Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 292 bits (748), Expect = 1e-83 Identities = 171/473 (36%), Positives = 259/473 (54%), Gaps = 15/473 (3%) Query: 4 KLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVR 63 +L+++G+ ++ E PV +PATG + AS +DAAV AA AF W T + R Sbjct: 5 RLIVDGKPLA-MAETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDR 63 Query: 64 AECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLA- 122 A +L +AD IE A L S GKP+ +A + + A+ AR GL Sbjct: 64 AAAILAIADSIEAAKDELARLLSAEQGKPVPNAVGEIMGALA--------WARATAGLRP 115 Query: 123 AGEYLEGHTSM---IRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPL 179 A + L+ S+ + R PLGVVASI+PWN+P+M+A W + P L AGN VV+KPS TPL Sbjct: 116 AVDVLKDDDSVRVEVHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPL 175 Query: 180 TALKLAELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASS 239 AL++ E+A P GV+N + G + +G + HP + + TGS TG I++ A++ Sbjct: 176 AALRMVEIANAHLPPGVLNSVTGEVE-IGRAIASHPGIDKIVFTGSTPTGRSIMADGAAN 234 Query: 240 IKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK 299 +KR +ELGG IV DAD++ V + + N+GQ C A R+Y + I+D L EK Sbjct: 235 LKRLTLELGGNDAAIVLPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEK 294 Query: 300 LGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYY 359 L T G D +++ GP+ + + V ++A+A G + + GGE R+G+GY+ Sbjct: 295 LAEMARTAVVGPGSDAASQFGPVQNRKQFDLVRALADDARAHGG-RFLAGGEAREGDGYF 353 Query: 360 YAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAH 419 + +++ IV +E FGP++ V + + E + AN ++ GL SVW+ D A Sbjct: 354 FPLSVVVDVTDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAAL 413 Query: 420 RVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 + RL+ G WVN H + ++P GG K SG G + LYGLE+Y ++ V V Sbjct: 414 AFAQRLEAGTVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTVRV 466 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: 546 Number of extensions: 28 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: 474 Length of database: 469 Length adjustment: 33 Effective length of query: 441 Effective length of database: 436 Effective search space: 192276 Effective search space used: 192276 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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