Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate GFF2263 HP15_2213 3-ketoacyl-(acyl-carrier-protein) reductase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Marino:GFF2263 Length = 247 Score = 127 bits (319), Expect = 2e-34 Identities = 93/248 (37%), Positives = 131/248 (52%), Gaps = 11/248 (4%) Query: 15 SLKGKRVLVTGGGSGIGAGIVEGFARQGADV--TFFDIAGAESQLLVERLSADGHKACFE 72 SL+GK LVTG GIG I A QGA+V T AGAES + L + G+K Sbjct: 2 SLEGKTALVTGATRGIGQAIARALAAQGAEVVGTATSEAGAES--ITNDLQSAGYKGYGM 59 Query: 73 RVDLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFF 132 +++ D AS++A + L + +G ILVNNA + + + + W L NL ++ Sbjct: 60 VMNVADPASIEAGLKELTEKSGAPLILVNNAGITRDNLLMRLKDDDWASVLETNLSSVYR 119 Query: 133 CAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRA 192 ++AV+ M G I+N+ S+ +G + Y KA +EG TRSLA+++ GI A Sbjct: 120 TSKAVLRGMAKAKWGRIINISSVVAGMGNAGQGNYCAAKAGVEGFTRSLAKEMSNRGITA 179 Query: 193 TCVIPGNVRTPRQLKWYSPEGEA--EIVAAQCLDGRLA-PEDVAAMVLFLASDDARLVTG 249 CV PG + T K + A EI+ A GRL PE+VAA+V FLASD A VTG Sbjct: 180 NCVAPGFIDTDMTKKLDDKQRGAMLEIIPA----GRLGEPEEVAAVVAFLASDAAGYVTG 235 Query: 250 HSYFVDAG 257 + V+ G Sbjct: 236 ETINVNGG 243 Lambda K H 0.321 0.137 0.409 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: 144 Number of extensions: 6 Number of successful extensions: 2 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: 259 Length of database: 247 Length adjustment: 24 Effective length of query: 235 Effective length of database: 223 Effective search space: 52405 Effective search space used: 52405 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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