Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::Q9STS1 (503 letters) >FitnessBrowser__MR1:200453 Length = 482 Score = 298 bits (763), Expect = 3e-85 Identities = 170/486 (34%), Positives = 255/486 (52%), Gaps = 24/486 (4%) Query: 7 RRQLFIGGQWTEPVLRKTLPVVNPATEDIIGYIPAATSEDVELAVEAARKAFTRNNGKDW 66 R+Q +I GQW + ++T+ + NPAT +I +P + + A+ AA A W Sbjct: 10 RQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPA-----W 64 Query: 67 ARATGAVRAKYLRAIAAKVIERKSELANLEAIDCGKPLDEAAWDMDDVAGCFEYYADLAE 126 T R LR + E +LA L + GKPL EA ++ A E++A+ A+ Sbjct: 65 RALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAK 124 Query: 127 GLDAKQKTPLSLPMDTFKGY-------ILKEPIGVVGMITPWNYPLLMAVWKVAPSLAAG 179 + DT G+ ++K+P+GV ITPWN+P M K AP+LAAG Sbjct: 125 RIYG----------DTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAG 174 Query: 180 CTAILKPSELASLTCLELADICREVGLPPGVLNILTGLGTEAGAPLASHPHVDKIVFTGS 239 CT ++KP+ T L LA + G+P GV +++TG G + ++P V K+ FTGS Sbjct: 175 CTMVVKPAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGS 234 Query: 240 TTTGSSIMTSAAKLVKPVSLELGGKSPIIVFDDVDIDKAVEWTMFGCFWTNGQICSATSR 299 T G +M A +K +SLELGG +P IVFDD +ID AVE M + GQ C +R Sbjct: 235 TNVGIKLMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANR 294 Query: 300 LLVHERIADEFLDKLVKWTKNIKISDPFEEGCRLGPVVSKGQYERVLKFVSNARNEGATV 359 + V + DEF +KL +K+ + G GP+++ E+V + +A +GATV Sbjct: 295 IYVQAGVYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATV 354 Query: 360 LCGGVRPEHLKKGYFVEPAIVSNVTTSMEIWREEVFGPALCVKTFSTEDEAIQLANDSQY 419 L GG H G F EP +++N SM + REE FGP + F+ D+ I+ AND+++ Sbjct: 355 LAGG--KVHELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEF 412 Query: 420 GLAGAVLSNDLERCDRVSKAFQAGIVWVNCSQPCFCQAPWGGTKRSGFGRELGEWGLENY 479 GLA D+ +V+++ + G+V VN AP+GG K SG GRE ++G+E Y Sbjct: 413 GLAAYFYGRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEY 472 Query: 480 LSVKQV 485 L +K + Sbjct: 473 LEIKYI 478 Lambda K H 0.318 0.135 0.421 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: 577 Number of extensions: 32 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: 503 Length of database: 482 Length adjustment: 34 Effective length of query: 469 Effective length of database: 448 Effective search space: 210112 Effective search space used: 210112 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Apr 09 2024. 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