Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate H281DRAFT_01630 H281DRAFT_01630 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__Burk376:H281DRAFT_01630 Length = 314 Score = 140 bits (354), Expect = 3e-38 Identities = 96/314 (30%), Positives = 156/314 (49%), Gaps = 31/314 (9%) Query: 53 PRLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAG-VSIFLK 111 PR ++ S +E + +WSEGP+W +G +LL+SD P + + +W +G VS F + Sbjct: 18 PRFKSLTLASASVECLYQGARWSEGPIWFGDGRYLLWSDIPNDRILRWDEASGAVSTFRQ 77 Query: 112 PSGHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKR 171 S +A NG G++ + TR + + + +V+ D Y+GKR Sbjct: 78 SSNNA-------------NGHTRDRQGRLVSCEHLTRRVTRTE-YDGSITVLADRYRGKR 123 Query: 172 FNSPNDLFFSKSGAVYFTDPPYGLTNLDESDIKEMNYNG-VFRL-SPDGRLDLIEAGLSR 229 FNSPND+ G+++F+DP +G+ E + +E + V+R+ G + ++ + Sbjct: 124 FNSPNDVVVKSDGSIWFSDPTFGIDGFYEGERQESELSACVYRIDGQTGEVSVVADDILG 183 Query: 230 PNGLALSPDETKLYVSNSDRASPNIWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDG 289 PNGLA SPDE+ LY+ S I + +D +G S L N + D G G PDG Sbjct: 184 PNGLAFSPDESVLYIVESRGEPRKIRAFDVDLDG---SGAALSN-NRVLIDAG-PGTPDG 238 Query: 290 MNIDKQGNLF------ASAPGGIYIFAPDGECLGLISGNPGQPLSNCCFGEKGQT-LFIS 342 +D GNL+ G+ +F P GE +G I+ + +N CFG + + LF++ Sbjct: 239 FRVDVHGNLWCGWGMGTDELDGVRVFTPQGEAIGHIA--LPERCANVCFGGRHRNRLFMA 296 Query: 343 ASHNVVRVRTKTFG 356 ASH + + T G Sbjct: 297 ASHGLYSLYVNTQG 310 Lambda K H 0.317 0.135 0.409 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: 400 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: 356 Length of database: 314 Length adjustment: 28 Effective length of query: 328 Effective length of database: 286 Effective search space: 93808 Effective search space used: 93808 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 (21.6 bits) S2: 49 (23.5 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