Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011782022.1 MVAN_RS24505 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000015305.1:WP_011782022.1 Length = 482 Score = 406 bits (1044), Expect = e-118 Identities = 216/467 (46%), Positives = 288/467 (61%), Gaps = 3/467 (0%) Query: 52 FVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEISVKERSSL 111 ++GG +TF V DP+ L TVAD +AR A+ AA W ++R + Sbjct: 15 WIGGEERQGTSTFSVLDPSDDEVLATVADATADDARDALDAACAVQGEWAATPARKRGEI 74 Query: 112 LRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVYGDIIYTSA 171 LR ++ + D++A ++T E GK E++GE+ Y A F WF+EEA R+ G A Sbjct: 75 LRSVFETITARADDIAALMTLEMGKVFAESKGEVTYGAEFFRWFAEEAVRIEGRYTPAPA 134 Query: 172 KDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPYSALALAQL 231 R LV KQ VG ITPWNFP AM TRK+G A AAGCT++VKPA++TP + L LA+L Sbjct: 135 GTGRILVTKQAVGPCYAITPWNFPLAMGTRKMGPAFAAGCTMIVKPAQETPLTMLLLAKL 194 Query: 232 ANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHHAANSVKRV 291 +AG+P GV +V+P S A V E L D + K++FTGST GK L+ +A+ + R Sbjct: 195 MAEAGLPKGVLSVLPTSNPGA--VTEALINDGRLRKLTFTGSTGVGKALVKQSADKLLRT 252 Query: 292 SMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDSFVTKFAEA 351 SMELGG APFIVFD A+VD AV GA+ +K RN G+ C +NR V + + F KF + Sbjct: 253 SMELGGNAPFIVFDDADVDAAVDGAILAKMRNGGEACTAANRIHVANAVREEFTEKFVKR 312 Query: 352 MKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQSGGNFFEPT 411 M + +G G +E +T GPLIN K V V + V+DAV++GATV GG GNF+ T Sbjct: 313 MSE-FTLGKGLDEKSTLGPLINAKQVATVTELVSDAVSRGATVAVGGVAPGGPGNFYPAT 371 Query: 412 LLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDPAQIWRVAE 471 +L++V D + EE FGPVAP+ FD EEE +A AN + GLA Y Y+Q + RVAE Sbjct: 372 VLTDVPADARILKEEVFGPVAPIAGFDTEEEGIAAANDTEYGLAAYVYTQSLDRALRVAE 431 Query: 472 QLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518 +E GMVGVN G+IS PFGG+K+SG GREG GI+EYL+ KY+ Sbjct: 432 NIESGMVGVNRGVISDAAAPFGGIKESGFGREGGTEGIEEYLDTKYI 478 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: 587 Number of extensions: 21 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: 482 Length adjustment: 34 Effective length of query: 489 Effective length of database: 448 Effective search space: 219072 Effective search space used: 219072 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