Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_011992983.1 XAUT_RS24665 2-(R)-hydroxypropyl-CoM dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_000017645.1:WP_011992983.1 Length = 250 Score = 149 bits (375), Expect = 7e-41 Identities = 89/248 (35%), Positives = 139/248 (56%), Gaps = 8/248 (3%) Query: 21 NKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVE-TVAAHWRERGADVHALKADV 79 ++V ++TGA+ G G AI F ++ R+ D+ AE +E T HW V ++ADV Sbjct: 2 SRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADV 61 Query: 80 SNQQDLHAMARHAVERHGRIDVLVNCAGV--NVFRDPLEMTE-EDWRRCFAIDLDGAWYG 136 +++ D++A +E+ G IDVLVN AG+ N L T E + + A+++ G + G Sbjct: 62 ADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLG 121 Query: 137 CKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 C+AVLP M+ QG G I+NIAS S PG Y +K +L LT+++ ++YA G+R N Sbjct: 122 CRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCN 181 Query: 197 AIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256 A+ PG IET + W D R + L P + IG +VA +FLA ++A ++N Sbjct: 182 AVCPGMIETPMT--QWR--LDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVN 237 Query: 257 ASCITIDG 264 + + +DG Sbjct: 238 GAALVMDG 245 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: 162 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: 250 Length adjustment: 25 Effective length of query: 247 Effective length of database: 225 Effective search space: 55575 Effective search space used: 55575 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