Align galactaro-1,5-lactonase (characterized)
to candidate BWI76_RS21470 BWI76_RS21470 gluconolaconase
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__Koxy:BWI76_RS21470 Length = 290 Score = 150 bits (379), Expect = 3e-41 Identities = 100/289 (34%), Positives = 132/289 (45%), Gaps = 13/289 (4%) Query: 6 IVDARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGN 65 + D + ECP W E ALYW DI + + R+ TG P+ C A G Sbjct: 7 LFDYTGHLPECPTWSEAEQALYWADIMECEIHRYDVRTGEHQVLQFPEEPGCFALRAKGG 66 Query: 66 WVAGMETGFFQLTPHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLN 125 ++ + +G + H G L + +P Q R NDG DR GRF+AG+ N Sbjct: 67 FIVALRSGIWLTDAH--GLLQRKVCDNPSNP-QLARFNDGGTDRDGRFYAGTFWGPGDFN 123 Query: 126 AAEGTLYRYTSGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGT 185 A L R S +P NGLAFS D R MY SD+ V D G Sbjct: 124 GA--LLMRIDSDLSPQVIQCDIHGANGLAFSEDKRWMYTSDTPNAVIYRTPLD---KRGE 178 Query: 186 PSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTM 245 R VF H G PDGAA+DA+GCYW D I RFSP G +PV+ PTM Sbjct: 179 AGKREVFRRFHPGEGIPDGAAIDAEGCYWSAMFDGWRIARFSPTGEQLEEHRLPVRCPTM 238 Query: 246 CAFGGSRLDTLFVTSIRDDQSEQS-----LSGGVFALNPGVVGLPEPTF 289 FGG+ + TL++T+ R++ + LSG +F L V G+ + F Sbjct: 239 VCFGGTDMKTLYITTTRENMDAEEVAKYPLSGAIFTLPVSVAGMKKLPF 287 Lambda K H 0.321 0.137 0.443 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: 338 Number of extensions: 19 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: 291 Length of database: 290 Length adjustment: 26 Effective length of query: 265 Effective length of database: 264 Effective search space: 69960 Effective search space used: 69960 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: 48 (23.1 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