Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_002877493.1 B506_RS01555 thiolase family protein
Query= SwissProt::Q8VPF1 (401 letters) >NCBI__GCF_000387565.1:WP_002877493.1 Length = 366 Score = 250 bits (638), Expect = 5e-71 Identities = 163/402 (40%), Positives = 223/402 (55%), Gaps = 42/402 (10%) Query: 3 REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62 +++YI A RTP GR+ LA A DL + ++ + + +D LD +++G AG Sbjct: 2 QDIYIVAAKRTPFGRYHKQLADFSAIDLGQIALRGAL-KEAGLDAKALDALFMGNVLSAG 60 Query: 63 EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122 +N+AR L AG+ V++N +C S + A A + G+ LV GG ESM+ Sbjct: 61 L-GQNIARQIALNAGMRQDSVAVSINEVCGSSLKAARLAEAQMLIGDLGLVAVGGSESMT 119 Query: 123 RAP----YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVS 178 AP + G DS G+ I TA+NVA +S Sbjct: 120 NAPKEIMFSDGLVDSFSGKSMGI-------------------------TAENVAKRNHIS 154 Query: 179 RADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKL 238 R D DAF+L S Q A +AQA G FA+EI+ + + DE++RPDT+LEALA L Sbjct: 155 RQDADAFSLSSHQKAVKAQAEGLFADEIIQI--------EDLKQDENVRPDTSLEALAGL 206 Query: 239 KPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIG 298 K D TVTAGNAS ++DG+ +ILA+AE V ++ L AK+ A G P MG G Sbjct: 207 KTSFLEDGTVTAGNASPISDGASMIILATAEKVAEYQLTPLAKLGAYAEVGYDPEFMGYG 266 Query: 299 PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHP 358 P A+RKLL+ VAD+D E+NEAFAA LAV R+L I A+VN GGAIALGHP Sbjct: 267 PYYAIRKLLDETGRQVADYDFFEINEAFAATTLAVARDLEI--PLAKVNKQGGAIALGHP 324 Query: 359 LGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400 LGASG RL+ TA QL++ GGQR + ++C+G G +A +E+ Sbjct: 325 LGASGTRLLATAARQLQR-GGQRAIASLCIGGGLAIAFEIEK 365 Lambda K H 0.317 0.134 0.379 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: 365 Number of extensions: 19 Number of successful extensions: 6 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: 366 Length adjustment: 30 Effective length of query: 371 Effective length of database: 336 Effective search space: 124656 Effective search space used: 124656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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