Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_086509800.1 BZY95_RS10050 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15736 (480 letters) >NCBI__GCF_002151265.1:WP_086509800.1 Length = 485 Score = 637 bits (1642), Expect = 0.0 Identities = 312/481 (64%), Positives = 387/481 (80%), Gaps = 3/481 (0%) Query: 3 LKDAQLFRQQAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP 62 LK+ QL+ A+IDG+WV AD+G+ I+V NPATGE GTVP++G AET RAI AAD AL Sbjct: 4 LKETQLYCPFAYIDGSWVAADSGEQIEVVNPATGETFGTVPRLGRAETERAIAAADAALV 63 Query: 63 AWRALTAKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEE 122 WRALTA+ERA L +W++L++E+QDDL +MT EQGKPL EA GEIAYAASF+ WFAEE Sbjct: 64 GWRALTAQERADILMKWHDLMMEHQDDLAMIMTHEQGKPLKEAAGEIAYAASFLRWFAEE 123 Query: 123 AKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPA 182 A+RIYG+ IP +P++R++V KQP+GV AITPWNFPAAMITRKAG ALAAGCT+VIKPA Sbjct: 124 ARRIYGETIPAAKPNQRIVVTKQPVGVVGAITPWNFPAAMITRKAGAALAAGCTIVIKPA 183 Query: 183 SQTPFSALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLM 242 SQTPFSA AL LA RAGIP+GV +VV G A +I +T +P+VRK++FTGSTE+GR+LM Sbjct: 184 SQTPFSATALALLAERAGIPRGVFNVVPGRASEIASAMTESPLVRKITFTGSTEVGRELM 243 Query: 243 AECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVY 302 A+ ++ I+K+SLELGGNAPFIVF+DADLD AVEGA+ +K+RN GQTC+C NR +Q SV Sbjct: 244 AQASRHIQKISLELGGNAPFIVFEDADLDAAVEGAMAAKFRNAGQTCICTNRFLVQSSVI 303 Query: 303 DAFAEKLKAAV-AKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGK-- 359 +AF EKL A+ ++LK+G+G E GPLIDEKAVAKV EH+ DA+ KGA LL GG Sbjct: 304 NAFCEKLAVAMNSELKVGDGTEPDINIGPLIDEKAVAKVSEHVHDAVDKGAELLLGGNPH 363 Query: 360 SMEGNFFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419 + GNFF PT++ D VA EETFGPLA +F F+DE + + M+NDT++GLASYFY+R Sbjct: 364 PLGGNFFSPTLISFANADMKVAHEETFGPLAAVFPFEDEEDAVQMANDTQYGLASYFYSR 423 Query: 420 DLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 479 DLGRV+RVA+ALEYGMVG+NTGLISN APFGG+KASGLGREG GIE++LE KYLC+ Sbjct: 424 DLGRVWRVADALEYGMVGINTGLISNTAAPFGGVKASGLGREGGHQGIEEFLETKYLCID 483 Query: 480 I 480 + Sbjct: 484 L 484 Lambda K H 0.317 0.135 0.390 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: 692 Number of extensions: 22 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: 480 Length of database: 485 Length adjustment: 34 Effective length of query: 446 Effective length of database: 451 Effective search space: 201146 Effective search space used: 201146 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 Apr 09 2024. 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