Align galactaro-1,5-lactonase (characterized)
to candidate Ac3H11_2337 hypothetical protein, not 6-phosphogluconolactonase
Query= reanno::HerbieS:HSERO_RS15795 (352 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2337 Length = 391 Score = 324 bits (830), Expect = 3e-93 Identities = 175/354 (49%), Positives = 237/354 (66%), Gaps = 6/354 (1%) Query: 2 IATSALSLATSHAGAATIAYVSHADSQDIYVLRLN-NDGSVNLIDKVDTGSTVMPLAISP 60 +A AL+LA AGAAT YVS+ADSQD+ V L+ N G++ +D G MP+A+SP Sbjct: 41 LAALALALAAPGAGAATWVYVSNADSQDVSVFELDRNAGALKPVDTTALGGMAMPMAVSP 100 Query: 61 DRKYLYASLRREPYAVASYAIDPASGKLKALSKAPLADNMANIATDRSGRYLLAASYFGN 120 D+K LY +LR +P+ V S AIDPASGKL+ L +APLAD+MANI TD +GR+L AASY G+ Sbjct: 101 DKKVLYVALRSQPFRVVSLAIDPASGKLRKLGEAPLADSMANIDTDATGRWLFAASYPGH 160 Query: 121 KISVNAIGSDGAVQTPPLAVIPTGKNAHSVQVDPANAFVFASNLGSDVILQYRFDPASGA 180 KI+VN+IG DGAV +IPT +AH++ D AN V A++LG D + +RFD +G Sbjct: 161 KITVNSIGKDGAVGAVQ-QLIPTAPHAHAIHADAANRHVLATSLGGDNLSAWRFDAETGK 219 Query: 181 VTPNTPP-SVASKAGAGPRHFVFSPDQRFLYCANELDATVSTYAYDRQAGTLTLLGSDSA 239 +T + P + + +GPRHFV+ QR LY NELDA+V AYD++ GTL + + Sbjct: 220 LTAHEPALTTVTPEKSGPRHFVWDKAQRSLYLLNELDASVHVMAYDKERGTLRAVQRATT 279 Query: 240 LPEGFQSSEQLAAADLHLTPDGRFLYATERTSNTLTGYRVDRASGKLTRILNIPTETQPR 299 LP GF AAD+HL+PDGR LYA+ERTS+TL+ +RVD A+G+L + +PTE PR Sbjct: 280 LPAGFAGKPW--AADIHLSPDGRTLYASERTSSTLSSFRVDAATGQLQPLGQVPTEKTPR 337 Query: 300 AFNIDPQGRYLLAVGQKA-GLTSYAIDAASGTLTPLFRYTLGRNPNWVEIIDLP 352 F +D GR+L+A GQ++ + + ID A+G R G+NPNWVEI+DLP Sbjct: 338 GFAVDSSGRFLIAAGQESHHVALHPIDPATGIPGAATRVPAGKNPNWVEIVDLP 391 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: 449 Number of extensions: 28 Number of successful extensions: 15 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: 391 Length adjustment: 30 Effective length of query: 322 Effective length of database: 361 Effective search space: 116242 Effective search space used: 116242 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