Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_015446415.1 R2APBS1_RS00470 aldehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >NCBI__GCF_000230695.2:WP_015446415.1 Length = 496 Score = 262 bits (670), Expect = 2e-74 Identities = 159/467 (34%), Positives = 258/467 (55%), Gaps = 21/467 (4%) Query: 29 DPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSLVLNRLADVLEQSLEELA 88 DP TG+ +P + ++++ A AA A AW++ +P ER+LV++ V ++ EE+ Sbjct: 36 DPYTGDTLVTIPLAATQDVDDAYLAAGAAQAAWAATAPAERALVMHNAVRVFDERREEIL 95 Query: 89 QAESKDQGKTLTLART-MDIPRSVLNFRFFASSNLHHVSECTQMSHL-GCMHYTVRTPVG 146 ++ G T A D R+V A+S + V+ S + G + R +G Sbjct: 96 SWLIREAGSTRLKANIECDSARAVT---LEAASFPYRVAGRILASDIPGKENRVYRRALG 152 Query: 147 IAGLISPWNLPLYLLTWKIAPAIAA--GNTVIAKPSEMTSVTAWMF-CKLLDKAGVPPGV 203 + G+ISPWN PL+L +APA+A GN V+ KP+ T V+ + K+ ++AG+PPGV Sbjct: 153 VIGIISPWNFPLHLTQRSLAPALALALGNAVVVKPASDTPVSGGLLLAKIFEEAGLPPGV 212 Query: 204 INIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQL--SAPHCKKLSLELGGKNPAI 261 +N++ G G +G+ V+HP+ LISFTGS + I +L S H K+++LELGG +P + Sbjct: 213 LNVIVGAGSEIGDYFVAHPQPRLISFTGSTAVGQGIGRLASSGTHLKRVALELGGNSPFV 272 Query: 262 IFEDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSD 321 + DA++E+ A V F +QG+IC+ +RI V ++ F+KRFV TR +VG P+D Sbjct: 273 VLGDADVEQAARAAVFGRFLHQGQICMSVNRIIVDAQLHDAFVKRFVARTRTLQVGDPND 332 Query: 322 PSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPTVITDI 381 + +G +I A L + + A+ +GA L G D LP P V TD+ Sbjct: 333 IATAIGPIIDAAQLRGIVEKIALAKQQGATELLGGEADGQLLP----------PHVFTDV 382 Query: 382 KDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSG 441 +S +E FGP+ +V E + + AN+ YGL++ V+ D+ R R A+++++G Sbjct: 383 PADSSLFRDESFGPIVPIVRAKDEADALRLANATGYGLSSAVFCGDIDRGVRFAQRIEAG 442 Query: 442 LVWTNCWLIR-ELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITIKY 487 + N + E ++PFGG K+SGIGR G + D FT I++++ Sbjct: 443 MTHVNDMSVNDEPHVPFGGEKNSGIGRFGGEWIIDEFTAAHWISVQH 489 Lambda K H 0.319 0.134 0.404 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: 513 Number of extensions: 20 Number of successful extensions: 7 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: 487 Length of database: 496 Length adjustment: 34 Effective length of query: 453 Effective length of database: 462 Effective search space: 209286 Effective search space used: 209286 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 (21.8 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