Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate BWI76_RS21470 BWI76_RS21470 gluconolaconase
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Koxy:BWI76_RS21470 Length = 290 Score = 155 bits (393), Expect = 8e-43 Identities = 93/282 (32%), Positives = 136/282 (48%) Query: 5 LTAPEPVWALGAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCL 64 + P+P++ L E P W + + AL++ DI IHR+D +GE + P + G Sbjct: 1 MAEPQPLFDYTGHLPECPTWSEAEQALYWADIMECEIHRYDVRTGEHQVLQFPEEPGCFA 60 Query: 65 PAANGKFVAGLQTGLAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGE 124 A G F+ L++G+ + D + D R NDG D GR + GT Sbjct: 61 LRAKGGFIVALRSGIWLTDAHGLLQRKVCDNPSNPQLARFNDGGTDRDGRFYAGTFWGPG 120 Query: 125 SEATGRIYRLGGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILG 184 + R+ D + +NG A S D R +Y DT VI+ + G G Sbjct: 121 DFNGALLMRIDSDLSPQVIQCDIHGANGLAFSEDKRWMYTSDTPNAVIYRTPLDKRGEAG 180 Query: 185 DSRVFATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVA 244 VF EG PDG A+DAEGC W +++G + R+SP GE L+ PV T V Sbjct: 181 KREVFRRFHPGEGIPDGAAIDAEGCYWSAMFDGWRIARFSPTGEQLEEHRLPVRCPTMVC 240 Query: 245 FGGPDLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGM 286 FGG D++T+Y TT +++DA+ A+ P +G +F VSV GM Sbjct: 241 FGGTDMKTLYITTTRENMDAEEVAKYPLSGAIFTLPVSVAGM 282 Lambda K H 0.319 0.139 0.439 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: 312 Number of extensions: 22 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: 295 Length of database: 290 Length adjustment: 26 Effective length of query: 269 Effective length of database: 264 Effective search space: 71016 Effective search space used: 71016 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 (21.7 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