Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 320 bits (820), Expect = 7e-92 Identities = 184/467 (39%), Positives = 271/467 (58%), Gaps = 5/467 (1%) Query: 7 INGELVSGE-GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAE 65 ING V+ + GE+ V NPA G +++ + A + A+ AAD A+ W T K R+ Sbjct: 16 INGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAKTAKERSA 75 Query: 66 CLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGE 125 L + ++I A+L + GKPL A E+ +FA A+ + G E Sbjct: 76 VLRRWFELIMAAQNDLAKLMTAEQGKPLAEA-KGEVAYGASFVEWFAEEAKRVYGDTIPE 134 Query: 126 YLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185 ++ G ++ ++P+GVVA+I PWN+PL M K APALAAG VV+KP+E TPL+AL LA Sbjct: 135 HMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 194 Query: 186 ELAKDI-FPAGVINILF-GRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243 ELA+ FP GV N++ G K VG LT +PKVR +S TGS G+ +++ A+++K+ Sbjct: 195 ELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMAQCAATVKKL 254 Query: 244 HMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAA 303 +ELGG AP +VFDDAD++A V G Y N GQ C A R+ Q GIYD +L A Sbjct: 255 SLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDAFTARLAEA 314 Query: 304 VATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPT 363 VA LK G + + GPL + + +V + + +A A G +V+ GG++ G ++ PT Sbjct: 315 VAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKG-ARVVMGGKRHARGGTFFEPT 373 Query: 364 LLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSA 423 +LA D A ++E FGPV + F EE+ V AND+++GLA+ +++DVGR RVS Sbjct: 374 ILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVGRVWRVSR 433 Query: 424 RLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 L+YG +N + P GG K SG G++ S YG+ED+ V+++ Sbjct: 434 ALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGIEDFLEVKYL 480 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: 514 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 474 Length of database: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 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