Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011427659.1 RHE_RS23010 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000092045.1:WP_011427659.1 Length = 484 Score = 511 bits (1315), Expect = e-149 Identities = 254/473 (53%), Positives = 339/473 (71%), Gaps = 6/473 (1%) Query: 53 VGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSS 110 + RW+ A+ V +PA+G LG+V D G E A+ AA A W + + ER++ Sbjct: 15 IADRWIEAEGRASAMVRNPATGEVLGSVPDFGAAETEEAIAAAVVAQKLWAKKTAGERAT 74 Query: 111 LLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTS 170 +L+ W+ LMI+N+D+LA I+T E GKPL EA+GEI Y A F+EWF+EEARR+ G+I+ Sbjct: 75 VLKTWHRLMIENRDDLAMILTLEQGKPLAEAKGEITYGASFIEWFAEEARRINGEIVPGH 134 Query: 171 AKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQ 230 DKR LVL+QP GV + ITPWNFP+AMITRK+G ALAAGC VV+KPA TP+SA+A+A Sbjct: 135 QPDKRILVLRQPAGVVAAITPWNFPNAMITRKIGPALAAGCAVVLKPALQTPFSAIAIAV 194 Query: 231 LANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKR 290 LA +AG+P G+ N++ A +G L V ++FTGST TG++L A ++K+ Sbjct: 195 LAERAGLPAGLLNIVTGD---AAAIGGALTASRDVRVLTFTGSTRTGELLYRQCAPTIKK 251 Query: 291 VSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAE 350 + +ELGG APFIVFD A++D AV GA+ +KFRN GQTCVC+NR VQ G++++F K AE Sbjct: 252 LGLELGGNAPFIVFDDADLDAAVEGAIIAKFRNNGQTCVCANRLYVQDGVYEAFAAKLAE 311 Query: 351 AMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFEP 410 A+ K L+VGNG E GPLI++ AV KVE H+ DAVAKGA +VTGGKRH GG+FFEP Sbjct: 312 AVSK-LKVGNGLERDVVLGPLIDDNAVAKVESHIQDAVAKGAGIVTGGKRHALGGHFFEP 370 Query: 411 TLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRVA 470 T+L +V M EETFGP+AP+ +F E++ + AN + GLA YFY++D ++++RVA Sbjct: 371 TILRDVAAGMQVAREETFGPLAPLFRFRDEQDVIEQANDTEFGLASYFYARDLSRVFRVA 430 Query: 471 EQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 E LE GMVGVN GL+S+ E PFGGVK SGLGREGS++G+DEY E+KYVC GG+ Sbjct: 431 EALEYGMVGVNTGLVSTAEAPFGGVKMSGLGREGSRHGLDEYTELKYVCLGGI 483 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: 629 Number of extensions: 22 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: 484 Length adjustment: 34 Effective length of query: 489 Effective length of database: 450 Effective search space: 220050 Effective search space used: 220050 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