Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF3753 PS417_19210 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__WCS417:GFF3753 Length = 394 Score = 250 bits (639), Expect = 4e-71 Identities = 165/413 (39%), Positives = 230/413 (55%), Gaps = 33/413 (7%) Query: 1 MRDVFICDAIRTPIGR-FGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQ 59 MR+V I D++RT + + F G R DD+AA + AL+ N + V++ G + Sbjct: 1 MREVVIVDSVRTGLAKSFRGKFNQTRPDDMAAHCVNALLTRN-GIDPATVEDCIVGAGSN 59 Query: 60 AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119 G N+ R +L+ L G+TLNR C+SG+ AI A IASG ++ +AGGVES Sbjct: 60 EGAQGYNIGRNVAVLSQLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVES 119 Query: 120 MSRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMP--ETADNVADDYQVS 177 +S +K +T INPL+K Q P +TA+ VA Y VS Sbjct: 120 ISLT--------------LKSVNTD---NLINPLLKEQVPGLYFPMGQTAEIVARRYSVS 162 Query: 178 RADQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHK-----KGET-----IVERDEHLRP 227 R +QD +AL+SQQ+ A AQA G F +EIVP+ + +K GE +V+RD+ RP Sbjct: 163 REEQDMYALQSQQRTAQAQADGLFDDEIVPMAVKYKVEDKNTGEAQVLDGVVDRDDCNRP 222 Query: 228 ETTLEALTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASG 287 +TTL +L LKPV D +VTAGN+S ++DGA+ ++ S E GL P+A G Sbjct: 223 DTTLASLQGLKPVFAEDGSVTAGNSSQLSDGASMTLVMSLEKALALGLKPKAFFRGFTVA 282 Query: 288 GVAPRVMGIGPVPAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNP 347 G P MGIGPV +V KL + G+ V+D D+ ELNEAFASQ L L + D + N Sbjct: 283 GCEPDEMGIGPVFSVPKLLKAKGLQVADIDLWELNEAFASQCLYARNRLEI--DNAKYNV 340 Query: 348 NGGAIALGHPLGMSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 NGG+I++GHP GM+G+R V + +L++ R G+ TMCVG G G E V Sbjct: 341 NGGSISIGHPFGMTGSRQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFEAV 393 Lambda K H 0.318 0.134 0.383 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: 378 Number of extensions: 18 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: 400 Length of database: 394 Length adjustment: 31 Effective length of query: 369 Effective length of database: 363 Effective search space: 133947 Effective search space used: 133947 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 (21.7 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