Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_011840126.1 RSPH17029_RS00190 SDR family oxidoreductase
Query= reanno::HerbieS:HSERO_RS05210 (261 letters) >NCBI__GCF_000015985.1:WP_011840126.1 Length = 260 Score = 241 bits (614), Expect = 1e-68 Identities = 123/249 (49%), Positives = 163/249 (65%), Gaps = 2/249 (0%) Query: 13 FPSLKGKRVFITGGGTGIGAAIVEAFAQQGAHVAFVDIATEASEALCNEVAAAGHPKPLF 72 FP LKG VF++GGG+GIGAA+ E F +QGA VAFV + + A C+ + A +PLF Sbjct: 11 FPDLKGASVFLSGGGSGIGAALTEGFLRQGAQVAFVQRSD--ATAFCDRMEAETGARPLF 68 Query: 73 RHCDLRDIPAFQATIAELQAQLGDFDVLVNNAANDQRHKLEEVTLEYWNDRIAINQRPSF 132 CD+ DIPA + +AE+ + G VLVN AA+D RH EVT +YW+ A+N + F Sbjct: 69 LPCDVTDIPALRQALAEVAERQGPIRVLVNAAAHDDRHTTAEVTEDYWDRAQAVNLKHYF 128 Query: 133 FAVQSVVEGMKRRGGGSIINFSSISWHQSGGGFPVYTTAKASTLGLTRGLARDLGPHKIR 192 FA Q+V+ GMK GGGSI+NFSSIS+ G+P YTTA + GLTR LAR+ GP +IR Sbjct: 129 FAAQAVIPGMKAAGGGSIVNFSSISYMMGNAGYPAYTTANSGINGLTRSLAREFGPDRIR 188 Query: 193 VNTVTPGWVMTERQIKLWLDEEGKKAIARNQCLQGDLLPWHLARMVLFLAADDSAMCTAQ 252 VN + PGWV+TERQ LW+ E+G +A QCL+ L+P + VLFLA++ S M T Q Sbjct: 189 VNALAPGWVLTERQKDLWVTEDGLQAHLDRQCLKEALVPADIVGGVLFLASEASRMMTGQ 248 Query: 253 EFIVDAGWV 261 ++D G V Sbjct: 249 ALVIDGGVV 257 Lambda K H 0.321 0.134 0.411 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: 179 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: 261 Length of database: 260 Length adjustment: 25 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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 Apr 10 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