVPVAFLTAFYGLSVLAEVAA
GQKVLVHAGTGGVGMAAVSLARYWGAEVFVTASRAKWDTLRAMGFDDIHISDSRSLEFEEAFLRATEGSGVDVVLNSLAGEFTDASLRLLPSGGRFIELG
KTDIRDGQTVAERHRGVRYRAFDLVEAGPDRIAAMLSEVVGLLAAGVLARLPVKTFDARCAPAAYRFVSQARHIGKVVLTIPDGPGGQSGLAGGTVVVTG
GTGMAGSAVATHLVRRHGVANLVLVSRSGEQADRAAEVAALLREGGAQVAVVSCDVADRDALAALLAGLDPRYPLKGVFHAAGVLDDAVITGLTPDRVDT
VLRAKVDGAWNLHELTEDMDLSAFVVFSSMAGIVGTPAQGNYAAANAFLDGLVAYRRSRGLAGLSVAWGLWEQASAMTRHLGERDRARMTQAGLAPLTTE
QALGFLDTALQADRAVVVAARLDRAALAGAGAALPALFSQLAAGPTRRRIDAADTAVSMSGLVSRLHALTPERRQRELTDLVISNAAAVLGRSSSVDINA
HKAFQDLGFDSLTAVELRNRLKTATGLTLSPTLIFDYPTPATLAEHLDSRLVTASGSDQQSLSDRVDDITRELVVLLDQPDLSANVKAHLRTRLQTMLTS
LTTEDDDIAAATESQLFAILDEELGS

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• data from Culviner et al (2025) (55,259 Mtb clinical isolates)
  • overall pN/pS for Rv1661: 0.905027791
  • lineage-specific pN/pS in L1: 0.91605703
  • lineage-specific pN/pS in L2: 0.938906525
  • lineage-specific pN/pS in L3: 0.825081848
  • lineage-specific pN/pS in L4: 0.918965147

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	YES
omega peak height (95%CI lower bound)	2.37 (0.88)	1.74 (1.03)
codons under selection		414, 415, 416, 417, 418, 419, 420, 421, 422
omega plots
genetic variants*	link	link
statistics at each codon	link	link