Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_012465362.1 CLIM_RS02000 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000020465.1:WP_012465362.1 Length = 458 Score = 241 bits (616), Expect = 3e-68 Identities = 151/461 (32%), Positives = 249/461 (54%), Gaps = 9/461 (1%) Query: 24 IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83 I +NPATE V++ P D +A++AA W + ERA + +++ +RER Sbjct: 2 IVTINPATEGVLAEYPAMSHGDINEAVNAAYLDFTRWRQVSIPERARLMLRVAELLRERK 61 Query: 84 SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRY-EGEIIQSDRPGENILLFKRA 142 +E L E GK A EV +A D+ A A Y E E + D G+ +++F+ Sbjct: 62 AEYGTLATREMGKPFAQAAAEVEKSAWVCDFYAAHAEGYLEPETVDMDG-GKGMVVFE-P 119 Query: 143 LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVF 202 LG+ G++PWNFP++ + R PAL+ GN +++K + A A ++ + G P ++ Sbjct: 120 LGLVLGVMPWNFPYWQVFRFAVPALMAGNGVIVKHAPNVTGCAAAIEQVFRDAGFPENLY 179 Query: 203 NLVLGRGETVGQELAG----NPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPA 258 + + V + L G +P V VS+TGS +AG + A A + + + +ELGG P Sbjct: 180 RTLHIELQDVDR-LTGIVIEHPFVKAVSVTGSTAAGRAVAARAGRALKRSVMELGGNDPY 238 Query: 259 IVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPA 318 IV+DDADLE AV SR++NSGQ C A+R V + I +F L E M + G+P Sbjct: 239 IVLDDADLEKAVTVCAASRLLNSGQSCIAAKRFIVHRSIRSRFEGMLLERMLGAKTGDPF 298 Query: 319 ERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMS 378 + + +GP+ A +V ++V +V +GA V GG EG+GY+YPPT+L V++ M+ Sbjct: 299 D-SATEVGPIARADLRLQVHRQVEESVAQGAVVLCGGVLPEGQGYFYPPTILTGVKKGMA 357 Query: 379 IMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYIN 438 EE FGPV ++ ++A+++ANDS+YGL S++++ + A + L+ G +IN Sbjct: 358 AYGEEIFGPVATIIEAADDDEAVAIANDSEYGLGSAVFSADTLRAAEIASRLETGNCFIN 417 Query: 439 RENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQS 479 + G ++SG G +G+ E+ + ++L++ Sbjct: 418 AMVKSDPRMPFGGVKQSGYGRELSSYGIKEFTNIRSLFLEA 458 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: 468 Number of extensions: 23 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: 458 Length adjustment: 33 Effective length of query: 446 Effective length of database: 425 Effective search space: 189550 Effective search space used: 189550 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