Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_019895364.1 A377_RS0106205 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000384235.1:WP_019895364.1 Length = 457 Score = 248 bits (634), Expect = 2e-70 Identities = 151/450 (33%), Positives = 239/450 (53%), Gaps = 3/450 (0%) Query: 28 NPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASEIS 87 NP T + P + A++ +++A W ERA+ L +++ + E ++ Sbjct: 6 NPTTGQAMEGYPAMSGSEIDAAVELSQQAFQGWRKTGFAERATLLHQVADLMNEDEERLA 65 Query: 88 ALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRALGVTT 147 L+ E GK + A EV + A+ A Y + + + + LG Sbjct: 66 RLMTVEMGKPIKEARGEVQKAIWCARHYADHAEGYLAPVTLASDASHSYVQHL-PLGPLL 124 Query: 148 GILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNLVLG 207 GILPWN PF+L R APAL+ GNT ++K P A A A++ +++G P G+F + Sbjct: 125 GILPWNAPFWLAFRFGAPALMAGNTCLMKHDSHVPACAEAIAELFEKVGAPEGLFQNMRV 184 Query: 208 RGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDDADLE 267 E V + + +P V VS+TGS SAG ++ + AA++I LELGG P++V+ DAD+ Sbjct: 185 HNEQVAR-IIEHPAVQAVSLTGSSSAGSQVASLAARHIKPAVLELGGSDPSLVLADADVN 243 Query: 268 LAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIAMGP 327 A + + SR+IN+GQ C A+R+ V+ +YDQFV L + A++ G+P E + +GP Sbjct: 244 KAAEVLALSRIINAGQSCIAAKRLIVEAPVYDQFVEHLTNQLAALKLGDPCEES-TQVGP 302 Query: 328 LINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEETFGP 387 + E + ++V V +GAR GG+ G G++YP T+L DV M EETFGP Sbjct: 303 IAREDLREGLHRQVTETVNQGARCLLGGEMPPGPGFFYPVTVLADVTPGMQASCEETFGP 362 Query: 388 VLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFEAMQG 447 + V+ D E A++MANDSDYGL +SI+T + A + ++ G+ IN + Sbjct: 363 IAVVMKADNAEQALAMANDSDYGLAASIWTADTAKAEAMSREIEAGQVAINGIVKTDPRL 422 Query: 448 FHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 G ++SG G G HG+ E++ Q V++ Sbjct: 423 PSGGIKRSGYGRELGPHGIREFVNVQQVWV 452 Lambda K H 0.318 0.135 0.392 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: 506 Number of extensions: 35 Number of successful extensions: 4 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: 479 Length of database: 457 Length adjustment: 33 Effective length of query: 446 Effective length of database: 424 Effective search space: 189104 Effective search space used: 189104 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: 51 (24.3 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