Align galactaro-1,5-lactonase (characterized)
to candidate BWI76_RS02900 BWI76_RS02900 6-phosphogluconolactonase
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >FitnessBrowser__Koxy:BWI76_RS02900 Length = 383 Score = 136 bits (342), Expect = 1e-36 Identities = 120/381 (31%), Positives = 184/381 (48%), Gaps = 34/381 (8%) Query: 2 IATSALSLATSHAGAAT-IAYVSHADSQDIYVLRLNNDGSVNLI-DKVDTGS--TVMPLA 57 + ++LSL + A A T A+V + + R D + DK + LA Sbjct: 7 LLVASLSLLAAGAAAQTHYAWVGTYNPNGEGLYRFTVDSQTGALRDKALVAKLPNLAQLA 66 Query: 58 ISPDRKYLYASLRREPYAVASYAIDPASGKLKALSK-APLADNMANIATDRSGRYLLAAS 116 +S D K LYA+ + V ++ I ++G+L L++ A ++ GR+LL A+ Sbjct: 67 VSADGKTLYAASEVDKGVVQAWRIG-SNGELSELNQVASGGAGPVYLSLTPDGRHLLVAN 125 Query: 117 YFGNKISVNAIGSDGAV---------QTPPLAVIPT-------------GKNAHSVQVDP 154 Y I+V + +G + Q P A P G +AH V DP Sbjct: 126 YVSGSIAVLPVKEEGNLGEAVDIHQDQGPAGAERPAAAVEGSFAISDHNGPHAHMVAADP 185 Query: 155 ANAFVFASNLGSDVILQYRFDPASGAVTPNTPPSV-ASKAGAGPRHFVFSPDQRFLYCAN 213 + FV++++LG D I QYR D ASG +TPN PP + AS GAGPRHFVF+P L+ N Sbjct: 186 SGRFVYSTDLGLDRIYQYRLDNASGKLTPNDPPFIDASSPGAGPRHFVFTPQGDGLWLIN 245 Query: 214 ELDATVSTYAYDRQAGTLTLLGSDSALPEGFQSSEQLAAADLHLTPDGRFLYATERTSNT 273 E +T++ Y D+Q+G L + SALPE ++ + AA L L+ DG+ LY R N+ Sbjct: 246 EEASTLTFYHLDKQSGLLREGKTVSALPEEYKGTS--FAAGLVLSRDGKQLYVANRLHNS 303 Query: 274 LTGYRVDRASGKLTRILNIPTE-TQPRAFNIDPQGRYLLAVGQKA-GLTSYAIDAASGTL 331 + + V A G L+ +I T PR +D Q ++L + Q++ +T + + G L Sbjct: 304 IAHFTV-LADGSLSHQEDIWTRGDYPRTLTLDSQEQWLYVMNQRSDNITRFRVAPKDGRL 362 Query: 332 TPLFRYTLGRNPNWVEIIDLP 352 T YT P+ + I P Sbjct: 363 TFSPDYTPVGGPSQMVISAQP 383 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: 448 Number of extensions: 36 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: 383 Length adjustment: 30 Effective length of query: 322 Effective length of database: 353 Effective search space: 113666 Effective search space used: 113666 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