Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3); L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31) (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I
Query= BRENDA::P49419 (539 letters) >FitnessBrowser__Marino:GFF2064 Length = 489 Score = 215 bits (548), Expect = 3e-60 Identities = 143/477 (29%), Positives = 227/477 (47%), Gaps = 15/477 (3%) Query: 47 LREENEGVYNGSW--GGRGEVITTYCPANNEPIARVRQASVADYEETVKKAREAWKIWAD 104 LRE+ NG W G+ PAN E +A V D ++ A AW W Sbjct: 11 LREQ--AYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAAWPAWRS 68 Query: 105 IPAPKRGEIVRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMI 164 PA +R I+R+ + L + L L++ E GK L E GEV ++ ++ Sbjct: 69 TPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFAEEAKRA 128 Query: 165 GGPILPSERSGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTS 224 G ++P ++ PVG+V IT +NFP+A+ A A+ G + K A T Sbjct: 129 YGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVKPAEDTP 188 Query: 225 LISVAVTKIIAKVLEDNKLP-GAICSLTCG---GADIGTAMAKDERVNLLSFTGSTQVGK 280 L ++A+T + E+ +P G I +TC +G+ + + V +SFTGST VGK Sbjct: 189 LSALAITALA----EEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPVGK 244 Query: 281 QVGLMVQERFGRSLLELGGNNAIIAFEDADLSLVVPSALFAAVGTAGQRCTTARRLFIHE 340 + + + LELGGN I F+DADL V + + GQ C A R+++ Sbjct: 245 LLMRQASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYVQA 304 Query: 341 SIHDEVVNRLKKAYAQIRVGNPWDPNVLYGPLHTKQAVSMFLGAVEEAKKEGGTVVYGGK 400 ++D +LK A +++ VG + GPL A++ +E+A +G V GG+ Sbjct: 305 GVYDAFAEKLKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALGGR 364 Query: 401 VMDRPGNYVEPTIVTGLGHDASIAHTETFAPILYVFKFKNEEEVFAWNNEVKQGLSSSIF 460 G + EPTI+T + IA ETF P+ +FKF+ ++E A N+ + GLS+ + Sbjct: 365 AHSLGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAYFY 424 Query: 461 TKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 ++++ R+ W + + G++ VN E+ FGG K +G GRE +YM Sbjct: 425 SRNIHRV--WRVAEELESGMIGVNEGIISTEV-APFGGVKESGLGREGSHYGLDEYM 478 Lambda K H 0.318 0.136 0.417 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: 688 Number of extensions: 28 Number of successful extensions: 3 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: 539 Length of database: 489 Length adjustment: 35 Effective length of query: 504 Effective length of database: 454 Effective search space: 228816 Effective search space used: 228816 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