Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 318 bits (814), Expect = 3e-91 Identities = 180/467 (38%), Positives = 266/467 (56%), Gaps = 2/467 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 Y+DG +V DV++PAT +I+ +PD A + R+AIDAAE A W A +RA Sbjct: 28 YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPWRQRTAKDRA 87 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + + I ++ L+ E GK A E+++ A +I + AE +R G++I + Sbjct: 88 AVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGKRAYGDLIPT 147 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 +L+ K+ +GV + PWNFP +I RK APAL G +V+KP+E TP +A+A A Sbjct: 148 TASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 207 Query: 190 KIVDEIGLPRGVFNLVLGR-GETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 ++ GLP+G+FN+V R VG E+ GN KV +S TGS G+ +MA A+ + KV Sbjct: 208 ELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAETVKKV 267 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 LELGG AP IV DD DL+ AV + S+ NSGQ C C R VQ GIY+ F +L E Sbjct: 268 SLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAVKLAEK 327 Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368 A+ G+ A + GPLINAAA+ +V VA AV +GARV GG+ G ++ PT Sbjct: 328 AAAMAVGH-ALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRPHALGGGFWQPT 386 Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428 +L DV M EETFGPV P++ F+T +AI++AN S++GL Y++++ + + Sbjct: 387 VLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRDVARVFRVAE 446 Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 L+ G +N G ++SG+G K+GL ++++T+ V Sbjct: 447 ALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYV 493 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: 529 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: 499 Length adjustment: 34 Effective length of query: 445 Effective length of database: 465 Effective search space: 206925 Effective search space used: 206925 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