Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_012115248.1 XAUT_RS16460 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000017645.1:WP_012115248.1 Length = 492 Score = 335 bits (860), Expect = 2e-96 Identities = 181/462 (39%), Positives = 270/462 (58%), Gaps = 1/462 (0%) Query: 9 MYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIER 68 M I G +V A I+V NPAT +I IP A + R+AI+AA A W A A ER Sbjct: 22 MLIGGAWVDADSGATIEVNNPATGEIIGTIPKAGAAETRRAIEAASEAFKTWRATTAAER 81 Query: 69 ASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 A+ L K++ I + A E++A++ E GK A+ E+ +A Y+ + AE ARR G++I Sbjct: 82 AAKLHKLADLITQNADELAAILTTEQGKPLAEAKGEIGASAGYVRWFAEEARRLYGDVIP 141 Query: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188 S IL+ K +GV T + PWNFP +++RK+ AL G T+V KPSE TP + +A+ Sbjct: 142 SPWGNRRILVTKEPVGVVTAVTPWNFPSSMLSRKIGAALAAGCTVVAKPSELTPYSGLAW 201 Query: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248 + + G+P GV N+V+G +G E+ NP V V+ TGS G+ +M +A + K+ Sbjct: 202 GVLAEMAGIPAGVVNIVVGEAPAIGGEMTSNPLVKKVTFTGSTPVGKLLMKQSADTMKKI 261 Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308 +ELGG AP +V DDADL+LAV+ + S+ N GQ C CA R YVQ GIYD F + EA Sbjct: 262 SMELGGNAPFLVFDDADLDLAVEQAIASKFRNVGQTCVCANRFYVQAGIYDAFAAKFAEA 321 Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368 + ++ GN + +A GPLI+ AL +VE+ + A+++GA V GGK G ++ PT Sbjct: 322 SKKLKVGNGLDEGVVA-GPLIDDRALAKVERLLKDALDKGATVLTGGKQPALGGTFFEPT 380 Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428 +L Q+M+ +E FGP+ P+ F+T E A+S AND++YGL +T++L A + + Sbjct: 381 VLAGATQDMAFARDEIFGPLAPLFKFETEEQAVSYANDTEYGLACYFFTKDLGRAFRVAE 440 Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYL 470 L++G+ IN G ++SG+G K+G +YL Sbjct: 441 KLEYGQVGINAGVITTEVAPFGGVKESGMGREGSKYGCDDYL 482 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: 556 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: 492 Length adjustment: 34 Effective length of query: 445 Effective length of database: 458 Effective search space: 203810 Effective search space used: 203810 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 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