Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_097070256.1 CRO22_RS11275 aldehyde dehydrogenase EutE
Query= BRENDA::B0K315 (466 letters) >NCBI__GCF_900217815.1:WP_097070256.1 Length = 533 Score = 452 bits (1163), Expect = e-131 Identities = 230/435 (52%), Positives = 301/435 (69%), Gaps = 4/435 (0%) Query: 35 GIFNDVNEAVECAKEAQKKFALMDLEKREEIIAAIREACVNNARL--LAEIACSETGRGR 92 GIF ++ A+ A EAQKK+ + R+ + IR + A L ++ + +TG G Sbjct: 98 GIFETMDAAINAAAEAQKKYLFCSMADRKRFVDGIRSIFTDPAILERISRLTVEQTGMGN 157 Query: 93 VEDKVAKNILAAKKTPGTEDLKPTAWTGDRGLTLVEMAPVGVIASITPVTNPTATIINNT 152 VE K+ KN LAA+ +PG EDL A +GD GLTLVE++P GVI +ITP TNPT TII N Sbjct: 158 VEHKIIKNRLAAENSPGIEDLVTEAQSGDDGLTLVELSPYGVIGAITPTTNPTETIICNG 217 Query: 153 ISMLAAGNAVVFNPHPSAKKTSNKAVEIINEAILKVGAPNGLVCSINNPTIQTAQKLMEH 212 I MLAAGNA VF+PHP A+ S A+++IN + +GAP LV ++ P+I+ +M H Sbjct: 218 IGMLAAGNAAVFSPHPRARGVSLLAIKLINRKLAALGAPANLVVTVQAPSIENTNAMMAH 277 Query: 213 PEVNMVVVTGGKAVVQTALRCGKKVIGAGAGNPPVVVDETADIVKAAHDIACGASFDNNL 272 P+V M+V TGG A+V+T + GKK IGAGAGNPPVVVDETADI KAA DI GASFD+N+ Sbjct: 278 PKVRMLVATGGPAIVRTVMSTGKKAIGAGAGNPPVVVDETADIPKAALDIVNGASFDHNM 337 Query: 273 PCIAEKEIIAVERIADTLLERMKREGAYVLHGKDIDRMTE--LIFQGGAINKDLIGRDAH 330 PCIAEKE I V ++AD L+ M R GAY++ + E ++ + G D +G+ A Sbjct: 338 PCIAEKEAIVVTQVADFLISEMCRNGAYLVKDPAVIAKLEARVLTEKGGPKTDCVGKSAV 397 Query: 331 FILSQIGIETGKDIRLVVMPVDVSHPLVYHEQLMPVIPFVTVPTVEEAINLAVKAEGGNR 390 ++L Q+G++ G ++RLV+M HP V E +MP++P V VP V+EAI+LAV E GNR Sbjct: 398 WLLDQVGVKVGPEVRLVLMEATKDHPFVQEELMMPILPLVRVPDVDEAIDLAVDLEHGNR 457 Query: 391 HTAMMHSKNVENMTAFARAIQTTIFVKNAPSYAGIGFGGEGYTTFTIAGPTGEGLTSART 450 HTA+MHS NV +T A+ IQTTIFVKN PSYAGIG GGEGYTTFTIAGPTGEGLTSAR+ Sbjct: 458 HTAIMHSTNVRKLTKMAKLIQTTIFVKNGPSYAGIGVGGEGYTTFTIAGPTGEGLTSARS 517 Query: 451 FTRQRRCVLVDAFRI 465 F R+R+CV+V+A + Sbjct: 518 FARRRKCVMVEALNV 532 Lambda K H 0.317 0.133 0.377 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: 630 Number of extensions: 26 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: 466 Length of database: 533 Length adjustment: 34 Effective length of query: 432 Effective length of database: 499 Effective search space: 215568 Effective search space used: 215568 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 24 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