Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ga0059261_2675 Ga0059261_2675 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Korea:Ga0059261_2675 Length = 242 Score = 134 bits (336), Expect = 2e-36 Identities = 91/254 (35%), Positives = 141/254 (55%), Gaps = 23/254 (9%) Query: 18 RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77 RL+ K+ L+T A QGIG A V AF + AR++ +D++AE ++ + GA+ L Sbjct: 3 RLEGKIALVTAAGQGIGRATVEAFVREGARVIATDVRAEALDGL------EGAETRQL-- 54 Query: 78 DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWYGC 137 DV+++ + A+A E ++VL NCAG L+ E+ W ++++ + Sbjct: 55 DVTSKDAVAAIAAEFPE----LNVLYNCAGFVHAGTILDCDEDAWEFSQSLNVTAQYRMI 110 Query: 138 KAVLPQMIEQGVGSIINIASTHSS-HIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196 +AVLP MI +G GSIIN++S SS +P F Y K ++GLT+++ I+Y KG+R N Sbjct: 111 RAVLPHMIARGGGSIINMSSVCSSIKAVPNRFAYGATKAAVIGLTKSVAIDYVTKGIRCN 170 Query: 197 AIAPGYIETQLNVDYWN---GFADPYAE--RQRALDLHPPRRIGQPIEVAMTAVFLASDE 251 AI PG +ET + + F YAE ++A+ R G+ E+A AV+LASDE Sbjct: 171 AICPGTVETPSLIQRLHDTGDFEKAYAEFTARQAMG-----RFGRTSELAALAVYLASDE 225 Query: 252 APFINASCITIDGG 265 + F + IDGG Sbjct: 226 SAFTTGTVNVIDGG 239 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: 135 Number of extensions: 5 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: 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 (21.8 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