Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_014266126.1 ACIX8_RS14625 SDR family oxidoreductase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >NCBI__GCF_000178955.2:WP_014266126.1 Length = 255 Score = 132 bits (331), Expect = 1e-35 Identities = 86/251 (34%), Positives = 133/251 (52%), Gaps = 8/251 (3%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQ-GADVVAIKA 77 LK K ++TGAA GIG AI FA+ QA +V+ D+ +K A E+ A I Sbjct: 4 LKGKRAVVTGAASGIGLAIAELFAAHQADVVLLDLDAQKTAGAAKAIAEKTSASATGIAC 63 Query: 78 DVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGC 137 DVSR ++A + G++D+LVNCAG+ + L T ED R +++++ G + Sbjct: 64 DVSRAD---SVAEAFSQAGGQLDILVNCAGIAHVGNLLSTTPEDMDRLYSVNVRGTYLCM 120 Query: 138 KAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNA 197 +A + M+E G I+N+AS +T + F Y + K +L +T + +Y +GIR N Sbjct: 121 QAAIKPMLEAKHGVILNLASIAATAGLTDRFAYSMTKGAVLSMTLSAAKDYISQGIRCNC 180 Query: 198 IAPGYIETQLNVDYW--NGFADPHAERQRAF-DLHPPRRIGQPIEVAMTAVFLASDEAPF 254 I+P + T VD + + AE+ +A P R+G P E+A+ A++L SDEA F Sbjct: 181 ISPARVHTPF-VDGFLAKNYPGQEAEKMKALAQAQPIGRMGTPAEIAVLALYLCSDEASF 239 Query: 255 INASCITIDGG 265 + IDGG Sbjct: 240 LTGVDYPIDGG 250 Lambda K H 0.321 0.138 0.424 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: 141 Number of extensions: 5 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: 272 Length of database: 255 Length adjustment: 25 Effective length of query: 247 Effective length of database: 230 Effective search space: 56810 Effective search space used: 56810 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 (21.9 bits) S2: 47 (22.7 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