Align galactaro-1,5-lactonase (characterized)
to candidate H281DRAFT_03238 H281DRAFT_03238 6-phosphogluconolactonase
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >FitnessBrowser__Burk376:H281DRAFT_03238 Length = 366 Score = 323 bits (829), Expect = 3e-93 Identities = 173/351 (49%), Positives = 240/351 (68%), Gaps = 7/351 (1%) Query: 1 LIATSALSLATSHAGAATIAYVSHADSQDIYVLRLNN-DGSVNLIDKVDTGSTVMPLAIS 59 L+A +S AT AAT AY+S+ADSQDI V L+ +G++ ++ V TVMP+A+S Sbjct: 13 LLAGVTMSAATH---AATYAYMSNADSQDISVFSLDTANGALKPVETVGLAGTVMPMALS 69 Query: 60 PDRKYLYASLRREPYAVASYAIDPASGKLKALSKAPLADNMANIATDRSGRYLLAASYFG 119 P+ LYA +R +PY V S+AI+P G+L L KAPLA++MA ++TD SGRYL +ASY G Sbjct: 70 PNHLRLYAGVRSKPYRVVSFAINPLDGRLSELGKAPLAESMAYVSTDASGRYLFSASYGG 129 Query: 120 NKISVNAIGSDGAVQTPPLAVIPTGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASG 179 N ++VN+I S+G V +I TG AH+++ P N +VFAS LGSD L+ +FDP+ G Sbjct: 130 NLLAVNSIDSNG-VALDVQQIIKTGPMAHAIRNAPDNRYVFASVLGSDAWLRLKFDPSKG 188 Query: 180 AVTPNTPPSVASKAGAGPRHFVFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDSA 239 ++T + P+ + A +GPRHFVFSPD RF+Y +ELD + A+D Q ++ + + S Sbjct: 189 SLTEDATPAYSLAAKSGPRHFVFSPDHRFVYLIDELDGKLHVLAFDNQRDSVKPVQTISI 248 Query: 240 LPEGFQSSEQLAAADLHLTPDGRFLYATERTSNTLTGYRVDRASGKLTRILNIPTETQPR 299 LP F S ++ AD+H+TPDGRF+YA+ERTS+TL YRV+RASGKLTRI TE QPR Sbjct: 249 LPPNF-SGDKPWGADVHITPDGRFVYASERTSSTLAAYRVERASGKLTRIGTYATEKQPR 307 Query: 300 AFNIDPQGRYLLAVGQ-KAGLTSYAIDAASGTLTPLFRYTLGRNPNWVEII 349 FN+DP G YLLAVGQ L++Y ID +G L+ L +Y +G+ NW+EI+ Sbjct: 308 GFNVDPSGNYLLAVGQLSTSLSAYRIDPKTGALSALGQYPVGKGANWIEIV 358 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: 506 Number of extensions: 38 Number of successful extensions: 12 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: 366 Length adjustment: 29 Effective length of query: 323 Effective length of database: 337 Effective search space: 108851 Effective search space used: 108851 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