Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_059152595.1 V474_RS16615 SDR family oxidoreductase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >NCBI__GCF_001046635.1:WP_059152595.1 Length = 248 Score = 141 bits (356), Expect = 1e-38 Identities = 84/247 (34%), Positives = 132/247 (53%), Gaps = 10/247 (4%) Query: 20 KNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVV-AIKAD 78 +++V ++TG A GIGEA+V ++ A++VI+D + ++A + GAD A K D Sbjct: 5 QDRVAIVTGGASGIGEAVVKDLLAEGAKVVIADFDLDGATRLADTY---GADRARAFKVD 61 Query: 79 VSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPL-QMTEEDWHRCFAIDLDGAWYGC 137 VS + + A A+E G + + VN AG+ PL + +DWHR +DL +YG Sbjct: 62 VSDAEAVEASVAFAVETFGALHLAVNNAGIGAPSTPLADIAIDDWHRVVGVDLHSVFYGM 121 Query: 138 KAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNA 197 K +P M++ G G+I+N+AS G Y +KH ++G+T+ ++YA +GIRVNA Sbjct: 122 KYQIPAMLKSGGGAIVNMASILGAAGWAGSAAYVTSKHAVVGMTKTAALDYAGQGIRVNA 181 Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINA 257 + P ++ET G ER LH R+ +P E+A FL SD A F+ Sbjct: 182 VGPAFVETPA-----LGKTMTDEERSVLAGLHAFNRLARPEEIAAFTSFLLSDRASFMTG 236 Query: 258 SCITIDG 264 + +DG Sbjct: 237 TYYPVDG 243 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: 175 Number of extensions: 14 Number of successful extensions: 4 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: 248 Length adjustment: 24 Effective length of query: 248 Effective length of database: 224 Effective search space: 55552 Effective search space used: 55552 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