Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_092344789.1 BLU87_RS03510 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::A6T8Z5 (462 letters) >NCBI__GCF_900107645.1:WP_092344789.1 Length = 452 Score = 414 bits (1063), Expect = e-120 Identities = 215/448 (47%), Positives = 285/448 (63%), Gaps = 2/448 (0%) Query: 11 SVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALRARGEE 70 S+NP TGEV+ + S+ +V I Y+ WR T A+R L + LR R +E Sbjct: 5 SLNPATGEVLETFDEWSDEQVATTIEAVHGAYQNWRTTSFAERKSLLLKAAVILRQRKDE 64 Query: 71 VAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEYRPLGAI 130 A M+ LEMGKP+ + R E+ K A +C++YAE+ MLA E + +++ + +RP G + Sbjct: 65 FATMMALEMGKPVVEGRAEIEKCALVCNYYAENAEQMLAPEPIASDASRSYVAFRPQGIV 124 Query: 131 LAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGVFGWVN 190 LAVMPWNFP WQV R A P L+AGN +LKHA NV A + ++F AG P VF + Sbjct: 125 LAVMPWNFPFWQVFRFAAPALMAGNVGVLKHASNVPRCALAIEQVFVEAGYPADVFRTLM 184 Query: 191 ATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLNDADLD 250 + V+Q+I + A T+TGS AG+ + ++GA LKK V+ELGGSDPFIVLNDADLD Sbjct: 185 IGSGKVAQVIEHPYVVATTLTGSDIAGRKVAEKSGAMLKKSVMELGGSDPFIVLNDADLD 244 Query: 251 EAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQNYVGPM 310 A AVT R NSGQ C A+KRFI+E GI E F KF +AALKMGDP DE VGP Sbjct: 245 LAASVAVTARCINSGQSCIAAKRFIVEDGIYETFLEKFKANMAALKMGDPCDETTQVGPQ 304 Query: 311 ARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQELFGPV 370 AR DL ELH+QV ++ +GA ++LG + G +Y PT+L V+ GM + +E FGPV Sbjct: 305 AREDLMRELHRQVEGSVAKGAKVILGG--MPGEAAFYPPTILTQVSKGMPAYNEEFFGPV 362 Query: 371 ATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCASDARVA 430 A + +DA+ AL +AND+EFGL +V+T D + ++ A E+ G VF+N SD R+ Sbjct: 363 AIVIRVKDAEEALFVANDTEFGLGGSVWTRDIIKGEKIAGEIRSGAVFVNSMTKSDPRLP 422 Query: 431 FGGVKKSGFGRELSHFGLHEFCNAQTVW 458 FGGV SGFGRELSH+G+ EF N QTVW Sbjct: 423 FGGVGISGFGRELSHYGIKEFVNIQTVW 450 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: 510 Number of extensions: 14 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: 452 Length adjustment: 33 Effective length of query: 429 Effective length of database: 419 Effective search space: 179751 Effective search space used: 179751 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