Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_059151340.1 V474_RS09995 SDR family oxidoreductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_001046635.1:WP_059151340.1 Length = 273 Score = 137 bits (344), Expect = 3e-37 Identities = 90/272 (33%), Positives = 135/272 (49%), Gaps = 28/272 (10%) Query: 18 RLKNKVVLLTGAAQ--GIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHAL 75 R KV ++TG+ + G+GE+I + + A+LVISDI + A++ + Sbjct: 2 RFAGKVAVVTGSGRKGGLGESIARRLSEEGAKLVISDIGGSRDAATPDAMIGGTAEMQDI 61 Query: 76 KA-----------DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPL-EMTEEDWR 123 A DV + + A+A HA+ HG +D+ VN AG+ PL E++ +DWR Sbjct: 62 AASLPTQASTFACDVRDPAQVAALADHAITTHGSLDIWVNNAGIGYIMKPLGEVSPDDWR 121 Query: 124 RCFAIDLDGAWYGCKAVLPQMIEQGVGS-IINIASTHSSHIIPGCFPYPVAKHGLLGLTR 182 ++L GAW+G +A +MI+QG G I+NIAS + P Y +KHGL+GL R Sbjct: 122 AVIDVNLTGAWFGLQAAAERMIKQGRGGRIVNIASQAAKSGFPHAQAYTASKHGLVGLVR 181 Query: 183 ALGIEYAPKGVRVNAIAPGYIETQLNVDYWNGFADPYAERQ---------RALDLHPPRR 233 + IE P+G+ VN + P ++ T L W + +AE Q R P R Sbjct: 182 SASIELGPEGITVNNVCPNHVTTGLG--KWQN--EHFAELQGISVEEYLKRMAGRIPMGR 237 Query: 234 IGQPIEVAMTAVFLASDEAPFINASCITIDGG 265 G P + A FL SDEA +I + + GG Sbjct: 238 PGLPQDTASAVAFLCSDEAAYITGESMNVSGG 269 Lambda K H 0.321 0.137 0.419 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: 164 Number of extensions: 11 Number of successful extensions: 5 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: 273 Length adjustment: 25 Effective length of query: 247 Effective length of database: 248 Effective search space: 61256 Effective search space used: 61256 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: 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