Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB
Query= BRENDA::A0A0E3T3B5 (503 letters) >FitnessBrowser__Phaeo:GFF2074 Length = 488 Score = 317 bits (811), Expect = 8e-91 Identities = 191/466 (40%), Positives = 260/466 (55%), Gaps = 9/466 (1%) Query: 29 NPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWALAPGAVRAKYLRAIAAKIAER 88 +PA+ ++ +P A A DVE AV AAR A DWA R K L +A IAE Sbjct: 23 DPASGEVWAMMPEARASDVEAAVAAARAAF---HAPDWAGMTATGRGKLLYRLADLIAEN 79 Query: 89 KSEIAKLEAIDCGKPLDEAAWDIDDVSGCFEYYADLAEGLDAQQKTPISLPMEQFKSHVL 148 +A+LE D GK + E + I V+ + YYA LA+ ++ PI P + + Sbjct: 80 AETLAQLETRDTGKIIRETSAQIAYVADYYRYYAGLADKIEGAH-LPIDKP--DMEVWLR 136 Query: 149 KEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSELASVTCLELADVCREVGLPP 208 +EP+GVV + PWN L +A K+ PALAAGC +LK SE A LE A + + G P Sbjct: 137 REPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLKASEEAPAPLLEFARIFDQAGFPR 196 Query: 209 GVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIMTAAAQLVKPVSLELGGKSPIV 268 GVLN++TG G + GA L +HP +D IAFTG T ++ +A+ + SLELGGKSP + Sbjct: 197 GVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARHVVRNSAENLASTSLELGGKSPFI 256 Query: 269 VFDDVDIDKAAEWTAFGIFWTNGQICSATSRLIIHENIAAKFLDRLVQWCKNIKIADPLE 328 VF+DVDID A IF GQ C A SRLII I A+FL RL + +NI+I P Sbjct: 257 VFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQIKAQFLHRLKEKAENIRIGAPEL 316 Query: 329 EGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGGARPEHLKKGFFIEPTII-TDVTTSM 387 +GP+ + Q + ++ +A + + GAR+++GG E +G F PTI+ Sbjct: 317 PETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQPLE--GEGNFFPPTILDCSEAPEA 374 Query: 388 QIWREEVFGPVLCVKTFSSEDEALELANDSHYGLGAAVISKDLERCERVSKALQAGIVWI 447 REE FGPVL V F +E EAL LAND+ +GL + V ++DL R R+ + ++AGIVW+ Sbjct: 375 PCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGVFTRDLTRAHRMIRGIRAGIVWV 434 Query: 448 NCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYLTVKQVTEYVSDDP 493 N + AP+GG SG GRE G +Y VK V SDDP Sbjct: 435 NTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTVWLRTSDDP 480 Lambda K H 0.319 0.136 0.419 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: 592 Number of extensions: 25 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: 503 Length of database: 488 Length adjustment: 34 Effective length of query: 469 Effective length of database: 454 Effective search space: 212926 Effective search space used: 212926 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