Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4184 Length = 498 Score = 554 bits (1427), Expect = e-162 Identities = 271/480 (56%), Positives = 356/480 (74%), Gaps = 3/480 (0%) Query: 46 LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105 LL+ D + G+W+ + F V DPA+G KL VA+ G +A AA+ AA A+ WK + Sbjct: 16 LLKTDGLINGQWVVGSSRFDVNDPATGLKLADVANLGPADAEAAIAAANAAWGPWKTKTA 75 Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165 KERS +LRKW+DL++ N+D+L +I+TAE GKPL EA+GE+ Y A F+EWF+EEA+R+ G+ Sbjct: 76 KERSIILRKWFDLLMANQDDLGRIMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRINGE 135 Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225 + ++R +VLKQP+GV + ITPWNFP AMITRKV ALAAGC VV+KPAE TP +A Sbjct: 136 TLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPAELTPLTA 195 Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285 LA A+LA +AGIP GV+N++P + +G+VLC +V ISFTGST G+IL+ +A Sbjct: 196 LAAAELAIRAGIPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVGRILMAQSA 255 Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345 +VK++S+ELGG APFIVFD A++D AV GA ASK+RNAGQTCVC+NRF VQ G++D FV Sbjct: 256 PTVKKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQEGVYDEFV 315 Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS-- 403 KFA A K+ +VGNGFE G QGPLI E A+ KV++HV+DA+AKG VV GG+R + Sbjct: 316 AKFA-AKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGGQRLTALG 374 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 G FFEPT+++N T DMLC EETFGP APV KF E+EA+ AN + GLA YFYS+D Sbjct: 375 SGQFFEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLASYFYSRDV 434 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 +I+RV E LE GMVG N G++++ PFGGVKQSGLGREGS +G+D+Y+E+KY+C G + Sbjct: 435 GRIFRVTEALEYGMVGANVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIKYLCLGDI 494 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: 668 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: 523 Length of database: 498 Length adjustment: 34 Effective length of query: 489 Effective length of database: 464 Effective search space: 226896 Effective search space used: 226896 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 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