Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 7025403 Shewana3_2558 3-oxoacyl-[acyl-carrier-protein] reductase (RefSeq)
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__ANA3:7025403 Length = 248 Score = 103 bits (256), Expect = 4e-27 Identities = 75/244 (30%), Positives = 120/244 (49%), Gaps = 6/244 (2%) Query: 15 SLKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERV 74 SL GK LVTG GIG I E GA V + + + E L G K + Sbjct: 6 SLAGKVALVTGASRGIGRAIAETLVEAGAIVVGTATSEKGAAAIQEYL---GDKGFGLVL 62 Query: 75 DLTDVASLQAVIARLIKGAGGFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCA 134 ++TD S+ + + + AG DILVNNA + + + + W++ + NL +F + Sbjct: 63 NVTDSQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNLTSLFRLS 122 Query: 135 QAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATC 194 + V+ M + G I+N+GS+ +G + V Y KA + G T+SLAR++ I Sbjct: 123 KPVMRTMMKKRFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVASRQITVNA 182 Query: 195 VIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLA-PEDVAAMVLFLASDDARLVTGHSYF 253 + PG ++T + E + + + +Q RL +++A VLFLASD A +TG + Sbjct: 183 IAPGFIQT--DMTDELTEDQQKAIMSQVPMERLGQAQEIANAVLFLASDSAAYITGETLH 240 Query: 254 VDAG 257 V+ G Sbjct: 241 VNGG 244 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: 120 Number of extensions: 5 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: 248 Length adjustment: 24 Effective length of query: 235 Effective length of database: 224 Effective search space: 52640 Effective search space used: 52640 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 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