Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_086509800.1 BZY95_RS10050 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_002151265.1:WP_086509800.1 Length = 485 Score = 646 bits (1667), Expect = 0.0 Identities = 313/479 (65%), Positives = 390/479 (81%), Gaps = 1/479 (0%) Query: 3 LKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALP 62 LK+ +L+ AY+DG+WV AD+G+ I+V NPATGE G+VP++G AET RAI AAD AL Sbjct: 4 LKETQLYCPFAYIDGSWVAADSGEQIEVVNPATGETFGTVPRLGRAETERAIAAADAALV 63 Query: 63 AWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEE 122 WRALTA+ERA+ L +W DLM+E+QDDLA +MT EQGKPL EA GEIAYAASFL WF EE Sbjct: 64 GWRALTAQERADILMKWHDLMMEHQDDLAMIMTHEQGKPLKEAAGEIAYAASFLRWFAEE 123 Query: 123 AKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPA 182 A+RIYG+TIP +P++RI+V KQP+GV AITPWNFP+AMITRKAG ALAAGCT+V+KPA Sbjct: 124 ARRIYGETIPAAKPNQRIVVTKQPVGVVGAITPWNFPAAMITRKAGAALAAGCTIVIKPA 183 Query: 183 SQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLM 242 SQTP+SA ALA LAERAGIP+GVF+VV G A E+ +T +P+VRK+TFTGSTE+GR+LM Sbjct: 184 SQTPFSATALALLAERAGIPRGVFNVVPGRASEIASAMTESPLVRKITFTGSTEVGRELM 243 Query: 243 AECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVY 302 A+ ++ I+K+SLELGGNAPFIVF+DADLDAAVEGA+ +K+RN GQTC+C NR VQ V Sbjct: 244 AQASRHIQKISLELGGNAPFIVFEDADLDAAVEGAMAAKFRNAGQTCICTNRFLVQSSVI 303 Query: 303 DAFVDKLKAAV-AKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361 +AF +KL A+ ++L +G+G E + GPLID KAVAKV EH+ DAV KGA+++ GG PH Sbjct: 304 NAFCEKLAVAMNSELKVGDGTEPDINIGPLIDEKAVAKVSEHVHDAVDKGAELLLGGNPH 363 Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421 LGG FF PT++ + V+ +ETFGPLA VF F+DE + + M+NDT++GLASYFY+R Sbjct: 364 PLGGNFFSPTLISFANADMKVAHEETFGPLAAVFPFEDEEDAVQMANDTQYGLASYFYSR 423 Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480 DL RV+RVA+ LEYGMVGINTGLISN APFGG+KASGLGREG GIE++LE KYLC+ Sbjct: 424 DLGRVWRVADALEYGMVGINTGLISNTAAPFGGVKASGLGREGGHQGIEEFLETKYLCI 482 Lambda K H 0.317 0.135 0.391 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: 676 Number of extensions: 20 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: 483 Length of database: 485 Length adjustment: 34 Effective length of query: 449 Effective length of database: 451 Effective search space: 202499 Effective search space used: 202499 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