Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_157063607.1 VV02_RS11195 aldehyde dehydrogenase family protein
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_001190945.1:WP_157063607.1 Length = 486 Score = 422 bits (1086), Expect = e-122 Identities = 228/480 (47%), Positives = 305/480 (63%), Gaps = 10/480 (2%) Query: 41 DLHADLLRGDSFVGGRW--LPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFS 98 D+H +LL +GG+W + ATF V DP++GA L VAD + + A+ AA +A + Sbjct: 11 DVHKELL-----IGGQWSAADSDATFEVLDPSTGAVLAEVADASPADGQRALDAAVEAQA 65 Query: 99 SWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEE 158 ++ + +ER +L K Y L+ + D+LA ++T E GKPL EA+GEI Y+A F F+ E Sbjct: 66 AFAATTPRERYDILMKAYGLLHERIDDLALLMTLEMGKPLAEAKGEITYAAEFFRHFAFE 125 Query: 159 ARRVYGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPA 218 A R+ G A R L+ KQPVG +ITPWNFP AM TRK+G A+AAGCT V+KPA Sbjct: 126 ALRIDGGYQTAPAGGARFLISKQPVGPCLLITPWNFPMAMGTRKIGPAIAAGCTSVIKPA 185 Query: 219 EDTPYSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGK 278 TP S LAL + +AG+P GV N++ C A +V E L K+SFTGST GK Sbjct: 186 HQTPLSMLALGAILTEAGVPDGVVNIVTC--MNAGDVMEPLIKSGKARKLSFTGSTKVGK 243 Query: 279 ILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQR 338 +LL A+ V R SMELGG APFIVF+ A++D+AV GAMA+K RN G+ C +NR V Sbjct: 244 VLLEQCADKVLRTSMELGGNAPFIVFEDADMDEAVKGAMAAKMRNMGEACTAANRIFVHE 303 Query: 339 GIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGG 398 + D F + ++AM + L+VG G E+G GPLI+E +KV + DA A+GATV+TGG Sbjct: 304 NVIDEFGKRLSQAMSE-LKVGRGTEDGVQVGPLIDEAGRQKVIDLLEDATARGATVLTGG 362 Query: 399 KRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYF 458 G FF PT+L+ V D +EE FGPVAP+ F E+E VA AN GL Y Sbjct: 363 DAPDGDGFFFTPTVLTGVPHDARMTSEEIFGPVAPLTPFTTEKEVVAAANDTPYGLVSYV 422 Query: 459 YSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518 ++ D + RVAE +E GMVG+N+G++S+ PFGG+K+SGLGREG GIDE+LEVKY+ Sbjct: 423 FTNDLRRALRVAEAIESGMVGLNQGVVSNPAAPFGGIKESGLGREGGSVGIDEFLEVKYI 482 Lambda K H 0.318 0.135 0.400 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: 649 Number of extensions: 24 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: 523 Length of database: 486 Length adjustment: 34 Effective length of query: 489 Effective length of database: 452 Effective search space: 221028 Effective search space used: 221028 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