Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate Ga0059261_1893 Ga0059261_1893 Gluconolactonase
Query= uniprot:Q888H2 (294 letters) >FitnessBrowser__Korea:Ga0059261_1893 Length = 295 Score = 157 bits (398), Expect = 2e-43 Identities = 103/283 (36%), Positives = 141/283 (49%), Gaps = 15/283 (5%) Query: 15 ESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSRGGWIAGMENGL 74 E PVW R+ AL++VDI + +HR+D + RSW AP + + G ++AG++ GL Sbjct: 20 EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79 Query: 75 YHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMAAGAVVGALYRY 134 P D T L E A G R NDG D GR W GTM D G +YR Sbjct: 80 AIFDPADRSF---TPLTDPEPALPGNRLNDGTVDPAGRLWFGTM--DDGESEATGRIYRL 134 Query: 135 SAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTDSGTPHDRRLFV 194 G A+ + + NG A SPDG+T+Y D+ V A D G D R+F Sbjct: 135 G-GDGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG---DDGILGDSRVFA 190 Query: 195 DMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKKPAMCAFGGPNL 254 + N G PDG A+DA+GC WI + V R++P G+L + PV AFGGP+L Sbjct: 191 TIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDL 250 Query: 255 DTLFVTSIRPGGDL---SDQPLAGGVFALR---PGVKGLEEPV 291 T++ T+ D +++P AG +FA R PG+ G E V Sbjct: 251 RTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGMPGTEVSV 293 Lambda K H 0.320 0.138 0.441 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: 381 Number of extensions: 32 Number of successful extensions: 5 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: 294 Length of database: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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