Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_007474687.1 CMTB2_RS05650 aldehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000170735.1:WP_007474687.1 Length = 491 Score = 257 bits (656), Expect = 8e-73 Identities = 160/446 (35%), Positives = 240/446 (53%), Gaps = 20/446 (4%) Query: 81 CGVPEARAAVRAAYDAFSSWKEISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKE 140 C + +A+ A+ A +AF + K+ ++ +R + + + + K+E AK IT E KP+ Sbjct: 55 CNIEDAKRALEVAKNAFENTKKSTLAQRIAWIEDVAKKLQEKKEEFAKYITLEVAKPISH 114 Query: 141 AQGEILYSAFFLEWFSEEARRVYGDIIYTSAK----DKRGLVLKQPVGVASIITPWNFPS 196 A+ E+ L+ + E + G+ I T A + P GV ITP+NFP Sbjct: 115 ARVEVERCIENLKICAAEGYHILGETIPTDATFTGAKTTAFYKRVPAGVVVAITPFNFPL 174 Query: 197 AMITRKVGAALAAGCTVVVKPAEDTPYSALALAQL--ANQAGIPPGVYNVIPCSRTKAKE 254 ++ K+G AL AG +VV+KP + PY+A A A+L ++ IP + V + + Sbjct: 175 NLVAHKLGPALIAGNSVVLKPTPEAPYTAYAFAKLFIESEYAIPNALSVVYGDA-----D 229 Query: 255 VGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRVSMELGGLAPFIVFDSANVDQAVA 314 VG L T P+ ISFTGS A GKI+ A +K+VS+ELGG A + SAN+D A + Sbjct: 230 VGSTLVTSPIPRVISFTGSVAVGKIITQSA--GIKKVSLELGGNAATFIESSANLDYAAS 287 Query: 315 GAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAEAMKKSLRVGNGFEEGTTQGPLINE 374 F N+GQ C+ R V +++ F K + K L+VGN FEE T GPLINE Sbjct: 288 RCAVGAFANSGQVCISLQRIYVDEKVYEEFAKKLGDEASK-LKVGNPFEEDTFMGPLINE 346 Query: 375 KAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFEPTLLSNVTRDMLCITEETFGPVAPV 434 +A + E + AV++GA ++ GGKR GN PT+L++VT DM + EE F P+ + Sbjct: 347 EAAIRAENWIKSAVSEGARIIAGGKRE---GNILYPTILADVTDDMKIVCEEVFAPIVSL 403 Query: 435 IKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRVAEQLEVGMVGVNE--GLISSVECPF 492 +K EEAV N + GL +S + R E E G V +N+ L ++ P+ Sbjct: 404 VKVRGYEEAVEKMNNSPYGLQYSMFSNRVDLMNRAIEDFEAGGVIINDIPTLRFDIQ-PY 462 Query: 493 GGVKQSGLGREGSKYGIDEYLEVKYV 518 GG+K SG+GREG K+ I+E E+K + Sbjct: 463 GGIKLSGIGREGPKFAIEEMTEIKSI 488 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: 539 Number of extensions: 22 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: 523 Length of database: 491 Length adjustment: 34 Effective length of query: 489 Effective length of database: 457 Effective search space: 223473 Effective search space used: 223473 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