Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_047007132.1 AAW01_RS09770 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_001010925.1:WP_047007132.1 Length = 476 Score = 325 bits (832), Expect = 3e-93 Identities = 180/464 (38%), Positives = 268/464 (57%), Gaps = 9/464 (1%) Query: 46 LLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISV 105 L+ G+ GG T V +PA+ LGT+ + A+ AA F W+ S Sbjct: 10 LIAGEKVTGGG----RDTEEVINPATEEVLGTLPHATSDDLDRALDAAQSGFREWRSTSA 65 Query: 106 KERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGD 165 +R+++L +L+ + K+++A +T E GKPL + +GE +YSA LE++++EA+R YG Sbjct: 66 DKRATILTNAANLIRERKEDIAGWLTREQGKPLGDGRGEAMYSANLLEFYAQEAKRTYGR 125 Query: 166 IIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSA 225 + + R V PVG + PWNFP+ + RK+G ALAAGC+V+VKP+E+TP + Sbjct: 126 TL-VRGEGSRVEVQYHPVGPVAGFAPWNFPAINVMRKIGGALAAGCSVIVKPSEETPAAG 184 Query: 226 LALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAA 285 +AL Q AG+P G + C V E L P++ K++FTGST GK L AA Sbjct: 185 IALVQALLDAGVPGGA---VQCVFGVPSNVSEHLLASPIIRKLTFTGSTPVGKHLAKLAA 241 Query: 286 NSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFV 345 + +K +MELGG P +VFD +VD+AV +K+RNAGQ CV RFL++ I + F Sbjct: 242 DDLKITTMELGGHGPVLVFDDCDVDKAVKTMAGNKYRNAGQVCVSPIRFLIEESIFEQFR 301 Query: 346 TKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGG 405 F E +K +RVGNG E+GT GP+ N + E ++K + +A GA ++TGG+ + G Sbjct: 302 DSFVERAEK-VRVGNGLEDGTDMGPMANARGRENIQKLIANAKEAGANLLTGGEVIGNQG 360 Query: 406 NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQ 465 F +PT+LS V + E FGPVA + E+ + AN GLA Y ++ D A+ Sbjct: 361 FFHQPTVLSEVPTSADIMNNEPFGPVAILNPMSGEDAMIEEANRLPYGLAAYAWTDDAAR 420 Query: 466 IWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGI 509 R+A ++E GM+ +N G +S+V+ PFGGVK SG G E + G+ Sbjct: 421 RRRLAAEVEAGMLAINGGSVSTVDAPFGGVKWSGYGSEDGREGV 464 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: 607 Number of extensions: 23 Number of successful extensions: 4 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: 476 Length adjustment: 34 Effective length of query: 489 Effective length of database: 442 Effective search space: 216138 Effective search space used: 216138 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