Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q8VWZ1 (503 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 226 bits (575), Expect = 2e-63 Identities = 160/502 (31%), Positives = 249/502 (49%), Gaps = 18/502 (3%) Query: 1 MAITVSSRQLFIDGEWRVPILNKRIPNINPSTENIIGDIPAATKEDVDLAVDAAKRAISR 60 M + +L IDG++ +NP+T++++ +P AT +VD AV AAK A Sbjct: 1 MTVAAPRIRLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAF-- 58 Query: 61 KNGRDWSAASGSLRARYLRAIAAKIKEKKDELGKLESIDCGKPLEEALADLDDVVACFEY 120 + W RAR I+E EL S + GK + +A D+ + E+ Sbjct: 59 ---KTWRKTPIGTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEH 115 Query: 121 YAGLAEELDSKQKAPISLPMDTFKSYILKEPIGVVALITPWNYPFLMATWKIAPALAAGC 180 A + + ++ +DT Y L +P+GV A ITP+N+P ++ W A+A G Sbjct: 116 AAAIGNLQLGELANNVANGVDT---YTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGN 172 Query: 181 AAILKPSELASVTCLELGEICKEVGLPRGVLNIVTGLGHEAGASLASHPDVDKISFTGSS 240 +LKPSE + + L E+ E G+P+GVLN+V G G E ++ HPD+ +SF GS+ Sbjct: 173 TFVLKPSEQDPMVTMRLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGST 231 Query: 241 ATGSKIMTTAAQLVKPVSLELGGKSPIVVFEDVDLDKVAEWTVFGCFFTNGQICSATSRL 300 G+ + A+ K V +G K+ VV D + ++ V F GQ C A S L Sbjct: 232 RVGTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTL 291 Query: 301 IVHESIAVEFVDKLVKWAENIKISDPLEEGCRLGPIVSEAQYKKVLNCISSAKSEGATIL 360 ++ A +V LV A+ +K+S G +GP++S + ++V I+S +GAT+ Sbjct: 292 VL-VGEARSWVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLD 350 Query: 361 TGGRRP--EHLKKGYFVEPTIITDVTTSMQIWREEVFGPVLAVKTFSTEEEAINLANDTH 418 GR P + +KG FV PTI + VTT M+I++EE+FGPVL + T E+AI L N Sbjct: 351 LDGRNPQVDGFEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNP 410 Query: 419 YGLGSAVMSNDLERCERLSKALQAGIVWINCAQPSFIQA-PWGGIKRSGFGRELGEWGLE 477 G G+AV + + + + G V IN P + + G + S G +LG +G + Sbjct: 411 NGNGTAVFTQSGAAARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLG-DLGPYGKQ 469 Query: 478 ---NYLSVKQVT-RYTSDEPWG 495 Y K +T R+ DE G Sbjct: 470 VVMFYTQTKTITARWFDDETLG 491 Lambda K H 0.317 0.134 0.402 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: 494 Number of extensions: 28 Number of successful extensions: 6 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: 501 Length adjustment: 34 Effective length of query: 469 Effective length of database: 467 Effective search space: 219023 Effective search space used: 219023 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 (21.6 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