Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_008534338.1 RHE_RS29885 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000092045.1:WP_008534338.1 Length = 495 Score = 522 bits (1344), Expect = e-152 Identities = 262/481 (54%), Positives = 341/481 (70%), Gaps = 6/481 (1%) Query: 46 LLRGDSFVGGRWLPTPAT---FPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102 L+R VGG+W V +P++ L ++ G+ E RA++ AA A W + Sbjct: 16 LVREQMLVGGKWSSEGVNGTRINVLNPSTMDVLASLPSAGLAEVRASIDAAKAAQKKWAK 75 Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162 +S KERS ++RK+Y+ ++ N ++LA I+T+E GKPL EA+GEI Y A ++EWF EEA+RV Sbjct: 76 VSAKERSLIMRKFYEEVVANAEDLAVILTSEMGKPLAEARGEIAYGASYIEWFGEEAKRV 135 Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222 YGD I DKR LV+KQPVGV + I PWNFPSAM+ RK+ ALA+GC +V KPA +TP Sbjct: 136 YGDTIPGHQADKRLLVIKQPVGVVAAIAPWNFPSAMVCRKIAPALASGCAIVFKPAAETP 195 Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282 SALALA LA +AGIP G+++V+P A+ GE +C++P+V K++FTGST G+IL+ Sbjct: 196 LSALALAILAERAGIPDGLFSVLPTDN--ARMFGEEVCSNPVVKKLTFTGSTEVGRILMA 253 Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342 A + ++S+ELGG APFIVFD A++DQAV GAM SKFRNAGQTCVC+NR VQ GIHD Sbjct: 254 QGAQKIMKLSLELGGNAPFIVFDDADLDQAVEGAMLSKFRNAGQTCVCANRIYVQSGIHD 313 Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402 FV K A + +L+V +GFE G T GPLIN++AV K+ H++DAV KGATVV GG R Sbjct: 314 RFVEKLAMRVS-ALQVLDGFESGATIGPLINDEAVAKLYGHIDDAVTKGATVVVGGDRDA 372 Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462 GG F +PTLLS T+DM EETF P+APV KFD EE + +AN + GLA YF++ D Sbjct: 373 RGGTFVQPTLLSGATKDMKVAREETFAPLAPVFKFDTVEEVIELANDTEFGLAAYFFAND 432 Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522 +W+V E LE GMVGVN GLIS+ PFGGVKQSG GREGSKYG+D++L +KYVC GG Sbjct: 433 LRNVWKVTEALEYGMVGVNTGLISTELAPFGGVKQSGFGREGSKYGMDDFLSMKYVCMGG 492 Query: 523 L 523 + Sbjct: 493 I 493 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: 652 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: 495 Length adjustment: 34 Effective length of query: 489 Effective length of database: 461 Effective search space: 225429 Effective search space used: 225429 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 Apr 09 2024. 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