Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_001046645.1:WP_066609128.1 Length = 487 Score = 322 bits (825), Expect = 2e-92 Identities = 180/469 (38%), Positives = 262/469 (55%), Gaps = 3/469 (0%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 +I G +V A + V NPAT A+I +PD D AI AAE A P W+A A +RA Sbjct: 16 FIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFPAWKAQTAGDRA 75 Query: 70 SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129 + L + A + +++ ++ E GK AE E+ + A +I + AE RR +G I+ + Sbjct: 76 AVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEEGRRVDGGIVPA 135 Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189 IL+ K +GV+ I PWNFP +I RK APAL G +V+KPSE TP A+A A Sbjct: 136 PEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPSELTPFTALALA 195 Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249 K+ +E G+P GVFN+V G +G L +P V +S TGS G +M A I +V Sbjct: 196 KLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSLLMRQCADTIKRVS 255 Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309 ELGG AP IV DDAD+++AV + + S+ N+GQ C CA R+ VQ G+YDQF +L A+ Sbjct: 256 FELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVYDQFAEKLARAV 315 Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKG-YYYPPT 368 A++ P +R +GPLIN AA+E+V+ V A+ GA + F A + G + P Sbjct: 316 SALKVA-PGDRTGSTIGPLINVAAVEKVQAHVEDALSHGATL-FAQAANDATGARFATPV 373 Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428 +L ++M + EETFGPV P+ F E+ I +AN + YGL + YT+NL+ A + + Sbjct: 374 ILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTENLHRAFRVAE 433 Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 L+ G +N G + SG+G G+ EYL+T+ ++ Sbjct: 434 RLEAGMVALNSGAIAMEVAPFGGVKMSGLGREGAHAGIEEYLETKAFHI 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: 533 Number of extensions: 29 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: 487 Length adjustment: 34 Effective length of query: 445 Effective length of database: 453 Effective search space: 201585 Effective search space used: 201585 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