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) >NCBI__GCF_000009985.1:WP_011383730.1 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:
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