Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_086510804.1 BZY95_RS15485 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_002151265.1:WP_086510804.1 Length = 481 Score = 613 bits (1580), Expect = e-180 Identities = 292/479 (60%), Positives = 380/479 (79%), Gaps = 3/479 (0%) Query: 6 AKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWR 65 A +F +A++ G W DA+ + V NPA GE + SVP + A + R A+ AA+ A PAWR Sbjct: 5 ADIFSDKAFIGGQWRDAE--RRFDVTNPANGETLASVPDLSADDARDAVAAAEAAWPAWR 62 Query: 66 ALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKR 125 TAK+RA LR WFD ++ +Q+ LAR+MT+EQGKPLAE++GE+AY ASF+E++ E+AKR Sbjct: 63 RQTAKQRAALLRAWFDAIMAHQESLARMMTLEQGKPLAESRGEVAYGASFVEFYAEQAKR 122 Query: 126 IYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQT 185 + G+T+P H DKRI+V ++P+GV AAITPWNFP AMITRK PALAAGC +V+KPA T Sbjct: 123 MAGETLPSHGADKRILVFREPVGVVAAITPWNFPLAMITRKCAPALAAGCPVVIKPAEAT 182 Query: 186 PYSALALAELAERAGIPKGVFSVVTGSA-GEVGGELTSNPIVRKLTFTGSTEIGRQLMAE 244 P +ALALA LAE+ G P GV +VVT S E+G LTS+P VRK++FTGST +G++L+A+ Sbjct: 183 PLTALALARLAEQVGFPAGVLNVVTASRPAEIGEVLTSDPRVRKVSFTGSTAVGKRLLAQ 242 Query: 245 CAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDA 304 CA +KK S+ELGGNAPFIVFDDADLDAAVEGA+ SKYRN+GQTCVC NRL VQ GVY+A Sbjct: 243 CAGTVKKASMELGGNAPFIVFDDADLDAAVEGAVASKYRNSGQTCVCTNRLLVQSGVYEA 302 Query: 305 FVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALG 364 FV+KL A VA+L +GNGL+ GV GPLI+ AV KV+ HIADA++KGA++V GG+PHALG Sbjct: 303 FVEKLAARVAQLKVGNGLDEGVVQGPLINQAAVDKVQSHIADALAKGARLVCGGEPHALG 362 Query: 365 GTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLA 424 GTFF+PT++ DV V+++ETFGPLAPVFRF + + IAM+N TEFGLA+YFYARD Sbjct: 363 GTFFQPTVVADVTDEMRVAREETFGPLAPVFRFDSDEQAIAMANATEFGLAAYFYARDYR 422 Query: 425 RVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483 R++ V E LEYGMV +N G++S E+APFGG+K SGLGREGS +G++++ E+KY+C+GG+ Sbjct: 423 RIWHVMEGLEYGMVAVNEGILSTELAPFGGVKESGLGREGSHHGLDEFTELKYVCVGGL 481 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: 681 Number of extensions: 15 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: 483 Length of database: 481 Length adjustment: 34 Effective length of query: 449 Effective length of database: 447 Effective search space: 200703 Effective search space used: 200703 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