Align Gluconolactonase; EC 3.1.1.-; EC 3.1.1.17 (characterized, see rationale)
to candidate RR42_RS30140 RR42_RS30140 gluconolaconase
Query= uniprot:Q88NN7 (293 letters) >FitnessBrowser__Cup4G11:RR42_RS30140 Length = 292 Score = 155 bits (392), Expect = 1e-42 Identities = 101/278 (36%), Positives = 144/278 (51%), Gaps = 12/278 (4%) Query: 14 GESPVWHPGEQALYWVDIPARQLHRWQAADGKHQCWQGDEMLACIARSGQG-WVAGMESG 72 GE PVWH G A+Y+VDI R++HR+ A G + W D I G ++ GM+ G Sbjct: 17 GEGPVWHQGSSAVYFVDIKGRRIHRFAIATGAMRSWPVDSQPGFIVPLDDGGFLCGMQDG 76 Query: 73 IFQLQAKADGSLDSRLLSNVQHAQAGMRFNDGRCDRQGRFWAGTMLLDMQQGAHVGALYR 132 +++ ADG+ R L V+ G R NDG D GR W GTM D + A G+LY+ Sbjct: 77 LYRFDP-ADGAC--RRLKEVEPDLPGNRINDGFVDPAGRLWFGTM--DDGEAAPSGSLYQ 131 Query: 133 HDGEGHLHLQQDGMIVPNGLAFSPDGKRMYLSDSHPNVQKVWAFDYDTDSGTPHGKHLFV 192 +G + G ++ NG A SPD + +Y +D+ + V+AFD D G + F Sbjct: 132 VGDDGRTWRRDSGYVITNGPAMSPDARTLYHADTVKRL--VYAFDVGQD-GALSRRREFA 188 Query: 193 DMRNYPGRPDGAAIDQDGCYWICGNDAGQIHRFTPEGRLDRSLSVPVKKPAMCAFGGASL 252 + G PDG A+D DG WI +I R++P+GRL + P AFGG L Sbjct: 189 RLCG-TGYPDGMAVDADGHLWIAVFGGARIERWSPDGRLAGVVRFPCDNVTKLAFGGDDL 247 Query: 253 DILYVTSIRP--TGIDLSDQPLAGGVFALDPGTKGLEE 288 +YVT+ R + L+ QPLAGG+F+ T+GL + Sbjct: 248 RTVYVTTARKGLSPAALALQPLAGGLFSFRAPTRGLPQ 285 Lambda K H 0.320 0.139 0.455 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: 440 Number of extensions: 34 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: 293 Length of database: 292 Length adjustment: 26 Effective length of query: 267 Effective length of database: 266 Effective search space: 71022 Effective search space used: 71022 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