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 BWI76_RS13210 BWI76_RS13210 aldehyde dehydrogenase
Query= SwissProt::Q9DBF1 (539 letters) >FitnessBrowser__Koxy:BWI76_RS13210 Length = 479 Score = 206 bits (524), Expect = 2e-57 Identities = 145/461 (31%), Positives = 226/461 (49%), Gaps = 10/461 (2%) Query: 61 GRGEV-ITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGD 119 GRG+ I PA ++R+ S +D I A++A W +PA +R +RKI Sbjct: 18 GRGDAWIDVINPATEALLSRIPDGSAEDARRAILAAERAQPGWEALPAIERARWLRKIAA 77 Query: 120 AFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALI 179 RE+ + + L+ E GKI EV D DY A +R G + S+R G ++ Sbjct: 78 GIRERAEEIAALIVAEGGKIQQLAAVEVSFTADYLDYMAEWARRYEGEIVQSDRTGENIL 137 Query: 180 EMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSVAVTKIIAQVLE 239 LG+ I +NFP + A ALITGN + K + T ++A AQ++ Sbjct: 138 VFKRALGVTTGILPWNFPFFLIARKLAPALITGNTIVIKPSEFTPNNAIA----FAQIVH 193 Query: 240 DNLLPGAICSLVCG-GADIGTTMARDERVNLLSFTGSTQVGKEVALMVQERFGKSLLELG 298 D LP + +LV G G +G +A + +V ++S TGS G+++ + K LELG Sbjct: 194 DIGLPKGVFNLVLGRGETVGQELASNPKVAMVSMTGSVAAGEKIMAAAAKNITKVCLELG 253 Query: 299 GNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNEVVDRLRSAYSQIR 358 G I +DADL L V +V+ + V +GQ C V R+++ + I++ V+RL A ++ Sbjct: 254 GKAPAIVMDDADLELAVKAVVDSRVINSGQVCNCVERVYVQKGIYDRFVNRLGEALKAVQ 313 Query: 359 VGNPWD-PNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMDHPGNYVEPTIVTGL 417 G+P +I GPL A++ + V +A QG V GGK + G + PT++ + Sbjct: 314 FGDPASRDDIAMGPLINAAALARVEQKVAKAVAQGARVALGGKAVTGRGYFYPPTLLLDV 373 Query: 418 AHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPKGSD 477 + IVH+ETF P+L V F EE N+ GL+SSI+T+DL + + KG Sbjct: 374 RQEMDIVHEETFGPVLPVVAFDTLEEALAMANDSDYGLTSSIYTRDLNVAMKAI--KGLK 431 Query: 478 CGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518 G +N A + G G + +G G G +Y++ Sbjct: 432 FGETYINRENFEA-MQGFHAGWRKSGIGGADGRHGLNEYLQ 471 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: 646 Number of extensions: 33 Number of successful extensions: 3 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: 479 Length adjustment: 34 Effective length of query: 505 Effective length of database: 445 Effective search space: 224725 Effective search space used: 224725 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