Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Echvi_4411 Echvi_4411 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__Cola:Echvi_4411 Length = 292 Score = 105 bits (262), Expect = 1e-27 Identities = 77/245 (31%), Positives = 116/245 (47%), Gaps = 7/245 (2%) Query: 16 LKGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVD 75 LKGK +VTGG IG I A GA V ++ + Q +V+ + A+G KA ++D Sbjct: 44 LKGKVAVVTGGSGAIGRAICCRLAADGALVVVCGMSHDKMQGVVDEIGANGGKAVKRQLD 103 Query: 76 LTDVASLQAVIARLIKGAGGFDILVNNAANDDRHA---IDEITEAYWDERLSVNLKHIFF 132 ++ + L + G DILVN A R A I E+ D L VNL+ Sbjct: 104 ISSEEKIIEFYQWLKESYGQLDILVNCAGGSARQASRPIYELETETIDTTLHVNLRGAIL 163 Query: 133 CAQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRA 192 + M A G IV++ S+ G + Y KA I T+S+A +LG+ GI A Sbjct: 164 VTREASKIMVAAKRGTIVSVTSVIGEHGKAKFSEYAAAKAGIIAFTKSIAMELGKLGITA 223 Query: 193 TCVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLAPEDVAAMVLFLASDDARLVTGHSY 252 CV PG V Q +P A++ ++ PED++ MV +L ++ + +TG ++ Sbjct: 224 NCVSPGIV----QRGTITPAQMAKLKKTNYMNDYGRPEDISEMVAYLTREEGKFITGQNF 279 Query: 253 FVDAG 257 VD G Sbjct: 280 KVDGG 284 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: 151 Number of extensions: 6 Number of successful extensions: 3 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: 292 Length adjustment: 25 Effective length of query: 234 Effective length of database: 267 Effective search space: 62478 Effective search space used: 62478 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