Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 348 bits (892), Expect = e-100 Identities = 188/465 (40%), Positives = 279/465 (60%), Gaps = 2/465 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 YI+G +V + + V NPA ++I R+P A + R+AI+AA+RA W+A A ER+ Sbjct: 15 YINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAKTAKERS 74 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + LR+ I ++++ L+ E GK A+ EVA+ A ++++ AE A+R G+ I Sbjct: 75 AVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRVYGDTIPE 134 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 PG I++ K +GV I PWNFP +I RK APAL G +V+KP+E TP +A+A A Sbjct: 135 HMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 194 Query: 190 KIVDEIGLPRGVFNLV-LGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 ++ + G P GVFN++ G + VG EL NPKV +S TGS G+ +MA A + K+ Sbjct: 195 ELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMAQCAATVKKL 254 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 LELGG AP +V DDADL+ AV + S+ N+GQ C CA R+ VQ GIYD F RL EA Sbjct: 255 SLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDAFTARLAEA 314 Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368 + A++ G P D GPLIN A+ +VE+ +A AV +GARV GGK G ++ PT Sbjct: 315 VAALKVG-PGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRHARGGTFFEPT 373 Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428 +L DV +M+ EETFGPV P+ F T E+A+ MAND+++GL + Y++++ + + Sbjct: 374 ILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVGRVWRVSR 433 Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 L++G IN G ++SG+G K+G+ ++L+ + Sbjct: 434 ALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVK 478 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: 543 Number of extensions: 27 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: 485 Length adjustment: 34 Effective length of query: 445 Effective length of database: 451 Effective search space: 200695 Effective search space used: 200695 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