Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate 7024914 Shewana3_2088 hypothetical protein (RefSeq)
Query= reanno::Korea:Ga0059261_1893 (295 letters) >FitnessBrowser__ANA3:7024914 Length = 300 Score = 161 bits (407), Expect = 2e-44 Identities = 101/270 (37%), Positives = 137/270 (50%), Gaps = 5/270 (1%) Query: 14 LGAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVG-FCLPAANGKFV 72 +G L EG +W ++W+ DI S I+RF AS ++ P +VG F L A + Sbjct: 15 VGNRLGEGVLWDDLHQSIWWTDILSSVIYRFHLASRSLETFPMPHRVGSFGLTAKPTTLI 74 Query: 73 AGLQTGLAIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGES--EATGR 130 G+AI+D D+S T L PE GNR NDG +D GR W GTM + + T Sbjct: 75 VAFDIGIAIYDIEDQSLTWLAQPESHFAGNRFNDGRIDRQGRFWAGTMVEQRDTLQQTAA 134 Query: 131 IYRLGGDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG-DDGILGDSRVF 189 +Y L G C + ISNG S DGRTLYH D+ I+ + G+L R+F Sbjct: 135 LYCLDEKGHCHQHLTNLEISNGLCWSVDGRTLYHADSPKHQIYQYDFDIEQGLLSRKRLF 194 Query: 190 ATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPD 249 A+ + FPDG VDA G +W + G V RY P GE+ ++ PV T +AFGG Sbjct: 195 ASTSHHI-FPDGSDVDAAGYLWNAQWGGGQVVRYRPDGEVDLILKLPVTHPTSIAFGGEK 253 Query: 250 LRTVYATTASKHLDADGRAEEPHAGDLFAF 279 + T+A LDA +EP AGD+F + Sbjct: 254 RDLLIVTSAKHSLDASQLDQEPQAGDVFIY 283 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: 317 Number of extensions: 20 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: 295 Length of database: 300 Length adjustment: 26 Effective length of query: 269 Effective length of database: 274 Effective search space: 73706 Effective search space used: 73706 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