Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_008484825.1 B3C1_RS10890 SDR family oxidoreductase
Query= reanno::acidovorax_3H11:Ac3H11_614 (280 letters) >NCBI__GCF_000299915.1:WP_008484825.1 Length = 256 Score = 273 bits (697), Expect = 4e-78 Identities = 135/252 (53%), Positives = 175/252 (69%), Gaps = 2/252 (0%) Query: 30 KFPSLQGRAVFVTGGGSGIGAAIVAAFAEQGARVAFVDVAREASEALAQHI-ADAGLPRP 88 ++PSL G+ VF+TGGGSGIGA++V AF QGA VAFVD+ S AL + + G P Sbjct: 6 QYPSLNGKVVFITGGGSGIGASLVEAFCRQGAIVAFVDILEAESRALVDRLNGELGRPLA 65 Query: 89 WWRVCDVRDVQALQACMADAAAELGSDFAVLVNNVASDDRHTLESVTPEYYDERMAINER 148 + C++ DV AL+ +A LG+ VLVNN ASD RH VTPEY+DER+ IN R Sbjct: 66 HFYPCNIIDVAALKGVIAAVGQTLGN-IGVLVNNAASDSRHDFREVTPEYWDERLNINLR 124 Query: 149 PAFFAIQAVVPGMRRLGAGSVINLGSTGWQGKGTGYPCYAIAKSSVNGLTRGLAKTLGQD 208 P FFA QAV P M+ LG G++IN GS W G P Y AKS+V GL+RGLA+ +G D Sbjct: 125 PQFFAAQAVYPQMQALGGGAIINFGSMSWHEGQGGMPGYTSAKSAVLGLSRGLARDMGAD 184 Query: 209 RIRINTVSPGWVMTERQIKLWLDAEGEKELARNQCLPDKLRPHDIARMVLFLASDDAAMC 268 IR+NT++PGWVMTERQ+KLW+ E ++++ +NQC+ L PH+IA M LFLASDD++MC Sbjct: 185 NIRVNTLTPGWVMTERQLKLWVTEETKQDIEKNQCIKTPLMPHNIAAMALFLASDDSSMC 244 Query: 269 TAQEFKVDAGWV 280 TAQ+F VD GW+ Sbjct: 245 TAQDFVVDGGWI 256 Lambda K H 0.320 0.133 0.405 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: 215 Number of extensions: 4 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: 280 Length of database: 256 Length adjustment: 25 Effective length of query: 255 Effective length of database: 231 Effective search space: 58905 Effective search space used: 58905 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 24 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