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 SMc04397 SMc04397 L-sorbosone dehydrogenase, NADP dependent protein
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Smeli:SMc04397 Length = 504 Score = 206 bits (525), Expect = 1e-57 Identities = 141/484 (29%), Positives = 232/484 (47%), Gaps = 25/484 (5%) Query: 54 VFNGSW--GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNI--WADIPAPK 109 + +G W G G I P + ++R + A+ D E I A++A++ W + A + Sbjct: 23 LIDGQWVDGAEGRTIERVAPGHGVVVSRYQAAAKADAERAIAAARRAFDEGPWPRMTASE 82 Query: 110 RGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTL 169 R I+ + D + + L L ++E GK + + GE+ D+ YAA L+R + G + Sbjct: 83 RSLILLRAADMIAARADELAFLDAVESGKPISQAKGELAGAADIWRYAAALARELSGESY 142 Query: 170 PSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIA 229 + G + P+G+V IIT +NFP + AL G + K + TS A Sbjct: 143 NTLGEGTLGVVLREPIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTS----A 198 Query: 230 VTKIIAKVLEDNLLPGAICSLTCG-GADMGTAMARDERVNLLSFTGSTQVGKQVALMVQE 288 T ++ ++LE +P + ++ G G + G + V+++SFTGST +G+ + Sbjct: 199 STLVLGEILEAAGVPQGVVNIIVGTGPEAGAPLTTHPHVDMVSFTGSTGIGQLTMANAAQ 258 Query: 289 RFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVD 348 K LELGG N I F DA+L + +A+F A AG+ C RL LH I +EV Sbjct: 259 TLKKVSLELGGKNPQIVFPDANLDEFIDAAVFGAYFNAGECCNAGSRLILHRDIAEEVTA 318 Query: 349 RLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMD-HPGN 407 R+ + ++++VG+P DP G + T Q + V A EG + +GG +D G Sbjct: 319 RIASLSAKVKVGDPLDPETQVGAIITPQHLQKIAGYVSSASNEGARIAHGGTTLDLGMGQ 378 Query: 408 YVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKD---- 463 ++ PTI++ + + + +E F P+L V F+ EE N + GLS+ ++++D Sbjct: 379 FMAPTILSAVRPEMAVAREEVFGPVLSVLTFEKTEEAIRIANSIDYGLSAGVWSRDFDTC 438 Query: 464 --LGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRST 521 +GR R G V +N GA FGG + +G GRE G A + Y T Sbjct: 439 LTIGRRVR--------AGTVWMNTFMDGAS-ELPFGGYRQSGLGRELGRHAVEDYTETKT 489 Query: 522 CTIN 525 ++ Sbjct: 490 LNMH 493 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: 584 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: 539 Length of database: 504 Length adjustment: 35 Effective length of query: 504 Effective length of database: 469 Effective search space: 236376 Effective search space used: 236376 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