Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate BPHYT_RS00120 BPHYT_RS00120 aldehyde dehydrogenase
Query= SwissProt::A1B4L2 (508 letters) >FitnessBrowser__BFirm:BPHYT_RS00120 Length = 506 Score = 792 bits (2045), Expect = 0.0 Identities = 384/493 (77%), Positives = 425/493 (86%) Query: 16 PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75 P++++Y NFIGGEWV PV G YF N +PITG I RS D+ELALDAAH AK WG Sbjct: 14 PYKKQYANFIGGEWVKPVGGEYFDNVSPITGEAFTSIPRSREADVELALDAAHRAKAAWG 73 Query: 76 ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135 TS +R+NI+++IADRME NL+ LA AET DNGKP+RETMAAD+PLAIDHFRYFAG +R Sbjct: 74 KTSAGDRSNILMRIADRMEANLQRLAVAETIDNGKPLRETMAADIPLAIDHFRYFAGAVR 133 Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195 AQEGSIS+ID DTVAYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+AAGNCVVLKPAEQT Sbjct: 134 AQEGSISEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQT 193 Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255 PA I+V LI DLLP GVLN+VNGFGLEAGKPLASS RIAKIAFTGETTTGRLIMQYAS Sbjct: 194 PASILVLVELIQDLLPAGVLNVVNGFGLEAGKPLASSKRIAKIAFTGETTTGRLIMQYAS 253 Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315 +N+IPVTLELGGKSPNIFF DV DD +FDKALEGF MFALNQGEVCTCPSRVLI E I Sbjct: 254 QNIIPVTLELGGKSPNIFFDDVMNADDSYFDKALEGFAMFALNQGEVCTCPSRVLIDEKI 313 Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375 YD+FMERA++RV AI QG P ++ TMIGAQAS EQ EKILSY+D+GK+EGAE L GG+ Sbjct: 314 YDRFMERALKRVAAITQGHPLDTRTMIGAQASQEQLEKILSYVDLGKQEGAECLIGGERN 373 Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435 L GELS GYY++PT+FRG+NKMRIFQEEIFGPVVSVTTFK + EALE+ANDTLYGLGAG Sbjct: 374 ALDGELSKGYYVKPTVFRGHNKMRIFQEEIFGPVVSVTTFKTEEEALEVANDTLYGLGAG 433 Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495 VW+RD YR GR I+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE HKMMLDHYQQTKN Sbjct: 434 VWTRDGTRAYRFGRQIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493 Query: 496 MLVSYSPKKLGFF 508 +LVSYS K LGFF Sbjct: 494 LLVSYSDKPLGFF 506 Lambda K H 0.319 0.136 0.411 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: 885 Number of extensions: 27 Number of successful extensions: 1 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: 508 Length of database: 506 Length adjustment: 34 Effective length of query: 474 Effective length of database: 472 Effective search space: 223728 Effective search space used: 223728 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