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_086509800.1 BZY95_RS10050 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9DBF1 (539 letters) >NCBI__GCF_002151265.1:WP_086509800.1 Length = 485 Score = 226 bits (576), Expect = 2e-63 Identities = 147/466 (31%), Positives = 228/466 (48%), Gaps = 11/466 (2%) Query: 56 NGSW--GGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNIWADIPAPKRGEI 113 +GSW GE I PA E V + + E I A A W + A +R +I Sbjct: 17 DGSWVAADSGEQIEVVNPATGETFGTVPRLGRAETERAIAAADAALVGWRALTAQERADI 76 Query: 114 VRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSER 173 + K D E L +++ E GK L E GE+ + A +R I G T+P+ + Sbjct: 77 LMKWHDLMMEHQDDLAMIMTHEQGKPLKEAAGEIAYAASFLRWFAEEARRIYGETIPAAK 136 Query: 174 PGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSVAVTKI 233 P ++ P+G+VG IT +NFP A+ AL G + K A T + A Sbjct: 137 PNQRIVVTKQPVGVVGAITPWNFPAAMITRKAGAALAAGCTIVIKPASQTPFSATA---- 192 Query: 234 IAQVLEDNLLPGAICSLVCGGA-DIGTTMARDERVNLLSFTGSTQVGKEVALMVQERFGK 292 +A + E +P + ++V G A +I + M V ++FTGST+VG+E+ K Sbjct: 193 LALLAERAGIPRGVFNVVPGRASEIASAMTESPLVRKITFTGSTEVGRELMAQASRHIQK 252 Query: 293 SLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNEVVDRLRS 352 LELGGN I FEDADL V + A AGQ C R + S+ N ++L Sbjct: 253 ISLELGGNAPFIVFEDADLDAAVEGAMAAKFRNAGQTCICTNRFLVQSSVINAFCEKLAV 312 Query: 353 AY-SQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMDHPGNYVEP 411 A S+++VG+ +P+I GPL ++AV+ V +A +G ++ GG GN+ P Sbjct: 313 AMNSELKVGDGTEPDINIGPLIDEKAVAKVSEHVHDAVDKGAELLLGGNPHPLGGNFFSP 372 Query: 412 TIVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWL 471 T+++ D + H+ETF P+ VF F+DEE+ + N+ + GL+S +++DLGR+ W Sbjct: 373 TLISFANADMKVAHEETFGPLAAVFPFEDEEDAVQMANDTQYGLASYFYSRDLGRV--WR 430 Query: 472 GPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517 + G+V +N + FGG K +G GRE G ++++ Sbjct: 431 VADALEYGMVGINTGLI-SNTAAPFGGVKASGLGREGGHQGIEEFL 475 Lambda K H 0.319 0.137 0.421 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: 641 Number of extensions: 42 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: 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 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