Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate HSERO_RS01265 HSERO_RS01265 acetyl-CoA acetyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >FitnessBrowser__HerbieS:HSERO_RS01265 Length = 398 Score = 295 bits (755), Expect = 2e-84 Identities = 182/411 (44%), Positives = 241/411 (58%), Gaps = 28/411 (6%) Query: 1 MNDAYICDAIRTPIGRYG-GALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQ 59 + DAYI A RTPIG+ G K+ R DDL I++ + + PG+D + ++D I GC+ Sbjct: 5 LQDAYIVAATRTPIGKAPRGMFKNTRPDDLLVRAIQSAVAQVPGLDPKLIEDAIVGCSFP 64 Query: 60 AGEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVES 119 G N+AR + LLAGLP G TINR C SG+ A+ AA I+ GEA +MIA G ES Sbjct: 65 EGAQGLNMARNAVLLAGLPNTIGGVTINRYCASGITAIAMAADRIRVGEADVMIAAGAES 124 Query: 120 MTRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRA 179 M+ P +MG S + D +G + M TAE VA+Q+ +SR Sbjct: 125 MSMVP-MMGFHPSININAFK--DENVGMAY------------GMGLTAEKVAQQWKVSRE 169 Query: 180 DQDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIR---------VTLDEHPR-ET 229 QD F+LAS QKA AQ G A E+ EI ++ + V+LDE PR ++ Sbjct: 170 AQDEFSLASHQKAIAAQEAGEFADEMTSFEIVERFPNLATGEIDVKTRTVSLDEGPRADS 229 Query: 230 SLESLARLKGVVRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGV 289 +L +LA+LK V G+VTAGN+S +DGA AL+I S++ +Q+ L AR V A GV Sbjct: 230 NLAALAKLKPVFAAKGSVTAGNSSQTSDGAGALIIVSEKILKQFNLTPLARFVSFAVRGV 289 Query: 290 EPRIMGIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNG 349 P IMGIGP A L+ G+T DQ+D IELNEAFA+Q LAV+ LGL D +VNP G Sbjct: 290 PPEIMGIGPKEAIPAALKAGGLTQDQIDWIELNEAFAAQALAVIGDLGL--DPSKVNPMG 347 Query: 350 GAIALGHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 GAIALGHPLGA+GA T +H L R N ++ + TMC+G G G A + ER+ Sbjct: 348 GAIALGHPLGATGAIRAATTIHALRRKNLKYGMVTMCVGTGMGAAGIFERV 398 Lambda K H 0.319 0.134 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 417 Number of extensions: 22 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory