Align gluconolactonase subunit (EC 3.1.1.17) (characterized)
to candidate Pf6N2E2_318 Gluconolactonase (EC 3.1.1.17)
Query= metacyc::MONOMER-13276 (356 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_318 Length = 363 Score = 134 bits (337), Expect = 4e-36 Identities = 113/378 (29%), Positives = 177/378 (46%), Gaps = 49/378 (12%) Query: 2 TTGRMSRRECLSAAVMVPIAAMTATATITGSAQAAKNNMNGSTIGKITKFSPRLDAILDV 61 T RR L +++V AA A + G AQA + I P + Sbjct: 8 TAADQGRRVFLKKSLVVSAAA-AALGNLPGLAQAEPLSQRYPD-PLINILDPSFMDLRIF 65 Query: 62 STPIEVIASDIQWSEGPVWVKNGNFLLFSDPPANIMRKWTP-DAGVSIFLKPSGHAEPIP 120 + +E +A+ ++W+EGPVWV +G +LL SD P N + +W G+S++ + S Sbjct: 66 NASVEKLATGLRWAEGPVWVGDGRYLLVSDIPNNRIVRWDEVTGGLSVYRENSNF----- 120 Query: 121 AGQFREPGSNGMKVGPDGKIWVADSGTRAIMKVDPVTRQR-----SVVVDNYKGKRFNSP 175 SNGM G++ V + T A + +TR +V+ D+++GK NSP Sbjct: 121 --------SNGMCRDRQGRLLVCEGSTTA-SEGRRITRTEHNGTITVLADSFEGKPLNSP 171 Query: 176 NDLFFSKSGAVYFTDPPYGL-TNLDESDIKEMNYNGVFRLSPD-GRLDLIEAGLSRPNGL 233 ND+ + G+V+FTDPP+ N + + + V+R+ + G++ + L+ PNGL Sbjct: 172 NDIVCKRDGSVWFTDPPFQTGNNYEGHKVTPAQPHAVYRIDGETGKVTRVIDDLAGPNGL 231 Query: 234 ALSPDETKLYVSNSDRASPN--IWVYSLDSNGLPTSRTLLRNFRKEYFDQGLAGLPDGMN 291 SPDE LYV RA PN IW ++ +G R RK A + DG+ Sbjct: 232 CFSPDEKILYVVEG-RAKPNRLIWAITVKDDGTLGER------RKHIEGLDYAAI-DGIK 283 Query: 292 IDKQGNLFASAPG------------GIYIFAPDGECLGLISGNPGQPLSNCCF-GEKGQT 338 D+ GNL+ G G+ +F P+G+ +G IS P N CF G +G Sbjct: 284 CDESGNLWCGWGGNGDPKADLEKLDGVRVFNPEGKAIGHISLPERCP--NVCFGGREGNR 341 Query: 339 LFISASHNVVRVRTKTFG 356 LF++ SH++ + T G Sbjct: 342 LFMAGSHSLYSLFVNTRG 359 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: 437 Number of extensions: 27 Number of successful extensions: 4 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: 363 Length adjustment: 29 Effective length of query: 327 Effective length of database: 334 Effective search space: 109218 Effective search space used: 109218 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