Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate RR42_RS34255 RR42_RS34255 aldehyde dehydrogenase
Query= SwissProt::A1B4L2 (508 letters) >FitnessBrowser__Cup4G11:RR42_RS34255 Length = 506 Score = 790 bits (2040), Expect = 0.0 Identities = 379/495 (76%), Positives = 429/495 (86%) Query: 14 ALPFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEK 73 A P++E+Y+N+IGG W+AP G+YF +P+TG ++ RS D++ ALDAAH AK Sbjct: 12 AYPYKEQYENYIGGAWLAPADGQYFEAISPVTGKPFTRVPRSNQKDVDAALDAAHRAKGA 71 Query: 74 WGATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGV 133 WG TS ERANI+ +IADR+E NL LA AET DNGKPIRET AADLPLA+DHFRYFAG Sbjct: 72 WGRTSTTERANILNRIADRIEANLVTLAVAETIDNGKPIRETTAADLPLAVDHFRYFAGC 131 Query: 134 LRAQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAE 193 +RAQEG IS+ID DTVAYHFHEPLGVVGQIIPWNFPLLMA WKLAPA+AAGNCVVLKPAE Sbjct: 132 IRAQEGGISEIDHDTVAYHFHEPLGVVGQIIPWNFPLLMATWKLAPALAAGNCVVLKPAE 191 Query: 194 QTPAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQY 253 QTPA I+V +IGDLLPPGVLN++NGFGLEAGKPLASS+RI+KIAFTGETTTGRLIMQY Sbjct: 192 QTPASILVLMEIIGDLLPPGVLNVINGFGLEAGKPLASSSRISKIAFTGETTTGRLIMQY 251 Query: 254 ASENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQE 313 AS+NLIPVTLELGGKSPNIFF DV DD +FDKALEGF MFALNQGEVCTCPSR LIQE Sbjct: 252 ASQNLIPVTLELGGKSPNIFFEDVLSADDAYFDKALEGFAMFALNQGEVCTCPSRALIQE 311 Query: 314 SIYDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGK 373 SIY++FMERA++RV AIKQG P + TMIGAQAS EQ EKILSY+D+GK+EGA+ L GG+ Sbjct: 312 SIYERFMERALKRVAAIKQGHPLDKATMIGAQASQEQLEKILSYIDLGKQEGAQCLIGGE 371 Query: 374 AADLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLG 433 LGG+L+ GYY++PT+F G+NKMRIFQEEIFGPVVSVTTFKD+ EALEIANDTLYGLG Sbjct: 372 RNALGGDLASGYYVKPTVFSGHNKMRIFQEEIFGPVVSVTTFKDEEEALEIANDTLYGLG 431 Query: 434 AGVWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQT 493 AGVW+RD +RMGRGI+AGRVWTNCYHAYPAHAAFGGYKQSGIGRE H+MMLDHYQQT Sbjct: 432 AGVWTRDGARAFRMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGRENHRMMLDHYQQT 491 Query: 494 KNMLVSYSPKKLGFF 508 KN+LVSYSP LGFF Sbjct: 492 KNLLVSYSPNALGFF 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: 24 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