Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_047092826.1 AAV99_RS05570 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_001013305.1:WP_047092826.1 Length = 476 Score = 244 bits (623), Expect = 5e-69 Identities = 145/473 (30%), Positives = 244/473 (51%), Gaps = 3/473 (0%) Query: 4 PVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEAL 63 P H + IDG+ + G DV+NPATE V+ +P D +A++AA+R EW Sbjct: 5 PTLH-LLIDGEQHSGDGRKTEDVINPATEEVLGTLPHATPADLDRALEAAQRGFHEWRRT 63 Query: 64 PAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYE 123 A +RAS L K + IRERA EI + E GK E +++A+ +++ A+ +R Sbjct: 64 SADKRASILTKAAGLIRERAKEIGETLCLEQGKPVAEGRGEASYSANLLEFYAQECKRIY 123 Query: 124 GEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPN 183 G + G + +G G PWNFP + RK+ AL G ++++KPSE TP Sbjct: 124 GRTLVRGE-GARAEVQYHPVGPIAGFAPWNFPAINVMRKIGGALAAGCSVIVKPSEETPA 182 Query: 184 NAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243 + IA + + + G+P GV V G V ++L G+P + ++ TGS G+++ AA Sbjct: 183 SGIAVVQALLDSGVPGGVVQCVFGVPSDVSEQLIGSPIIRKITFTGSTPVGKQLAKMAAD 242 Query: 244 NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303 ++ +ELGG P +V +D+DL + +V ++ N+GQVC R +++ I+D+F + Sbjct: 243 DLKIATMELGGHGPVLVFNDSDLTKVLDTMVANKFRNAGQVCVSPTRFLIEEDIFDKFRD 302 Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGY 363 E +A+ GN ++ MGP+ NA L+ + + +A A ++GA + GG+ + +G+ Sbjct: 303 GFVERAKALTVGNGMDKG-TDMGPMANARGLDNIAKLIANAQDKGANLLTGGERIGNQGF 361 Query: 364 YYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVA 423 ++ PT+L +V + IM+ E FGPV + A I AN YGL + +T + Sbjct: 362 FFQPTVLSEVPLDSDIMNNEPFGPVAILNAMPGEAAMIEEANRLPYGLAAYAWTNDPARR 421 Query: 424 MKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVY 476 + ++ G IN + G + SG G DG+ G+ + + ++ Sbjct: 422 RRLAAEVEAGMLAINTGGVSTVDAPFGGVKWSGYGSEDGREGVMACMVVKAIH 474 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: 568 Number of extensions: 24 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: 479 Length of database: 476 Length adjustment: 34 Effective length of query: 445 Effective length of database: 442 Effective search space: 196690 Effective search space used: 196690 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