Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 7026324 Shewana3_3466 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__ANA3:7026324 Length = 292 Score = 117 bits (294), Expect = 2e-31 Identities = 80/254 (31%), Positives = 123/254 (48%), Gaps = 8/254 (3%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGE-KVEKVAAHWREQ-GADVVAIK 76 LK KV L+TG+ GIG A A Q L++ + E + ++AA + EQ Sbjct: 34 LKGKVGLITGSTSGIGLATAHVLAEQGCHLILHGLMPEAEGRRLAAEFAEQYHIHTYFSN 93 Query: 77 ADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYG 136 AD+ + +HA ++ G ID+LVN AG+ + + W+ AI+L A++ Sbjct: 94 ADLRDPESIHAFMDAGVKALGSIDILVNNAGIQHTENVAHFPIDKWNDIIAINLSSAFHT 153 Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVN 196 + +P M E+ G IINIAS H Y AKHG++GLT+ + IE A +GI VN Sbjct: 154 IQQAVPAMAEKRWGRIINIASVHGLVASVNKAAYCAAKHGIVGLTKVVAIECAEQGITVN 213 Query: 197 AIAPGYIETQL------NVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASD 250 AI PG+++T L + G + A+ Q P + P ++ +FL S Sbjct: 214 AICPGWVDTPLINKQIEAIASNKGLSYDEAKYQLVTAKQPLPEMLDPRQIGEFVLFLCSS 273 Query: 251 EAPFINASCITIDG 264 A I + + +DG Sbjct: 274 AARGITGASLAMDG 287 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: 220 Number of extensions: 10 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: 292 Length adjustment: 26 Effective length of query: 246 Effective length of database: 266 Effective search space: 65436 Effective search space used: 65436 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