Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate GFF2758 HP15_2702 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Marino:GFF2758 Length = 685 Score = 408 bits (1049), Expect = e-118 Identities = 224/523 (42%), Positives = 313/523 (59%), Gaps = 12/523 (2%) Query: 4 LLKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYA 63 +LK+ +AGQW+ G L V G + + LD A + R+ GG L A+ + Sbjct: 7 VLKSFIAGQWV-GEKPAKALPSAVNGEIVAHTHDDTLDFKNAVEYGRKVGGKNLMAMDFQ 65 Query: 64 QRAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEV 122 +RA L + LQ + + YA++ ++G+T+ D+ +DIDGG TL YA +G L Sbjct: 66 ERALALKAMALYLQEHKKELYALSM-HTGSTKGDNGIDIDGGFGTLFSYASMGRRELPSG 124 Query: 123 HALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVK 182 + + +G L K+ F+ H+L P GVA+ I+A+NFP WG+ EK AP L+G+P IVK Sbjct: 125 NVVHEGPVTPLGKNNHFAGTHILVPRGGVAVHIDAYNFPVWGMLEKFAPTFLAGMPSIVK 184 Query: 183 PATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLR 242 PAT+T ++T+ V + ++G LP G+L +I GS+ L D + DVV+FTGSA TA LR Sbjct: 185 PATSTCYVTELAVRLMQESGALPEGSLQLIIGSTGDLFDHLEEQDVVTFTGSAATARKLR 244 Query: 243 AHPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRA 302 HP + R N EADSLNSAIL D TP+ FD+F+KE+ REMT K+GQKCTAIRR Sbjct: 245 NHPNIINRSIPFNAEADSLNSAILAPDVTPEHEEFDVFVKEIRREMTAKAGQKCTAIRRI 304 Query: 303 FVPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAY 362 FVP+ + V + LK +L+KITVG+P + VRMG+L S +Q E+V A I L + + L Sbjct: 305 FVPKDQVNAVCDKLKEQLSKITVGDPSVEGVRMGALASIDQLEDVKANIQELLKTSELVV 364 Query: 363 DSSAVPLIDAD-ANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALP 421 D A + PHL + +P+N HD+E FGPVA+V PY D Sbjct: 365 GGEGNFKATGDGTEKGAFIEPHLLLCRNPENGCGAHDIEAFGPVATVIPYETIDD----- 419 Query: 422 EAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMP 481 AV L RG+GSLV ++ + D A GR+A LA HGR+H + TGHG+ +P Sbjct: 420 ---AVELCSRGRGSLVTTLTTRDPAIAGRIAPLLAAFHGRLHLLDAEAAKESTGHGSPLP 476 Query: 482 MSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQ 524 M HGGPGRAGGGEELGG+RA+ Y +R+AIQ + + + +T+ Sbjct: 477 MLKHGGPGRAGGGEELGGIRAVHHYLQRTAIQGSPSMLAAVTR 519 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: 750 Number of extensions: 39 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: 531 Length of database: 685 Length adjustment: 37 Effective length of query: 494 Effective length of database: 648 Effective search space: 320112 Effective search space used: 320112 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: 53 (25.0 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