Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_063836871.1 BS73_RS00110 SDR family oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_20240 (272 letters) >NCBI__GCF_000744815.1:WP_063836871.1 Length = 345 Score = 140 bits (354), Expect = 3e-38 Identities = 84/250 (33%), Positives = 127/250 (50%), Gaps = 2/250 (0%) Query: 19 LKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERGADVHALQAD 78 L K +TGA GIG+A A + AR+ DI+ E A G A++ D Sbjct: 4 LTGKTAFVTGAGSGIGQACALRLAEEGARVAAVDIRLPAAEETAKRIEASGGTAVAVECD 63 Query: 79 VSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFR-DPLEMTEEDWRRCFAIDLDGAWYGC 137 VS + + A R VE G + V+VN AG+ D + +E+DW R +++ + Sbjct: 64 VSSGRQVAAAVSRTVEALGALHVIVNAAGILAAEGDVVACSEDDWDRVMGVNVKSMYLIG 123 Query: 138 KAVLPQMIEQGVGSIINIASVHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVNA 197 K +P+++ G GSI+NIASV +P Y +K +L LTR + ++YA +G+RVNA Sbjct: 124 KHGVPEILRAGGGSIVNIASVFGFTALPDECAYDASKGAVLNLTRQMAVQYAKQGIRVNA 183 Query: 198 IAPGYIETQLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVFLASDEAPFINA 257 + P +T L +D D AE+ P R+ +P E+A FLASD+A F+ Sbjct: 184 LCPSDCDTPL-LDALLAGGDVEAEKAELAKPIPMGRLARPEEIASGVAFLASDDAAFVTG 242 Query: 258 SCITIDGGRS 267 + +DGG S Sbjct: 243 VALPVDGGSS 252 Lambda K H 0.321 0.137 0.419 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: 192 Number of extensions: 9 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: 272 Length of database: 345 Length adjustment: 27 Effective length of query: 245 Effective length of database: 318 Effective search space: 77910 Effective search space used: 77910 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: 48 (23.1 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