Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 223 bits (569), Expect = 1e-62 Identities = 146/469 (31%), Positives = 229/469 (48%), Gaps = 10/469 (2%) Query: 42 LQDLGLREDNEGVFNGSW--GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAW 99 L D L D+ + NGSW GE + PA+ I RV + + I A +AW Sbjct: 4 LSDSALLRDHAYI-NGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAW 62 Query: 100 NIWADIPAPKRGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAG 159 W A +R ++R+ + + L +L++ E GK L E GEV ++ A Sbjct: 63 GPWKAKTAKERSAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAE 122 Query: 160 LSRMIGGPTLPSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKG 219 ++ + G T+P PG ++ P+G+V IT +NFP+A+ A AL G + K Sbjct: 123 EAKRVYGDTIPEHMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKP 182 Query: 220 APTTSLVSIAVTKIIAKVLEDNLLPGAICSLTCGGAD-MGTAMARDERVNLLSFTGSTQV 278 A T L ++A+ ++ + PG +T G +G + + +V LSFTGST+V Sbjct: 183 AEDTPLSALALAELAERA---GFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEV 239 Query: 279 GKQVALMVQERFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFL 338 GK + K LELGGN + F+DADL + A+ + GQ C RL + Sbjct: 240 GKLLMAQCAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLV 299 Query: 339 HESIHDEVVDRLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYG 398 + I+D RL A + ++VG + + GPL ++AV + + +A +G VV G Sbjct: 300 QDGIYDAFTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMG 359 Query: 399 GKVMDHPGNYVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSS 458 GK G + EPTI+ + D +ETF P+ +F+FK EEE N+ + GL++ Sbjct: 360 GKRHARGGTFFEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAY 419 Query: 459 IFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRE 507 +++D+GR+ W + + GIV +N E+ FGG K +G GRE Sbjct: 420 FYSRDVGRV--WRVSRALEYGIVGINEGLISTEV-APFGGVKESGLGRE 465 Lambda K H 0.319 0.137 0.417 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: 617 Number of extensions: 32 Number of successful extensions: 2 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: 539 Length of database: 485 Length adjustment: 35 Effective length of query: 504 Effective length of database: 450 Effective search space: 226800 Effective search space used: 226800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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