Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate Ac3H11_3089 Benzaldehyde dehydrogenase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3089 Length = 520 Score = 648 bits (1671), Expect = 0.0 Identities = 333/522 (63%), Positives = 391/522 (74%), Gaps = 8/522 (1%) Query: 1 MTELLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRAL 60 MTELL N AG+W GTG G L DPV G ALVRV + GLDLA AF+FAR+ GGAALRA Sbjct: 1 MTELLPNFAAGRWQHGTGPGTALWDPVLGTALVRVDAAGLDLAEAFAFARDMGGAALRAA 60 Query: 61 TYAQRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGASLG 120 TY +RAA LA +VK+LQ R YY IATAN+GT +NDSAVDIDG IFTL YA+ G +LG Sbjct: 61 TYRERAAMLAAVVKVLQTHRDSYYDIATANAGTVKNDSAVDIDGAIFTLGQYARWGDALG 120 Query: 121 EVHALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVI 180 +V ALRDG A L K+ F +QH+ P +GVALFINAFNFP+WGLWEKAAPALLSG+PVI Sbjct: 121 DVRALRDGGAVKLGKEPVFLSQHLQVPRQGVALFINAFNFPAWGLWEKAAPALLSGMPVI 180 Query: 181 VKPATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAAT 240 VKPATATAWLTQRMV DVVDAG+LP GALS+I GSSAGL+DQ++ FDVVSFTGSA+TA Sbjct: 181 VKPATATAWLTQRMVQDVVDAGVLPVGALSVIAGSSAGLMDQLQPFDVVSFTGSAETAGV 240 Query: 241 LRAHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300 +RAH A QR R N+EADSLNSA+L P + AF+L ++EVVREMTVKSGQKCTAIR Sbjct: 241 IRAHAAVAQRSVRANIEADSLNSALLLPGEAPGSEAFNLLVREVVREMTVKSGQKCTAIR 300 Query: 301 RAFVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVL 360 R VP + EA+ AKLA ITVGNPRND VRMGSLVSR Q +V G+ L+ A + Sbjct: 301 RILVPADVYDAAAEAIGAKLAGITVGNPRNDGVRMGSLVSRAQLASVREGLVTLQAHATV 360 Query: 361 AYDSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420 +D PL+DAD +AAC+ P L D D A +HDVEVFGPVA++ PYR Sbjct: 361 LHDGRHQPLVDADPAVAACMGPVLLGARDADAAQPVHDVEVFGPVATLLPYR-------- 412 Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480 AHA+ALA+RGQGSLV S+Y +D+A L AL +A SHGRVH ++P V + +GHGNVM Sbjct: 413 DSAHAIALAQRGQGSLVTSLYGSDEAALAHTALAVAASHGRVHVVTPDVAQTHSGHGNVM 472 Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTL 522 PMS HGGPGRAGGG ELGGLRAL FYH+RSA+QA+ A + L Sbjct: 473 PMSQHGGPGRAGGGAELGGLRALDFYHQRSAVQASPAVLAAL 514 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: 789 Number of extensions: 30 Number of successful extensions: 2 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: 520 Length adjustment: 35 Effective length of query: 496 Effective length of database: 485 Effective search space: 240560 Effective search space used: 240560 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