Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_017600331.1 D471_RS0120380 acetyl-CoA C-acetyltransferase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000341125.1:WP_017600331.1 Length = 395 Score = 265 bits (677), Expect = 2e-75 Identities = 157/395 (39%), Positives = 230/395 (58%), Gaps = 10/395 (2%) Query: 3 ALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGED 62 ++I RTP GR G+L A DL I++ +ER G+ +V ++ G QAG Sbjct: 4 SVIVGGARTPTGRLLGSLAGFSAADLGGFAIKAALER-AGISGEQVGYVVMGQVLQAGA- 61 Query: 63 NRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRA 122 + +R A + AG+P++VP T+N++C S LDA+ +A + + +GE +++AGG+ESMT A Sbjct: 62 GQIPSRQAAVKAGIPMSVPSVTINKVCLSGLDAIALADQLVTAGEFDVVVAGGMESMTNA 121 Query: 123 PFVMGKAESAFAR-SAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181 P ++ K+ F S + D T + + + +SM + E I RA+QD Sbjct: 122 PHLLPKSRKGFKYGSVEVLDAT-----AHDGLTDAFDNESMGASTERHNAKLGIGRAEQD 176 Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241 AFA RS QR AAA A G FA EI P+ IPQ+KGDP+V TDE RPDTT+ +LAKL+ Sbjct: 177 AFAARSHQRAAAAAAEGRFADEIVPVQIPQRKGDPVVFGTDEGVRPDTTVESLAKLRPAF 236 Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301 DGT+TAG +S ++DGA A+++ S A+ A + + P+ A Sbjct: 237 DGDGTITAGTSSQISDGAAAVVVMSRAKAEELGAPVLAEIGAHGNVAGPDNSLHSQPSNA 296 Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361 ++ L + G + +D+IE+NEAFAA G+ +DLG+ +D VN NGGAIAIGHP+GAS Sbjct: 297 IQHALTKAGRAVEDLDLIEINEAFAAVGIQSTKDLGVSEDI--VNVNGGAIAIGHPIGAS 354 Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALV 396 GAR+ +++L R GG +C G GQG AL+ Sbjct: 355 GARIALHLVHELRRRGGGLGAAALCGGGGQGDALL 389 Lambda K H 0.320 0.135 0.394 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: 449 Number of extensions: 27 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: 401 Length of database: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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 24 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