Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_059152522.1 V474_RS16500 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >NCBI__GCF_001046635.1:WP_059152522.1 Length = 472 Score = 519 bits (1337), Expect = e-152 Identities = 256/454 (56%), Positives = 326/454 (71%), Gaps = 1/454 (0%) Query: 6 ATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALR 65 A+ VS NP TGE +++ P+ + EV+A + +A +R WR TP+ R A RR+ LR Sbjct: 14 ASGGVSRNPATGETIATYPYQTVDEVEATMQASAEAFRVWRDTPMEQRVAAYRRLAETLR 73 Query: 66 ARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAV-IEY 124 R + +A +IT EMGK I AR E+ KSA DW AEHGPA+LA E V+ + V + Y Sbjct: 74 ERSDTLAALITAEMGKTIGAARSEIEKSAGTLDWLAEHGPAILADEPVSVDGDDEVHVSY 133 Query: 125 RPLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDG 184 P+G IL VMPWN P+WQV+R + PI+L+GN +LLKHAPNVMGSA L + + A+G P G Sbjct: 134 LPIGTILGVMPWNLPIWQVIRASGPIMLSGNGFLLKHAPNVMGSAYALQQAYEASGFPKG 193 Query: 185 VFGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVL 244 +FG +N N+ V+++I D RIAAVT+TGS+RAG A+ A A ALKK +LELGGSD FIVL Sbjct: 194 LFGNLNTDNETVARVIEDPRIAAVTLTGSMRAGAAVAATAARALKKSLLELGGSDAFIVL 253 Query: 245 NDADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQ 304 DA+LD AV A + R+ NSGQVC A+KRF+LE IA+ FTRKFV+A + LK+GDP D Sbjct: 254 ADANLDLAVAAGIQARFGNSGQVCLAAKRFLLERPIAQEFTRKFVEAASKLKVGDPLDAS 313 Query: 305 NYVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQ 364 +GPMAR DLRDELH+QV TL +GA LLLG +K+EG GN+YAPTVL +V GM F + Sbjct: 314 TALGPMARHDLRDELHEQVERTLAQGAKLLLGGQKVEGPGNFYAPTVLADVAPGMAAFEE 373 Query: 365 ELFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCA 424 E FGPVA +T D +HA+AL N SE+GL +++T D A+AQR AR LE GGVF+NG+ A Sbjct: 374 ETFGPVAAITMVEDVEHAIALTNASEYGLGGSLWTADTARAQRIARRLETGGVFINGFSA 433 Query: 425 SDARVAFGGVKKSGFGRELSHFGLHEFCNAQTVW 458 S+ R+ GGVKKSG+GRELSHFGL EF N Q VW Sbjct: 434 SNPRIPVGGVKKSGYGRELSHFGLREFTNPQAVW 467 Lambda K H 0.319 0.133 0.392 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: 575 Number of extensions: 22 Number of successful extensions: 2 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: 462 Length of database: 472 Length adjustment: 33 Effective length of query: 429 Effective length of database: 439 Effective search space: 188331 Effective search space used: 188331 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 (21.8 bits) S2: 51 (24.3 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