Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate BPHYT_RS13360 BPHYT_RS13360 aldehyde dehydrogenase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__BFirm:BPHYT_RS13360 Length = 531 Score = 960 bits (2482), Expect = 0.0 Identities = 491/529 (92%), Positives = 506/529 (95%) Query: 1 MTELLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRAL 60 MTELLKNHVAGQWIAG+G G+TLTDPVTGVALVRVSSEGLDLA AF FAR+ GGAALRAL Sbjct: 1 MTELLKNHVAGQWIAGSGTGVTLTDPVTGVALVRVSSEGLDLAHAFGFARDTGGAALRAL 60 Query: 61 TYAQRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120 TYAQRAARLADIVKLLQAKR DYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG Sbjct: 61 TYAQRAARLADIVKLLQAKRDDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120 Query: 121 EVHALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180 +VHALRDG + SLSKD+SFS QHVL+PTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI Sbjct: 121 DVHALRDGESVSLSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180 Query: 181 VKPATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAAT 240 VKPATATAWLTQRMVADVVDAGILPPGALS+ICGSSAGLLDQI+SFDVVSFTGSA TAAT Sbjct: 181 VKPATATAWLTQRMVADVVDAGILPPGALSVICGSSAGLLDQIQSFDVVSFTGSAQTAAT 240 Query: 241 LRAHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300 LRAHPAFVQRGARLNVEADSLNSAILCADA P TPAFDLFIKEVVREMTVKSGQKCTAIR Sbjct: 241 LRAHPAFVQRGARLNVEADSLNSAILCADAAPGTPAFDLFIKEVVREMTVKSGQKCTAIR 300 Query: 301 RAFVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVL 360 RAFVPE ALE VLEAL AKLAKITVG+PRND VRMGSLVSREQYENVLAGIAALREEAVL Sbjct: 301 RAFVPEGALEAVLEALNAKLAKITVGDPRNDTVRMGSLVSREQYENVLAGIAALREEAVL 360 Query: 361 AYDSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420 A+D SAVPLIDAD+NIAAC+APHLFVVNDPDNATLLHDVEVFGPVASVAPYRV TD L Sbjct: 361 AFDGSAVPLIDADSNIAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVATDAATL 420 Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480 PEAHAVALARRGQGSLVASIYSND+AHLGRLALELADSHGRVHAISPSVQ SQTGHGNVM Sbjct: 421 PEAHAVALARRGQGSLVASIYSNDEAHLGRLALELADSHGRVHAISPSVQQSQTGHGNVM 480 Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQATHWP 529 PMSLHGGPGRAGGGEELGGLRAL FYHRRSAIQAASAAIG+LTQATH P Sbjct: 481 PMSLHGGPGRAGGGEELGGLRALGFYHRRSAIQAASAAIGSLTQATHLP 529 Lambda K H 0.318 0.132 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: 963 Number of extensions: 17 Number of successful extensions: 1 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: 531 Length of database: 531 Length adjustment: 35 Effective length of query: 496 Effective length of database: 496 Effective search space: 246016 Effective search space used: 246016 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: 52 (24.6 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