Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= BRENDA::G5DDC2 (506 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 313 bits (801), Expect = 1e-89 Identities = 188/464 (40%), Positives = 262/464 (56%), Gaps = 14/464 (3%) Query: 14 FVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWARAP 73 F GE+RP + G+ PVVNP T + E G A DVDAAVAAA AA K +WA+ P Sbjct: 23 FFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQK-----EWAKRP 77 Query: 74 GAVRAKYLRAIAAKVIERKQELAKLEALDCGKPY-DEAAWDMDDVAGCFEYFADQAEALD 132 R K + + K+E+AKL AL+ GK E+ + ++ F +F A L Sbjct: 78 VRERGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPEL- 136 Query: 133 KRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKVAPALAAGCAAVLKPSEL 192 K + P + M T REP+GVVG I PWN PLL+ K+APA+ AG A V+K +E Sbjct: 137 KGETIPFNPSMLTMTV---REPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEE 193 Query: 193 ASVTCLELADICKEVGLPPGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIMAA 252 A + L + + V +P GV+NI++G GP+ GAPL AH DV KV FTGS ETGK + Sbjct: 194 APLAVLRVVQLINTV-IPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIVYKT 252 Query: 253 AAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGC-FWTNGQICSATSRLLVHTKIAK 311 AA + PVTLELGGKSP++V D D+D+A+ + G F GQ C+A+SR+ VH I Sbjct: 253 AAEKLIPVTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHD 312 Query: 312 EFNEKMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFILNAKSEGATILTGGVRPA- 370 F EK+ +K+ DPL+E +G +VS Q ++++ +I K GAT P+ Sbjct: 313 AFVEKLKEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSD 372 Query: 371 -HLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVI 429 L KG +++P I T + S I +EE+FGPV CV ++ +E I ANDT+YGLA + Sbjct: 373 PKLTKGLYVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIW 432 Query: 430 SGDRERCQRLSEEIDAGIIWVNCSQPCFCQAPWGGNKRSGFGRE 473 + D + ++AG + VN + +GG K SG G+E Sbjct: 433 TRDLKVAMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKE 476 Lambda K H 0.318 0.135 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: 585 Number of extensions: 27 Number of successful extensions: 6 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: 506 Length of database: 497 Length adjustment: 34 Effective length of query: 472 Effective length of database: 463 Effective search space: 218536 Effective search space used: 218536 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 (21.7 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