Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_058859372.1 AS188_RS14085 thiolase family protein
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_001482365.1:WP_058859372.1 Length = 397 Score = 342 bits (877), Expect = 1e-98 Identities = 199/401 (49%), Positives = 259/401 (64%), Gaps = 14/401 (3%) Query: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 +A I DA+RTPFGR+GGAL VR DDLAA + + R PG+D + +++++ G AN AGE Sbjct: 3 QAYIYDAVRTPFGRFGGALAGVRPDDLAAHVLGEQVGRAPGLDPAAIDEVVLGNANGAGE 62 Query: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 +NRNVARMA LLAGLP+ +PG+TVNRLCGSSLDA +A+R I +GE +++ GGVESM+R Sbjct: 63 ENRNVARMATLLAGLPVELPGTTVNRLCGSSLDAAIIASRQIGAGEADVVLVGGVESMSR 122 Query: 122 APFVMGKAESAF-ARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 AP+V+ K E + A + TT+GWR VN M+ ++ + S+ E E +A I R Sbjct: 123 APWVLPKTEKPYPAGDMTLASTTLGWRLVNKRMRPEWTV-SLGEATEQLAERHGITRDRM 181 Query: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 D FA RS Q A GF+ A LT+ Q G L T DE R +T+ LA LK V Sbjct: 182 DEFAYRSHQLTQQAWDEGFY----ADLTV-QVPGTEL--TRDESVRASSTVEKLAGLKTV 234 Query: 241 VRPD---GTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFG 297 RP+ GTVTAGNAS +NDGA A LL S KAA+L L+P AR+ G A P+ GF Sbjct: 235 FRPEEQGGTVTAGNASPLNDGASAALLGSEKAAELTGLQPLARIAGRGAAANEPQFFGFA 294 Query: 298 PAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHP 357 P A L + G+T + +ELNEAFAAQ LA + G+ D A VN +GGAIAIGHP Sbjct: 295 PVEAANSALRRAGITWDDVAAVELNEAFAAQSLACVDAWGI--DPAIVNRHGGAIAIGHP 352 Query: 358 LGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIE 398 LGASG R++ T L+ SG R+ + +CIGVGQG+A+V+E Sbjct: 353 LGASGTRILGTLARSLQASGQRWGVAAICIGVGQGLAVVLE 393 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: 436 Number of extensions: 15 Number of successful extensions: 4 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: 397 Length adjustment: 31 Effective length of query: 370 Effective length of database: 366 Effective search space: 135420 Effective search space used: 135420 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