Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate Ac3H11_138 Gluconolactonase
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_138 Length = 307 Score = 87.0 bits (214), Expect = 6e-22 Identities = 81/272 (29%), Positives = 126/272 (46%), Gaps = 35/272 (12%) Query: 76 EGPVWVKNGNFLLFSDPPANIMRKWTPDAGVSIFLKPSGHAEPIPAGQFREPGSNGMKVG 135 EGPV+ GN + P I R + P G A + A EP NGMK Sbjct: 45 EGPVFDGVGNLYVTDIPWGRIFR-----------IDPQG-AWTLVAEYDGEP--NGMKFM 90 Query: 136 PDGKIWVADSGTRAIMKVDPVTRQRSVVVDNYKGKRFNSPNDLFFSKSGAVYFTDPPYGL 195 G + + D +M++D T + ++ +RF NDL F G +YFTD G Sbjct: 91 DAGTLLITDY-KNGLMRLDIATGGVTPYLERRNSERFKGVNDLIFDADGNLYFTDQ--GQ 147 Query: 196 TNLDESDIKEMNYNGVFRLSPDGRLDLIEAGLSRPNGLALSPDETKLYVSNSDRASPNIW 255 + L + + ++RL P+G+LDL+ A + PNG+ALSPD LY++ + +W Sbjct: 148 SGLHDPSGR------LYRLRPNGQLDLLLANVPSPNGVALSPDGRVLYLAAT--RGNCVW 199 Query: 256 VYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMNIDKQGNLFASAPGGIYIFAPD--G 313 L +G S + F + G PDG+ +D G L + PG Y++ + Sbjct: 200 RVPLLPDG---SVAKVGQFFTSHGPSG----PDGLAVDTSGRLLVANPGLGYVWVLNHRA 252 Query: 314 ECLGLISGNPGQPLSNCCF-GEKGQTLFISAS 344 E + ++ G G +N F G+ GQT+F++ S Sbjct: 253 EPVLVLRGPAGASTTNLAFGGQGGQTVFVTDS 284 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: 479 Number of extensions: 48 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: 307 Length adjustment: 28 Effective length of query: 328 Effective length of database: 279 Effective search space: 91512 Effective search space used: 91512 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