Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate SM_b21635 SM_b21635 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Smeli:SM_b21635 Length = 688 Score = 460 bits (1183), Expect = e-134 Identities = 242/521 (46%), Positives = 335/521 (64%), Gaps = 11/521 (2%) Query: 5 LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64 L++++AG W+ G+ G+TL D TG + V S G+D A A ++ RE GG ALR +++ + Sbjct: 11 LESYIAGAWMRGSKDGVTLCDAATGAPVALVDSSGIDFAAALAYGREKGGPALRRMSFHE 70 Query: 65 RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123 RA L + + L ++ ++YA++TA +G TR DS +DI+GGI TL YA G L H Sbjct: 71 RAMMLKALAQALMERKEEFYALSTA-TGATRADSWIDIEGGIGTLFSYASKGRRELPNSH 129 Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 L DG E+LS+D +FSAQH+L+P +G+A+ INAFNFP WG+ EK AP LL+G+P IVKP Sbjct: 130 VLLDGDVEALSRDGTFSAQHILTPLQGIAVHINAFNFPCWGMLEKLAPTLLAGMPAIVKP 189 Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243 A+ TA+L + +V +VD G+LP GAL ++CGS LLD++ DVV+FTGSA T L+ Sbjct: 190 ASQTAYLAELVVRRIVDTGLLPEGALQLVCGSPGDLLDRVGDQDVVTFTGSATTGRKLKT 249 Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 HPA V R +EADSLN+A+L DA P F LF++EV REMT K+GQKCTAIRR Sbjct: 250 HPAIVGNSVRFTMEADSLNAAVLGLDAAPGAEEFGLFVREVAREMTSKAGQKCTAIRRVI 309 Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEA-VLAY 362 P A + ++ AL +LAK+ +G+P ++ VRMG L SR+Q E V A I L +A ++A Sbjct: 310 APRAHCDALITALGERLAKVPLGDPADENVRMGPLASRDQREEVRARILDLTTDAEIVAG 369 Query: 363 DSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALPE 422 D + L+ DA A + P L + PD A +HDVE FGPV++V PY + Sbjct: 370 DPARPQLVSGDAEAGAFLNPVLLYCDSPDAARSVHDVEAFGPVSTVMPYDTAEE------ 423 Query: 423 AHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMPM 482 AV L RRG+GSLV S+++ND L + +A HGRV + S TGHG+ +P Sbjct: 424 --AVDLVRRGRGSLVTSVFTNDPDIARELVIGMAPFHGRVMIGNRLSAKSSTGHGSPLPG 481 Query: 483 SLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLT 523 +HGGPGRAGGGEELGG+R + Y +R+A+Q A + +T Sbjct: 482 LVHGGPGRAGGGEELGGMRGVRHYMQRTAVQGAPGLVAAVT 522 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: 784 Number of extensions: 27 Number of successful extensions: 5 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: 688 Length adjustment: 37 Effective length of query: 494 Effective length of database: 651 Effective search space: 321594 Effective search space used: 321594 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