Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= BRENDA::P25526 (482 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 578 bits (1491), Expect = e-169 Identities = 292/477 (61%), Positives = 360/477 (75%), Gaps = 5/477 (1%) Query: 7 NLFRQQALINGEWLDANNGEA-IDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWR 65 NL ALI+G+W+ GEA DV NPA+G + +V +GA ET AIDAA+RALPAW Sbjct: 8 NLVETAALIDGQWV---RGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWA 64 Query: 66 ALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKR 125 A TAKER ILR W +L++ H DDLARLMT EQGKPLAEAKGE+ Y ASFI+WFAEE KR Sbjct: 65 ARTAKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKR 124 Query: 126 IYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185 YG TIP KRL IKQP+GV AAI PWNFP AMITRK GPALAAGCT+V+KPA++T Sbjct: 125 AYGHTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAET 184 Query: 186 PFSALALAELAIRAGVPAGVFNVVTGSAGA-VGNELTSNPLVRKLSFTGSTEIGRQLMEQ 244 P SALA+A LA AGVPAGV N+VT + + VG L + VRKLSFTGST IG+ L +Q Sbjct: 185 PLSALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQ 244 Query: 245 CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDR 304 CA +KK+SLELGGNAPFIVFDDADL+ AV+GA+ASK+RNAGQTCVCANRL VQ G++D Sbjct: 245 CAGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDA 304 Query: 305 FAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERG 364 FA +L + V+ L +G G GV IGPLI+EKA+ KV ++ A++ GA V+ GG H G Sbjct: 305 FAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLG 364 Query: 365 GNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLS 424 G+F+QPT+LV ++ +EE FGP+AP+ +F+ EA+ + AN T FGLAAYFY+RD+ Sbjct: 365 GHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVG 424 Query: 425 RVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481 R +RV E +E G+VGIN G+IS EVAPFGG+K SGLGREG+ G+++YLE KY+C G Sbjct: 425 RCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLCFG 481 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: 664 Number of extensions: 19 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