Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 3609507 Dshi_2891 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__Dino:3609507 Length = 242 Score = 131 bits (329), Expect = 2e-35 Identities = 88/252 (34%), Positives = 129/252 (51%), Gaps = 12/252 (4%) Query: 18 RLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKA 77 RL+ K ++TG G G IV FA++ A+++++DI E VA + A V Sbjct: 2 RLEGKTAIVTGGGSGFGAGIVRKFAAEGAQVIVADINKGAAEAVAEEYGGTAAQV----- 56 Query: 78 DVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQ-MTEEDWHRCFAIDLDGAWYG 136 DVS D +MA LA E HG D+LVN AG+ P++ +TEE++ R A++ + Sbjct: 57 DVS---DADSMAALA-EAHGAPDILVNNAGITHLPKPMEEVTEEEFDRVLAVNAKSVYLS 112 Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVN 196 + +P M +G G+I+NIAST P Y +K ++ T+A+ +E AP GIRVN Sbjct: 113 ARVFVPAMKARGSGAILNIASTAGVSPRPKLNWYNASKGWMITATKAMAVELAPFGIRVN 172 Query: 197 AIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256 A+ P ET L + D R + P R QP ++ A FL SDEA I Sbjct: 173 ALNPVAGETPLLASFMG--EDTPEMRAKFLATIPLGRFSQPEDLGNAAAFLCSDEASMIT 230 Query: 257 ASCITIDGGRSV 268 + +DGGR + Sbjct: 231 GVAMEVDGGRCI 242 Lambda K H 0.321 0.138 0.424 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: 134 Number of extensions: 5 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: 272 Length of database: 242 Length adjustment: 24 Effective length of query: 248 Effective length of database: 218 Effective search space: 54064 Effective search space used: 54064 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