Align Putative sugar lactone lactonase; EC 3.1.1.- (characterized, see rationale)
to candidate WP_011842721.1 RSPH17029_RS19585 SMP-30/gluconolactonase/LRE family protein
Query= uniprot:Q92RN9 (294 letters) >NCBI__GCF_000015985.1:WP_011842721.1 Length = 279 Score = 167 bits (424), Expect = 2e-46 Identities = 115/282 (40%), Positives = 151/282 (53%), Gaps = 21/282 (7%) Query: 19 LGEGPTFDPGTGTAWWFNITGRELHELHLESGRKAIHPLPFLGSVLAV--IDPLRQLIAS 76 +GEGP + P WF+I GR L L G A F +V A ID R L+A+ Sbjct: 13 VGEGPLWHPERQQFLWFDILGRRL----LGEGGAA---WTFDRAVTAAGWIDRDRLLVAT 65 Query: 77 DQGLFVRDTESSKLGHFATLE-EKPGNRSNDGRIHPCGALWIGTMGRSAEKHAGAIYHVA 135 + GL V D + L +E ++P RSNDGR G W GTMG+ A+ AG++Y Sbjct: 66 ETGLAVLDLQRRTLDPLLAVEADRPETRSNDGRADRQGGFWFGTMGKEAQSGAGSLYRYH 125 Query: 136 GSRVTKLYSNITIPNAICFSPDGATAYFTDTDVNQLMRVDIDPATALPTGDPVL---LSD 192 R+ +L +TIPNAICFSPDG TAY++DT QL+ A P G+ L L+D Sbjct: 126 RGRLERLVEGLTIPNAICFSPDGRTAYYSDT-ARQLVWTQRLDAEGWPVGERELFLDLAD 184 Query: 193 ESTSPGGVDGAVCDADGLIWNARWGASAVEVYKPDGQKVARYAVPATQPSCPAFVGAKAE 252 E +P DGAV DA+G A WGA AV + G++ R AV QPSCPAF G + + Sbjct: 185 EGLNP---DGAVIDAEGGFCCAAWGAGAVLRFDARGRQTHRLAVGGRQPSCPAFGGPEFD 241 Query: 253 RLLVTSAWQGMDDAARAADPHAGKTFELGIEVKGRFEPAFRL 294 RLLVT+A +GM+D P G + L ++G EP L Sbjct: 242 RLLVTTATEGMEDPG----PGEGLPYLLRPGLRGLAEPRVTL 279 Lambda K H 0.317 0.135 0.418 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: 315 Number of extensions: 20 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: 294 Length of database: 279 Length adjustment: 26 Effective length of query: 268 Effective length of database: 253 Effective search space: 67804 Effective search space used: 67804 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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