Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011423489.1 RHE_RS00470 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000092045.1:WP_011423489.1 Length = 494 Score = 543 bits (1398), Expect = e-159 Identities = 270/481 (56%), Positives = 345/481 (71%), Gaps = 6/481 (1%) Query: 46 LLRGDSFVGGRWLPTPA---TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102 LLR ++ G W P A TF V +PA+G L ++ D G E RAA+ AAY A +W Sbjct: 17 LLRDAGYINGVWTPGDAAAKTFDVLNPATGELLASLPDMGAAETRAAIDAAYAAQPAWAA 76 Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162 KERS +LRKW+DL++ N D LA I+TAE GKP EA+GEILY+A ++EW++EEA+R+ Sbjct: 77 RPAKERSQILRKWFDLIVANADALAAILTAEMGKPFPEARGEILYAAAYIEWYAEEAKRI 136 Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222 YG+ I ++DKR +V+KQPVGV ITPWNFP+AMI RK+ ALA GCTVV KPAE TP Sbjct: 137 YGETIPAPSQDKRMIVIKQPVGVVGTITPWNFPAAMIARKIAPALAVGCTVVSKPAEQTP 196 Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282 +A+ALA LA QAGIP GV+N+I +G LC + V KISFTGST G+IL+ Sbjct: 197 LTAIALAVLAEQAGIPAGVFNLI--VGLDGPAIGRELCGNDKVRKISFTGSTEVGRILMR 254 Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342 A+ +K+VS+ELGG APFIVFD A++D AV GA+ASK+RNAGQTCVC+NR +Q G++D Sbjct: 255 QCADQIKKVSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRLYIQSGVYD 314 Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402 +F K A A + VG+GF G GPLI+E+ + KVE HV DAVAKGA ++TGGKR Sbjct: 315 AFAAKLA-AKVADMSVGDGFRPGVEIGPLIDEQGLAKVEDHVGDAVAKGAKILTGGKRID 373 Query: 403 SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQD 462 G FF PT+L+ VTRDM EETFGPVAP+ +F+ E+ + AN + GLA YFY+ D Sbjct: 374 GAGTFFAPTVLTGVTRDMTVAREETFGPVAPLFRFETAEDVITQANDTEFGLAAYFYAGD 433 Query: 463 PAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGG 522 ++WRVAE LE GMVG+N GL+SS PFGG+KQSGLGREGS++G D+YLE+KY+C GG Sbjct: 434 LKKVWRVAEALEYGMVGINTGLMSSEMAPFGGIKQSGLGREGSRHGADDYLEMKYLCIGG 493 Query: 523 L 523 L Sbjct: 494 L 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: 685 Number of extensions: 27 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: 494 Length adjustment: 34 Effective length of query: 489 Effective length of database: 460 Effective search space: 224940 Effective search space used: 224940 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