Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate HSERO_RS19370 HSERO_RS19370 gluconolactonase
Query= metacyc::MONOMER-20628 (289 letters) >FitnessBrowser__HerbieS:HSERO_RS19370 Length = 302 Score = 172 bits (435), Expect = 1e-47 Identities = 107/295 (36%), Positives = 151/295 (51%), Gaps = 12/295 (4%) Query: 3 AQVTCVWDLKATLGEGPIWHGD--TLWFVDIKQRKIHNYHPATGERFSFDAPDQVTFLAP 60 A VT + LGE P+WH L+++DI + +H HP +G+ +D P++ + Sbjct: 9 AAVTVAFPEPMLLGESPLWHAQEAALYWIDIPGKAVHRLHPESGQHKRWDLPEEPGSIVR 68 Query: 61 IVGATGFVVGLKTGIHRFHPATG-FSLLLEVEDAALNNRPNDATVDAQGRLWFGTMHDGE 119 G VV ++TG+ + TG +LLL + R ND DA GR W GT+++ Sbjct: 69 HAQG-GLVVAIRTGMFHLNTDTGALTLLLAAPYDSSRIRFNDGRCDASGRFWCGTIYEPR 127 Query: 120 ENNSGSLYRMDLTGVARMDRDICITNGPCVSPDGKTFYHTDTLEKTI--YAFDLAEDGLL 177 + + G+LY + + + +NG S D + YH +T I Y +DLA G Sbjct: 128 DRDGGTLYCFERNALRDAHHAVVTSNGLAFSSDQRLMYHANTPAHRINLYDYDLAT-GAT 186 Query: 178 SNKRVFVQFALGDDV-----YPDGSVVDSEGYLWTALWGGFGAVRFSPQGDAVTRIELPA 232 SN R+ QF PDG+ VDS+G W A++ G +R SPQG+ + I LPA Sbjct: 187 SNCRLLRQFDSDKSAPDYGGRPDGAAVDSQGAYWCAMFEGGRVLRLSPQGEILQEIRLPA 246 Query: 233 PNVTKPCFGGPDLKTLYFTTARKGLSDETLAQYPLAGGVFAVPVDVAGQPQHEVR 287 T FGG DL+TLY TT R G S LAQYP +G V AV VDV GQ ++ R Sbjct: 247 RCPTMVAFGGDDLRTLYITTGRNGRSPAELAQYPESGCVLAVRVDVPGQLEYSYR 301 Lambda K H 0.321 0.139 0.442 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: 276 Number of extensions: 17 Number of successful extensions: 5 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: 289 Length of database: 302 Length adjustment: 26 Effective length of query: 263 Effective length of database: 276 Effective search space: 72588 Effective search space used: 72588 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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