Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_057509057.1 ABB28_RS13185 short-chain dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >NCBI__GCF_001431535.1:WP_057509057.1 Length = 255 Score = 209 bits (533), Expect = 4e-59 Identities = 116/255 (45%), Positives = 156/255 (61%), Gaps = 8/255 (3%) Query: 17 ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALK 76 +RL KV ++TGAA GIG AI F S A + D A + ++G Sbjct: 9 QRLAGKVAIVTGAANGIGAAIAGLFQSHGAIVAGYDQAAPGADDAVCALFQQG------- 61 Query: 77 ADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYG 136 DVS+ + A V +G++DVLV+ AG++VF PLE++ + W+R ++L G W Sbjct: 62 -DVSDADAVAAFVERVVSAYGQVDVLVSNAGMDVFSIPLELSSQTWQRNLDVNLGGHWNF 120 Query: 137 CKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 +AVLP M+ QG GS++NIAS H II G FPY VAKH L+GLT+ALG+EYA KG+R N Sbjct: 121 ARAVLPCMLRQGRGSVVNIASVHGHRIIQGAFPYNVAKHALIGLTKALGLEYADKGLRFN 180 Query: 197 AIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256 +I+PG I ++ DP R+ L PP+RIG+ EVA TA+FLASDEA FIN Sbjct: 181 SISPGLILVDRIEHWFESQPDPAQARREQEALLPPKRIGEASEVAQTALFLASDEARFIN 240 Query: 257 ASCITIDGGRSVMYH 271 A+ I IDGGRS +Y+ Sbjct: 241 AADILIDGGRSQLYY 255 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: 208 Number of extensions: 9 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: 272 Length of database: 255 Length adjustment: 25 Effective length of query: 247 Effective length of database: 230 Effective search space: 56810 Effective search space used: 56810 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