Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::A1B4L2 (508 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 699 bits (1805), Expect = 0.0 Identities = 333/504 (66%), Positives = 399/504 (79%) Query: 5 QTHPFRGVNALPFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELAL 64 Q P ++ F+ YDNFIGG++V PV G YF +P+ G ++AR +A DIELAL Sbjct: 6 QEKPATMLDRPDFKPHYDNFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELAL 65 Query: 65 DAAHAAKEKWGATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAI 124 DAAH A W TS ER+NI+LKIADR+E LE LA ET DNGKP+RET+ ADL L + Sbjct: 66 DAAHKAFPAWSRTSATERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVV 125 Query: 125 DHFRYFAGVLRAQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAG 184 DHFRYFAGV+RA+EGSI+++D TV+ + EP+G+VGQIIPWNFP+LMA WK+APA+AAG Sbjct: 126 DHFRYFAGVIRAEEGSIAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAG 185 Query: 185 NCVVLKPAEQTPAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGET 244 C ++KPAEQTPA IM+ +IGDLLP GVLN+VNGFG EAGKPLA S R+ K+AFTGET Sbjct: 186 CCTIVKPAEQTPASIMILMEVIGDLLPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGET 245 Query: 245 TTGRLIMQYASENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCT 304 TTGRLIMQYASENL PVT+ELGGKSPN+FF V DD+F DK LEG MFALNQGEVCT Sbjct: 246 TTGRLIMQYASENLNPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCT 305 Query: 305 CPSRVLIQESIYDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKE 364 CPSR+L+ E IYD FME+ + R +AI+ G P + TM+GAQAS +Q EKILSY+DIGK+E Sbjct: 306 CPSRILVHEKIYDAFMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQE 365 Query: 365 GAEVLTGGKAADLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEI 424 GAEVLTGG+ A L L GYY++PT+ +G+NKMR+FQEEIFGPV SV TFKD EA+ I Sbjct: 366 GAEVLTGGEVAKLNSGLENGYYVKPTLLKGHNKMRVFQEEIFGPVCSVATFKDVEEAISI 425 Query: 425 ANDTLYGLGAGVWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHK 484 +NDTLYGLGAGVW+RDA+ Y++ R IKAGRVW NCYHAYPAHA FGGYK+SG GRETH Sbjct: 426 SNDTLYGLGAGVWTRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHL 485 Query: 485 MMLDHYQQTKNMLVSYSPKKLGFF 508 MML+HY+Q KNML+SY KLGFF Sbjct: 486 MMLNHYRQNKNMLISYDKNKLGFF 509 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: 831 Number of extensions: 28 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: 509 Length adjustment: 34 Effective length of query: 474 Effective length of database: 475 Effective search space: 225150 Effective search space used: 225150 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