Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000496075.1:WP_023433101.1 Length = 492 Score = 318 bits (815), Expect = 3e-91 Identities = 181/472 (38%), Positives = 266/472 (56%), Gaps = 7/472 (1%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKVRA 64 I+G G +PATG+ + A+A VD AVRAAD AF + W + T R Sbjct: 10 IDGAFCEGGAGSFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTATQRG 69 Query: 65 ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124 + L +LAD++ EN Q AELE+R+ GK + + +I + D +R++AG A + G Sbjct: 70 KLLYRLADLVAENAQALAELETRDTGKIIRET-SAQIAYVADYYRYYAGLADKIEGAHLP 128 Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184 + +RR+P+GVVA++ PWN L ++A KL PALAAG VVLK SE P L Sbjct: 129 IDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGPAPLLAF 188 Query: 185 AELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243 A L FP GV+NIL G G G L HP V ++ TG AT HI+ H+A ++ Sbjct: 189 ARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSAENLAAV 248 Query: 244 HMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAA 303 +ELGGK+PV+VF+DAD+++V V + GQ C A R+ Q+GI D L+E+L Sbjct: 249 TLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDALLERLVQK 308 Query: 304 VATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG--NGYYYA 361 ++ G P + TE+GPL++ L + + + A G +++TGG + G G+Y+ Sbjct: 309 ARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGG-RLVTGGGRPDGFPAGHYFE 367 Query: 362 PTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRV 421 PT++ V++E+FGPV+SV F+ E + V +AN + YGLAS V+T + RAHR+ Sbjct: 368 PTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTASLTRAHRM 427 Query: 422 SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 ++ G WVNT+ + MP GG LSG G++ L DYT + V ++ Sbjct: 428 IRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAVWIR 479 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: 597 Number of extensions: 23 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: 474 Length of database: 492 Length adjustment: 34 Effective length of query: 440 Effective length of database: 458 Effective search space: 201520 Effective search space used: 201520 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