Align succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate WP_034410955.1 H566_RS0107095 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_11505 (480 letters) >NCBI__GCF_000482785.1:WP_034410955.1 Length = 486 Score = 613 bits (1581), Expect = e-180 Identities = 298/481 (61%), Positives = 373/481 (77%), Gaps = 4/481 (0%) Query: 1 MQLKDTLLFRQQAFIDGAWVDADNGQTINVTNPATGEILGTVPKMGAAETRRAIEAADKA 60 + L D L R+ FIDG W+ T++V +PA G ++ VP++GAAET A+ AA++A Sbjct: 6 LTLSDPSLLREACFIDGEWITG--ADTLDVIDPARGTLVARVPRLGAAETEAAVIAAERA 63 Query: 61 LPAWRALTAKERANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFA 120 LPAWRALTA ER+ L + +L+I+N +DLARL+T EQGKPLAE++GEI Y A ++ WFA Sbjct: 64 LPAWRALTADERSRLLMKLHDLLIDNVEDLARLLTAEQGKPLAESRGEIRYGAGYLRWFA 123 Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180 EEA+RIYG+ IP H DKRLI I+QP+GV AITPWNFP AMI RK PALAAGCTMVLK Sbjct: 124 EEARRIYGETIPAHAADKRLIAIRQPVGVVGAITPWNFPNAMIARKLAPALAAGCTMVLK 183 Query: 181 PASQTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQ 240 PA TP SAFALAELA+RAGIP+GV +V+TG A IG LT +P VRK++FTGST +G+ Sbjct: 184 PAELTPLSAFALAELARRAGIPRGVFNVLTGDAAAIGGVLTKHPAVRKITFTGSTAVGKL 243 Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300 L+A+ A +KKVS+ELGG+APFIVFDDADLD AVEGA+ +KYRN+GQTCVCANR +Q Sbjct: 244 LLAQAADTVKKVSMELGGHAPFIVFDDADLDAAVEGAVAAKYRNSGQTCVCANRFIVQAG 303 Query: 301 VYDAFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGKV 360 ++DAF EKL A LK+G G EGT GPLID +AVAKV+ H+ADA+ +GA ++ GG+ Sbjct: 304 IHDAFVEKLGARAAALKVGPGDAEGTVQGPLIDARAVAKVESHVADAIGQGARVVTGGRR 363 Query: 361 ME--GNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 E NF+ PT+L V + +A+EETFGP+AP+FRF+ EAE +A++N +E GLA YF+ Sbjct: 364 HEAGANFYAPTVLAGVTPAMRIAREETFGPVAPVFRFETEAEALALANASESGLAGYFFT 423 Query: 419 RDLGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 478 RD+GR FRVAEA+E GMVG+NTGLIS EVAPFGG+K SGLGREG + GIEDYLEIKYLC Sbjct: 424 RDIGRAFRVAEAMEVGMVGINTGLISTEVAPFGGVKQSGLGREGGRAGIEDYLEIKYLCF 483 Query: 479 G 479 G Sbjct: 484 G 484 Lambda K H 0.317 0.135 0.389 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: 628 Number of extensions: 12 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: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 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 24 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