Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >lcl|NCBI__GCF_000009985.1:WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase Length = 485 Score = 667 bits (1720), Expect = 0.0 Identities = 327/482 (67%), Positives = 387/482 (80%), Gaps = 1/482 (0%) Query: 1 MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60 + L+DS L R A ING W+ A +GE + VTNPA+G + VP MGA ETR AI+AA+RA Sbjct: 2 LDLSDSALLRDHAYINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRA 61 Query: 61 LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120 W+A TAKER+ +LR WF L+M Q+DLA+LMT EQGKPLAEAKGE++Y ASF+EWFA Sbjct: 62 WGPWKAKTAKERSAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFA 121 Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180 EE KR+YGDTIP H +R++V+K+PIGV AAITPWNFP AMITRK PALAAGC +V+K Sbjct: 122 EEAKRVYGDTIPEHMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVK 181 Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVT-GSAGAVGNELTSNPLVRKLSFTGSTEIGR 239 PA TP SALALAELA RAG P GVFNV+T G AVG ELT+NP VRKLSFTGSTE+G+ Sbjct: 182 PAEDTPLSALALAELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGK 241 Query: 240 QLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQD 299 LM QCA +KK+SLELGGNAPF+VFDDADLD AV GA+ASK+RN GQTCVCANRL VQD Sbjct: 242 LLMAQCAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQD 301 Query: 300 GVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGK 359 G+YD F +L +AV+ L +G GL+ GPLI+E+AV KVE HIADA+ KGARVV GGK Sbjct: 302 GIYDAFTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGK 361 Query: 360 AHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFY 419 H RGG FF+PTIL DV + ++EETFGP+APLFRFK E + + ANDTEFGLAAYFY Sbjct: 362 RHARGGTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFY 421 Query: 420 ARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMC 479 +RD+ RV+RV ALEYGIVGIN G+IS EVAPFGG+K SGLGREGSKYGIED+LE+KY+C Sbjct: 422 SRDVGRVWRVSRALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVKYLC 481 Query: 480 IG 481 +G Sbjct: 482 MG 483 Lambda K H 0.318 0.135 0.395 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: 718 Number of extensions: 18 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: 482 Length of database: 485 Length adjustment: 34 Effective length of query: 448 Effective length of database: 451 Effective search space: 202048 Effective search space used: 202048 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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