Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BPHYT_RS09900 BPHYT_RS09900 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__BFirm:BPHYT_RS09900 Length = 492 Score = 345 bits (885), Expect = 2e-99 Identities = 194/484 (40%), Positives = 285/484 (58%), Gaps = 11/484 (2%) Query: 1 MQHKLLINGELV-SGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQ 57 + H + INGE S G+ PV+NPAT + + +I +AS +D AVR + AAF W + Sbjct: 10 LPHTMFINGEKTGSAAGKTFPVFNPATAEEIAQIPDASEADIDHAVRTSKAAFESDAWRR 69 Query: 58 TTPKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARC 117 P VR LLKLAD++E + A LE+ N GK + + E+ V R+ AG A Sbjct: 70 MPPAVREGLLLKLADLVERHSDELATLETLNQGKLIGFSKMLEVAGSVQWLRYMAGWATK 129 Query: 118 LNGLAAGEYLE-----GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLK 172 + G + + + +R P GVVA+I PWN+PL+MA WK+APALA G VVLK Sbjct: 130 IEGSTFDLSIPFPPGTRYNASTKRVPAGVVAAIVPWNFPLLMAVWKIAPALACGCTVVLK 189 Query: 173 PSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEH 231 P+E TPLTA++LAELA + FPAGV N++ GRG+T G L HP V+ V+ TGS G Sbjct: 190 PAEETPLTAIRLAELAHEAGFPAGVFNVVTGRGETAGAALVRHPLVKKVTFTGSTEVGRI 249 Query: 232 IISHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKG 291 I A +KR +ELGGK+PVIV DD D +EG ++N GQ CTA R+Y + Sbjct: 250 IGRQCADDLKRASLELGGKSPVIVLDDCDPRKAIEGAAGAIFFNHGQVCTAGSRLYVARS 309 Query: 292 IYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGE 351 IYD +V+ + A + G+ D +T++GP+ S H ++V + + K G ++++ Sbjct: 310 IYDEVVQGIAAVADGITLGSGFDAATQMGPMVSARHRDKVAGMIAQGKDEGG-EIVSRDA 368 Query: 352 KRKGNGYYYAPTLLAG-ALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSV 410 + + GY+ PT++A A + A+V++EVFGPV+ P+D+ ++V+ AN S+YGL +SV Sbjct: 369 RVEREGYFVRPTVIANRACKPLAVVKEEVFGPVLVAMPYDDLDEVLAQANASEYGLGASV 428 Query: 411 WTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 WT + +A R+ ++ G WVNTH M+ MP GG K SG G++ +E YT + V Sbjct: 429 WTNQLDKALRLVDGIEAGTVWVNTHNMVDPAMPFGGFKASGIGREHGKSIIESYTESKSV 488 Query: 471 MVKH 474 + + Sbjct: 489 CIAY 492 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: 566 Number of extensions: 29 Number of successful extensions: 5 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: 492 Length adjustment: 34 Effective length of query: 440 Effective length of database: 458 Effective search space: 201520 Effective search space used: 201520 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