Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CA265_RS13660 CA265_RS13660 oxidoreductase
Query= reanno::pseudo6_N2E2:Pf6N2E2_5967 (272 letters) >FitnessBrowser__Pedo557:CA265_RS13660 Length = 262 Score = 154 bits (389), Expect = 2e-42 Identities = 93/257 (36%), Positives = 135/257 (52%), Gaps = 5/257 (1%) Query: 19 LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGA-DVHA--L 75 LK K+ L+TG GIG I A ++ Q+E + E + D H Sbjct: 7 LKGKIALVTGVTSGIGLGIAKMMAKAGCTVIGCAEQSETSDVAQRFLAEMESFDAHTDYF 66 Query: 76 KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWY 135 KAD+ +D+ + +GR+D+LV+ AG NVF TE++W+ ++L W Sbjct: 67 KADMVVTEDIDGLVSDITNDYGRLDILVSNAGQNVFTGLENSTEKNWQFNLDLNLSAHWR 126 Query: 136 GCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195 K ++ G II +AS H+ IPGC PY +AK L GL R+L IE+ P G+R Sbjct: 127 LAKRC-KSLLNTNNGVIIVMASNHAFASIPGCAPYNIAKTALTGLVRSLAIEWGP-GIRT 184 Query: 196 NAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255 IAPG+I+T N ++N F P ERQR ++LHP +++G E+ VFL+S+ A F Sbjct: 185 IGIAPGFIDTPGNQQWFNSFIQPEEERQRTINLHPVKKLGTVEEIGGWCVFLSSEYAGFA 244 Query: 256 NASCITIDGGRSVMYHD 272 + + IDGGRS M D Sbjct: 245 SGTTYLIDGGRSAMMQD 261 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: 182 Number of extensions: 8 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: 262 Length adjustment: 25 Effective length of query: 247 Effective length of database: 237 Effective search space: 58539 Effective search space used: 58539 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