Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_017867545.1 LACPOB_RS0104010 SDR family oxidoreductase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119 (272 letters) >NCBI__GCF_000349725.1:WP_017867545.1 Length = 254 Score = 153 bits (386), Expect = 4e-42 Identities = 89/252 (35%), Positives = 139/252 (55%), Gaps = 5/252 (1%) Query: 16 GERLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAI 75 G++L NKV ++TG+ G+G + FA++ A ++ +DI E+ +VA + G +AI Sbjct: 2 GKKLANKVAIITGSGSGMGAEMATLFAAEGASIVGADINIERANEVAEKIKTNGGQAIAI 61 Query: 76 KADVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPL-EMTEEDWRRCFAIDLDGAW 134 K DVS D+ + + A D G++D++VN AG+ P+ EMT E W R FA+++D Sbjct: 62 KTDVSCLADIKKVFKTAKDKFGQVDIVVNNAGIMDDFSPVGEMTNETWERAFAVNVDSVM 121 Query: 135 YGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVR 194 Y + + + + + G I+N AS T+ Y AKH ++GLT+ Y G+R Sbjct: 122 YATREAVKEFLPKKKGVILNTASVGGTNGGRAGAAYTAAKHAVVGLTKNTAFMYEKNGIR 181 Query: 195 VNAIAPGYIETQLNVDYWNGFADPHAERQRA-FDLHPPRRIGQPIEVAMTAVFLASDEAP 253 NAIAPG I T + N ++ ERQ+A L P +G +A TA+FL SD+A Sbjct: 182 TNAIAPGGISTNIGESIKNA-SEFGMERQKAGMGLMP--GMGSSSSIAKTALFLVSDDAD 238 Query: 254 FINASCITIDGG 265 F+N + +DGG Sbjct: 239 FVNGVIVPVDGG 250 Lambda K H 0.322 0.138 0.426 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: 155 Number of extensions: 7 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: 254 Length adjustment: 25 Effective length of query: 247 Effective length of database: 229 Effective search space: 56563 Effective search space used: 56563 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