Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 202371 SO3263 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)
Query= reanno::Korea:Ga0059261_1894 (259 letters) >FitnessBrowser__MR1:202371 Length = 255 Score = 107 bits (268), Expect = 2e-28 Identities = 79/241 (32%), Positives = 119/241 (49%), Gaps = 5/241 (2%) Query: 19 KRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVDLTD 78 K VL+TGG GIGAGI + FA G V + + + + + D K +D + Sbjct: 14 KLVLITGGSRGIGAGIAKAFAEAGYWVAITYLNHQDKAVSLANILGD--KVAAFALDQSK 71 Query: 79 VASLQAVIARLIKGAG-GFDILVNNAANDDRHAIDEITEAYWDERLSVNLKHIFFCAQAV 137 S++ I + K D+L+NN A +IT + L+ NL+ F AQA Sbjct: 72 PESIKQCITEVEKYFNRSIDVLINNGAIAQEKPFSDITADDFTTMLNTNLRGPFLLAQAC 131 Query: 138 VPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRATCVIP 197 +PAM+ G G I+N+GSI G + V Y KA + L++S+A+ RDGIR + Sbjct: 132 IPAMQQHGFGRIINIGSIGGQWGGYNQVHYAAAKAGLINLSQSIAKIYSRDGIRTNTIAI 191 Query: 198 GNVRTPRQLKWYSPEGEAEIVAAQCLDGRLAP-EDVAAMVLFLASDDARLVTGHSYFVDA 256 G V T + E + AA + GRL ED+A++ LFLAS D+ ++G + + Sbjct: 192 GLVATEMTEHELTTEAGKQKAAAIPV-GRLGKVEDIASIALFLASQDSDYLSGQTLNANG 250 Query: 257 G 257 G Sbjct: 251 G 251 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: 138 Number of extensions: 7 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: 255 Length adjustment: 24 Effective length of query: 235 Effective length of database: 231 Effective search space: 54285 Effective search space used: 54285 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