Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= BRENDA::A0A0E3T3B5 (503 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 311 bits (796), Expect = 4e-89 Identities = 180/477 (37%), Positives = 264/477 (55%), Gaps = 13/477 (2%) Query: 9 QLFIDGEWREPVLKKRIPIINPATEQIIGDIPAATAEDVEIAVEAARKALARNKGRDWAL 68 Q F+DG W + K + + NPA ++G +P A++ A+EAA +A W Sbjct: 23 QGFVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPA-----WRA 77 Query: 69 APGAVRAKYLRAIAAKIAERKSEIAKLEAIDCGKPLDEAAWDIDDVSGCFEYYADLAEGL 128 RAK LR + + +IA++ + GKPL EA ++ + E++A+ EG Sbjct: 78 LTAKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAE--EGK 135 Query: 129 DAQQKT-PISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPS 187 T P LP + V KEPIGV ITPWN+P M T K PALAAGC ++KP+ Sbjct: 136 RVYGDTIPQHLPGRRIV--VTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPA 193 Query: 188 ELASVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLASHPHVDKIAFTGSTMTGSKIM 247 +T L +A + G+P G+L+++TG G + +P V K+ FTGST G ++M Sbjct: 194 TATPLTALAMAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELM 253 Query: 248 TAAAQLVKPVSLELGGKSPIVVFDDVDIDKAAEWTAFGIFWTNGQICSATSRLIIHENIA 307 A VK VSLELGG +P +VF+D D+D+A + + GQ C +RL++ + Sbjct: 254 AQCAGTVKKVSLELGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVY 313 Query: 308 AKFLDRLVQWCKNIKIADPL-EEGCRLGPVVSGGQYEKILKFIATAKSEGARVLSGGARP 366 F +L + K +K+ L EG + GP++ EK+ I A +GARV+ GG R Sbjct: 314 DAFAAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKR- 372 Query: 367 EHLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDSHYGLGAAVI 426 H G F EPTI+ DVT +M++ REE FGPV + F +E+EA+ +AN + +GL A Sbjct: 373 -HELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFY 431 Query: 427 SKDLERCERVSKALQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYLTVK 483 S+D+ R RV++AL+ GIV IN AP+GG K SG GRE K+G+++YL +K Sbjct: 432 SRDIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYLEIK 488 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: 615 Number of extensions: 35 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: 503 Length of database: 497 Length adjustment: 34 Effective length of query: 469 Effective length of database: 463 Effective search space: 217147 Effective search space used: 217147 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