Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 324 bits (830), Expect = 5e-93 Identities = 185/472 (39%), Positives = 276/472 (58%), Gaps = 12/472 (2%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKVRA 64 ++G +SG PV +PAT V+ E ++ A + AV +A AF W P R Sbjct: 29 VSGPALSGRW--LPVTDPATEMVVAEAPDSDAADIARAVASAQRAFDSHVWRGLRPADRE 86 Query: 65 ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124 + L +L+++IE + + LE+ GK A ++ A + R+ AG A L G Sbjct: 87 KLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFVRYMAGWATKLEGQTLD 146 Query: 125 EYLE----GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180 + + RR+P+GVV +I PWN+PL +A WK+APALAAG VVLKPSE TPLT Sbjct: 147 NSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPALAAGCTVVLKPSEDTPLT 206 Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTA-S 238 AL+LA LA + P GV+N++ GRG T G L HP VR +S TGS A G+ ++ H A Sbjct: 207 ALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSFTGSTAVGK-VVGHAAVE 265 Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298 ++ R +ELGGK+P +V +DAD V +G+ T +++ GQ CTA+ R+ + +Y +++ Sbjct: 266 NMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTASSRLLVHRSLYRRVLD 325 Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY 358 +L ++ G+ D +T+ GPL+S AH RV + AKA G ++ GGE+ G Sbjct: 326 ELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEG-ATLVAGGERVHDAGC 384 Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418 + PT+ A +V++EVFGPV++V PFD+ E + AND+ YGLA+S+WT+ + A Sbjct: 385 FVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTPYGLAASLWTQSLSHA 444 Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 HR+ RLQ G WVN H +L + +P GG K SG G+D+ +E +T ++ V Sbjct: 445 HRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEGFTELKSV 496 Lambda K H 0.317 0.134 0.397 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: 537 Number of extensions: 22 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: 474 Length of database: 500 Length adjustment: 34 Effective length of query: 440 Effective length of database: 466 Effective search space: 205040 Effective search space used: 205040 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