Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ac3H11_1480 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_805 (497 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1480 Length = 486 Score = 313 bits (803), Expect = 7e-90 Identities = 184/478 (38%), Positives = 271/478 (56%), Gaps = 14/478 (2%) Query: 18 IEGRAYINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSR 77 ++ R YI+G++ DA +G T +P +G L+G I + AA Q A+ A F G W Sbjct: 12 LKARCYIDGQWVDADNGATLAVNNPANGALIGTIPNAGAAQTQTAIAAADRAF--GPWKD 69 Query: 78 LAPTKRKSTMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDK 137 R + R+ L+ QH E+LAL+ T + GKP++++ ++ AA + W E + Sbjct: 70 RTAEDRARILRRWFELMLQHQEDLALIMTSEQGKPLAEARG-EIAYAASYIEWFAEEARR 128 Query: 138 IYDEVAATPH-DQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKS 196 IY EV +P D+ +VTREPVGV AI PWNFP M K+ PAL+ G ++I+KP+ ++ Sbjct: 129 IYGEVIPSPWLDKRIVVTREPVGVCAAITPWNFPAAMITRKVAPALAAGCTIIVKPATQT 188 Query: 197 PLTAIRIAELAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYS 256 PL+A+ +AELA AG+P GV +V+ G +G L V L FTGST+I + L Sbjct: 189 PLSALAMAELAARAGVPAGVFSVITGDARPIGAELTASPVVRKLTFTGSTEIGRVLAAQC 248 Query: 257 GESNMKRVWLEAGGKSPNIVFADAPNLQDAAEAAAGAIAF---NQGEVCTAGSRLLVERS 313 + +K++ LE GG +P IVF DA D A AGA+A N G+ C +RLLV+ Sbjct: 249 APT-LKKMSLELGGNAPFIVFEDA----DLDAAVAGAMASKYRNTGQTCVCANRLLVQDG 303 Query: 314 IKDKFLPLVIEALKAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGKR 373 + D F + + A K G+ L+ G L+D + V + + A GAR+V GG+R Sbjct: 304 VYDAFAEKLARTVAALKVGHGLEEGVEQGPLIDEASLTKVEALVADAKARGARVVTGGRR 363 Query: 374 TLQETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAV 433 GGT+ EPTI ++ M++A+EEIFGPV + F + EAI +ANDT +GLAA Sbjct: 364 --HALGGTFYEPTILADITPDMRMAREEIFGPVAPLFRFHTEAEAIQMANDTEFGLAAYF 421 Query: 434 WTADISKAHLTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELK 491 ++ D+ + + AL+ G V +N APFGG KQSG GR+ S+H ++Y + K Sbjct: 422 YSRDVGRVWRVSGALQYGMVGINAGVISTAVAPFGGVKQSGMGREGSVHGIEEYVDTK 479 Lambda K H 0.316 0.132 0.390 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: 626 Number of extensions: 29 Number of successful extensions: 7 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: 497 Length of database: 486 Length adjustment: 34 Effective length of query: 463 Effective length of database: 452 Effective search space: 209276 Effective search space used: 209276 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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