Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 194 bits (492), Expect = 7e-54 Identities = 144/465 (30%), Positives = 213/465 (45%), Gaps = 14/465 (3%) Query: 4 KLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKV 62 +LLI+G+ + S Q V NPAT DVL ++ A+ +VD AV AA AF W +T Sbjct: 9 RLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKTWRKTPIGT 68 Query: 63 RAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA 122 RA LK +I EN A S GK + A D + +V A G Sbjct: 69 RARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGL-EVVEHAAAIGNLQLGEL 127 Query: 123 AGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTAL 182 A G + PLGV A I P+N+P M+ W A+A GN VLKPSE P+ + Sbjct: 128 ANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVTM 187 Query: 183 KLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIK 241 +L ELA + P GV+N++ G G+ V + + HP ++ VS GS G H+ + + + K Sbjct: 188 RLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLAGK 246 Query: 242 RTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLG 301 R +G K +V DA+ E + + + AGQ C AA + G + V L Sbjct: 247 RVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTL-VLVGEARSWVPDLV 305 Query: 302 AAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR-----KGN 356 A TLK A T++GP+ S + ERV + G + G + KGN Sbjct: 306 AKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEKGN 365 Query: 357 GYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVG 416 + PT+ +G D I Q+E+FGPV+ + + E + N + G ++V+T+ Sbjct: 366 --FVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGA 423 Query: 417 RAHRVSARLQYGCTWVNTHFML-VSEMPHGGQKLSGYGKDMSLYG 460 A + + G +N + V G + S G D+ YG Sbjct: 424 AARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLG-DLGPYG 467 Lambda K H 0.317 0.134 0.397 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: 518 Number of extensions: 33 Number of successful extensions: 5 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: 474 Length of database: 501 Length adjustment: 34 Effective length of query: 440 Effective length of database: 467 Effective search space: 205480 Effective search space used: 205480 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 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