Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ga0059261_3382 Ga0059261_3382 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::BFirm:BPHYT_RS16920 (266 letters) >FitnessBrowser__Korea:Ga0059261_3382 Length = 245 Score = 110 bits (276), Expect = 2e-29 Identities = 81/245 (33%), Positives = 123/245 (50%), Gaps = 13/245 (5%) Query: 25 RTVLITGGATGIGASFVEHFAAQGARVAF-FDIDASAGEALADELGDSKHKPLFLSCDLT 83 + L+TGG+ GIGA+ A +GA VA + A A +A E+ + L ++ D Sbjct: 6 KRALVTGGSRGIGAAIARRLAREGADVAITYASSAGAAAGVAAEIEALGRRALAITADNR 65 Query: 84 DIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQAV 143 D A++ A+ AALG I +LVNNA +++ E FDA +AVN+R F A +AV Sbjct: 66 DAAAVEAAVDQAAAALGGIDILVNNAGIFLAAPADDLSLEDFDATMAVNLRAPFVAVRAV 125 Query: 144 MEDMKAANSGSIINLGS-ISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLV 202 + M G I+ +GS ++ + G+ VY SK+AV L + LARDL I VNT+ Sbjct: 126 LPHM--GEGGRIVAIGSNVALVAPTPGFSVYSTSKAAVTMLHQALARDLAPRGITVNTVH 183 Query: 203 PGWVMTEKQKR---LWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDI 259 PG T+ D R ++ D D+A +LA+ ++R +T + Sbjct: 184 PGSTDTDMNPADGPHAADQIARTALGRFGSAD------DIASAVAYLASPEARSVTGTAL 237 Query: 260 VVDGG 264 +VD G Sbjct: 238 LVDSG 242 Lambda K H 0.320 0.134 0.388 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: 168 Number of extensions: 10 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: 266 Length of database: 245 Length adjustment: 24 Effective length of query: 242 Effective length of database: 221 Effective search space: 53482 Effective search space used: 53482 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 17 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