Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate RR42_RS23435 RR42_RS23435 gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__Cup4G11:RR42_RS23435 Length = 317 Score = 142 bits (357), Expect = 2e-38 Identities = 105/323 (32%), Positives = 158/323 (48%), Gaps = 39/323 (12%) Query: 47 KITKFSPRLDAILDVSTPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTPDAG- 105 +I SPR + I+ IA+ +W+EGPVW + LL+SD P N + +W + G Sbjct: 17 RIQALSPRFEKYHLPLAAIDRIATGGRWNEGPVWFGDARCLLWSDVPNNRILRWDEETGN 76 Query: 106 VSIFLKPSGHAEPIPAGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQRSVVVD 165 +IF KPS +A NG G++ + G R + + + +V+ D Sbjct: 77 TTIFRKPSNNA-------------NGNTRDRQGRLVTCEHGGRRVTRTE-YDGSITVLAD 122 Query: 166 NYKGKRFNSPNDLFFSKSGAVYFTDPPYGLTNL--DESDIKEMNYNGVFRLSP-DGRLDL 222 Y GK NSPND+ G+V+FTDPP+G+ E + E+ V+R+ P G L + Sbjct: 123 QYDGKPLNSPNDVVVKSDGSVWFTDPPFGIVGFYQGEKAVAELP-ERVYRIDPHTGELSV 181 Query: 223 IEAGLSRPNGLALSPDETKLYVSNSDRASPNIWVYSLDSNG--LPTSRTLLRNFRKEYFD 280 + +S PNGLA SPDE LYV S I + + +G L S+ L+ D Sbjct: 182 VADDVSGPNGLAFSPDEKLLYVIESRTRPRRIRAFHVSGDGESLTDSKVLI--------D 233 Query: 281 QGLAGLPDGMNIDKQGNLFAS------APGGIYIFAPDGECLGLISGNPGQPLSNCCFGE 334 G G PDG +D GNL+ G+ +FAPDGE +G I G P + +N CFG Sbjct: 234 AG-PGTPDGFRVDVDGNLWCGWGMGTPELDGVRVFAPDGEAIGHI-GLP-ERCANLCFGG 290 Query: 335 KGQT-LFISASHNVVRVRTKTFG 356 + + LF+++ ++ + T G Sbjct: 291 RHRNRLFMASCTSIYALYVNTQG 313 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: 413 Number of extensions: 34 Number of successful extensions: 6 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: 317 Length adjustment: 28 Effective length of query: 328 Effective length of database: 289 Effective search space: 94792 Effective search space used: 94792 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