Align galactaro-1,5-lactonase (characterized)
to candidate BWI76_RS08665 BWI76_RS08665 6-phosphogluconolactonase
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >FitnessBrowser__Koxy:BWI76_RS08665 Length = 331 Score = 193 bits (490), Expect = 6e-54 Identities = 115/329 (34%), Positives = 176/329 (53%), Gaps = 7/329 (2%) Query: 21 YVSHADSQDIYVLRLNNDGSVNLIDKVDTGSTVMPLAISPDRKYLYASLRREPYAVASYA 80 Y + +SQ I+V L+ G + L+ VD V P+ +SP+++YLY +R E + V +Y Sbjct: 6 YTASPESQQIHVWDLDLAGKLTLVQVVDAPGQVQPMVVSPNKEYLYVGVRPE-FRVLAYR 64 Query: 81 IDPASGKLKALSKAPLADNMANIATDRSGRYLLAASYFGNKISVNAIGSDGAVQTPPLAV 140 I P +G L +APL + +I+TD GR++ +ASY +SV + DG + +AV Sbjct: 65 IAPDNGALTFAGEAPLPGSPTHISTDHQGRFVFSASYNAGCVSVTPL-VDG-LPREAVAV 122 Query: 141 IPTGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASGAVTPNTPPSVASKAGAGPRHF 200 + + HS + P N ++ L D I + G + P V + GAGPRH Sbjct: 123 VEGLEGCHSANISPDNRTLWVPALKQDRICLFTLSD-DGFLAEQEPAEVTTVEGAGPRHM 181 Query: 201 VFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDSALPEGFQSSEQLAAADLHLTPD 260 VF P+Q++ YC NEL+++V + G + + + +P F AAD+HLTPD Sbjct: 182 VFHPNQQYGYCVNELNSSVDVWELKDPHGKIECVQTLDMMPPDFAGVRW--AADIHLTPD 239 Query: 261 GRFLYATERTSNTLTGYRVDRASGKLTRILNIPTETQPRAFNIDPQGRYLLAVGQKA-GL 319 GR LYA +RT++ +T + V L+ TETQPR FN+D G+YL+A GQK+ + Sbjct: 240 GRHLYACDRTASIITIFSVSEDGSVLSIEGYQNTETQPRGFNLDHSGKYLIAAGQKSHHI 299 Query: 320 TSYAIDAASGTLTPLFRYTLGRNPNWVEI 348 Y I+ G L RY +G+ P WV + Sbjct: 300 AVYEIEGEQGLLEEKGRYAVGQGPMWVVV 328 Lambda K H 0.316 0.131 0.375 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: 329 Number of extensions: 25 Number of successful extensions: 11 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: 352 Length of database: 331 Length adjustment: 29 Effective length of query: 323 Effective length of database: 302 Effective search space: 97546 Effective search space used: 97546 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