Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 213 bits (541), Expect = 2e-59 Identities = 155/464 (33%), Positives = 234/464 (50%), Gaps = 13/464 (2%) Query: 4 WINGDWITGQGASRVK-RNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62 +ING W+ Q R+ NP G ++ + AA+ QA AA A+ W + ER Sbjct: 15 YINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAKTAKERS 74 Query: 63 AVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIA-ISIKAYHVRTGEQRS 121 AV+ R+ L+ + + +L ++ E GKP EA EV + + + +A V Sbjct: 75 AVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRVYGDTIPE 134 Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181 MP + P GV+A P+NFP + PAL AG ++ KP+E TP S A+ Sbjct: 135 HMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 194 Query: 182 RLWQQAGLPPGVLNLVQGG--RETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKI 239 L ++AG PPGV N++ G + G L+A + L FTGS G L Q + +K Sbjct: 195 ELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMAQCAATVKK- 253 Query: 240 LALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARL- 298 L+LE+GGN P ++ + AD+DAAV + S + GQ C CA RLL++ G DAF ARL Sbjct: 254 LSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIY-DAFTARLA 312 Query: 299 -VAVSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSL 357 + ++ PG D Q G LI+E+A ++V A G R ++ + G + Sbjct: 313 EAVAALKVGPGLEGDFQQ---GPLINEEAVRKVERHIADAVAKGARVVMGGKRHARGGTF 369 Query: 358 LTPGII-EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFD 416 P I+ ++T EE FGP+ ++R+ T +EA+RMAN+T FGL+ S + + Sbjct: 370 FEPTILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVGRVW 429 Query: 417 QLLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460 ++ GIV N+ L + APFGG+ SG R + Y + Sbjct: 430 RVSRALEYGIVGINEGLI-STEVAPFGGVKESGLGREGSKYGIE 472 Lambda K H 0.318 0.134 0.412 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: 577 Number of extensions: 22 Number of successful extensions: 5 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: 492 Length of database: 485 Length adjustment: 34 Effective length of query: 458 Effective length of database: 451 Effective search space: 206558 Effective search space used: 206558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 17 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