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 BPHYT_RS32650 BPHYT_RS32650 aldehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__BFirm:BPHYT_RS32650 Length = 499 Score = 481 bits (1237), Expect = e-140 Identities = 241/478 (50%), Positives = 330/478 (69%), Gaps = 7/478 (1%) Query: 66 ITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDALREKI 125 I + P + I RV ++ + + + +AK+A+ W ++PAP+RGE+VR +G+ LREK Sbjct: 21 IAVHSPITGDLIGRVASNTVAEVDTALARAKEAYTAWRNVPAPRRGELVRLLGNRLREKK 80 Query: 126 QLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALMEQWNPL 185 Q LG +++LE GKIL EG+GEVQE +D+CD+A GLSR + G T+ SERPGH + E W+P+ Sbjct: 81 QALGSIITLETGKILQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHRMAETWHPM 140 Query: 186 GLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLED-NLLP 244 G +I+AFNFP AV+ WN A+AL+ GN +WK + T L ++AV +I+ + L++ P Sbjct: 141 GTCVVISAFNFPAAVWSWNAALALVCGNAVIWKPSEKTPLTALAVNQILTEALQEFGDAP 200 Query: 245 GAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELGGNNAII 304 + +L GG D+G + D R +++S TGST++G+ V + V +RFG+SLLELGGNNA I Sbjct: 201 AGLTALINGGRDVGAKLVADPRASIVSATGSTEMGRTVGVEVAKRFGRSLLELGGNNAGI 260 Query: 305 AFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIRVGNPWD 364 + AD L + LF+AVGTAGQRCT++RRLF+HES++D+ ++RLK YS++ +GNP + Sbjct: 261 VTQTADHELAMRGILFSAVGTAGQRCTSLRRLFVHESVYDKTIERLKQLYSKVPIGNPLE 320 Query: 365 PNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMD----HPGNYVEPTIVTGLVHD 420 L GPL KQ+ +A+++A EGG V+GG+ +D G YV P IV + Sbjct: 321 KGTLMGPLIDKQSYGRMQEALQQATAEGGK-VFGGERVDVKGYENGYYVRPAIVE-MPSQ 378 Query: 421 APIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSDCGI 480 +V KETFAPILYV ++ + + E NN GLSS +FT DL R+L GSDCGI Sbjct: 379 TSVVLKETFAPILYVLRYTDFADAVEANNAAVHGLSSCVFTTDLREAERFLSDSGSDCGI 438 Query: 481 VNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSTALPLAQGIKF 538 NVNI SGAEIGGAFGGEK TGGGRESGSDAWK YMRR+T T+NYS+ALPLAQGI F Sbjct: 439 ANVNIGPSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNTVNYSSALPLAQGIDF 496 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: 803 Number of extensions: 31 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: 499 Length adjustment: 35 Effective length of query: 504 Effective length of database: 464 Effective search space: 233856 Effective search space used: 233856 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