Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate SMa0717 SMa0717 hypothetical protein
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__Smeli:SMa0717 Length = 569 Score = 217 bits (552), Expect = 6e-61 Identities = 116/274 (42%), Positives = 154/274 (56%), Gaps = 1/274 (0%) Query: 15 GAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAG 74 GA L E PVWV+R+ L++VDI +HRFDP +G+ S + V LP N + Sbjct: 290 GAQLGEAPVWVEREKRLYWVDILHPAVHRFDPVTGKNESCNVAKLVSAVLPTRNEGLIVA 349 Query: 75 LQTGLAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEATGRIYRL 134 Q G+ FD F P +PEP LP NRLND VDP+GRLW G+M S TG +YRL Sbjct: 350 SQDGVEHFDFDRGDFNPFAEPEPGLPENRLNDAKVDPSGRLWVGSMRLDVSRPTGSLYRL 409 Query: 135 GGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAI-GDDGILGDSRVFATIP 193 G + +++NG A SPD T Y VDT+ G+I++ +G + + RVF T+P Sbjct: 410 TSAGEVTRAGSGFTVANGLAWSPDSSTFYFVDTVPGIIYAYDFDAREGSIANRRVFVTVP 469 Query: 194 NSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLRTV 253 +EG PDG AVDA+G VW +++G V RY P G L V PV T VAFGG +L T+ Sbjct: 470 EAEGRPDGLAVDADGGVWCAIWDGWRVNRYRPDGRLDRAVELPVPRPTSVAFGGDELATL 529 Query: 254 YATTASKHLDADGRAEEPHAGDLFAFRVSVPGMP 287 + T+A L A E P +G +FA G+P Sbjct: 530 FITSARTRLPASTLTEAPLSGGIFACNPGARGLP 563 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: 604 Number of extensions: 27 Number of successful extensions: 2 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: 569 Length adjustment: 31 Effective length of query: 264 Effective length of database: 538 Effective search space: 142032 Effective search space used: 142032 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: 50 (23.9 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