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 GFF3742 PGA1_262p01460 aldehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Phaeo:GFF3742 Length = 497 Score = 222 bits (565), Expect = 3e-62 Identities = 151/489 (30%), Positives = 235/489 (48%), Gaps = 11/489 (2%) Query: 42 LQDLGLREDNEGVFNGSW-GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWN 100 ++ L + + + + G W G EV ++ + QAS E T+ +A+ A Sbjct: 11 VRPLTMTDIQKNLIAGEWLAGESEVENRNPSDLSDLVGIFAQASADQLEATLDQAQVAQR 70 Query: 101 IWADIPAPKRGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGL 160 WA ++ ++ IG+ + + + LG L+S E GK L EG GEV Y A Sbjct: 71 EWAAYGLERKQAVLNAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAE 130 Query: 161 SRMIGGPTLPSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGA 220 G S RP + + +G V II+ +NFP A W A AL GN +WK A Sbjct: 131 CLRQIGENADSVRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPA 190 Query: 221 PTTSLVSIAVTKIIAKVLEDNLLPGAICSLTCG-GADMGTAMARDERVNLLSFTGSTQVG 279 T ++A +A+++E +P + SL G G +G + +VN +SFTGS VG Sbjct: 191 NITPASAVA----LAEIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVG 246 Query: 280 KQVALMVQERFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLH 339 K +A + K +E+G NA+ +DADL L + AL A G GQ+CT RL +H Sbjct: 247 KGIASAAIQNLTKVQMEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLVVH 306 Query: 340 ESIHDEVVDRLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGG 399 IHD V++L ++VG+ + + GP+ ++Q ++ + V+ K EG + GG Sbjct: 307 AGIHDAFVEKLVTGAKAMKVGHALEAGVQMGPVVSEQQLNENLAYVDLGKTEGAELACGG 366 Query: 400 K--VMDHPGNYVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSS 457 + M H G Y+ P + +D I +E FAP+ V K + +E N+ GL+S Sbjct: 367 QRLEMPHQGFYMSPGVFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTS 426 Query: 458 SIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTG-GGRESGSDAWKQY 516 I T+ L R + + + G+V VN+PT+G + FGG + G RE G A + Y Sbjct: 427 GIVTQSLARATHF--RRNARTGVVTVNLPTAGTDYHVPFGGRGDSSYGPREQGKAAAEFY 484 Query: 517 MRRSTCTIN 525 T I+ Sbjct: 485 TTVKTAYIS 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: 639 Number of extensions: 33 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: 497 Length adjustment: 35 Effective length of query: 504 Effective length of database: 462 Effective search space: 232848 Effective search space used: 232848 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