Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate AO353_22325 AO353_22325 short-chain dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__pseudo3_N2E3:AO353_22325 Length = 249 Score = 130 bits (327), Expect = 3e-35 Identities = 84/250 (33%), Positives = 135/250 (54%), Gaps = 5/250 (2%) Query: 17 ERLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQA-EKVETVAAHWRERGADVHAL 75 ++L K+ L+TG+++GIG AI A A ++++ ++ E + V + E GA +A+ Sbjct: 2 KKLHRKIALVTGSSKGIGAAIARQLAKDGATVIVNYTRSREDADRVVSQILETGARAYAI 61 Query: 76 KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWY 135 +ADVSN ++ A+ + V HG ID+LVN AGV E+TE+++ R F +++ G Sbjct: 62 RADVSNALEVKALFKAIVHEHGHIDILVNNAGVYATGALAEITEQEFNRQFNLNVLGL-I 120 Query: 136 GCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195 C + GSIINI+S+ +S Y +K + +T+ L E PK +RV Sbjct: 121 QCTQEAVAVFNPKGGSIINISSSVTSFTPANSTVYTASKGAVDAITKTLANELGPKNIRV 180 Query: 196 NAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255 N++ PG + T+ V F D + RQ+ + P RIG P ++A FLASD+A +I Sbjct: 181 NSVNPGLVVTE-GVHASGFFEDAF--RQKIEAITPLGRIGSPEDIAPAVAFLASDDAGWI 237 Query: 256 NASCITIDGG 265 + I GG Sbjct: 238 TGEILVIGGG 247 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: 142 Number of extensions: 7 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: 249 Length adjustment: 24 Effective length of query: 248 Effective length of database: 225 Effective search space: 55800 Effective search space used: 55800 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