Align xylono-1,5-lactonase (EC 3.1.1.110) (characterized)
to candidate CA265_RS13655 CA265_RS13655 hypothetical protein
Query= metacyc::MONOMER-20628 (289 letters) >FitnessBrowser__Pedo557:CA265_RS13655 Length = 291 Score = 152 bits (384), Expect = 8e-42 Identities = 100/272 (36%), Positives = 144/272 (52%), Gaps = 7/272 (2%) Query: 15 LGEGPIWHG--DTLWFVDIKQRKIHNYHPATGERFSFDAPDQVTFLAPIVGATGFVVGLK 72 LGEG WH F+DIK + I +PA G+ + LAP +V L+ Sbjct: 16 LGEGARWHAGWQKFLFIDIKGKLIGTCNPANGKVVTKKISAMPGMLAPAENDQ-LLVALQ 74 Query: 73 TGIHRFHPATGFSLLLEVEDAALNNRPNDATVDAQGRLWFGTMHDGEENNSGSLYRMDLT 132 I F+ ATG ++ L NR ND DA GRLW GTM+ ++ +G+LY + Sbjct: 75 GKIVLFNLATGKTINLAKFKEDPENRSNDGACDALGRLWVGTMNINAKHGAGNLYCYNGK 134 Query: 133 GVARMDRDICITNGPCVSPDGKTFYHTDTLEKTIYAFDL-AEDGLLSNKRVFVQFALGDD 191 V +++ ++NG C S D +T Y+ D+ I AFD G +SN+R+ V+ + Sbjct: 135 LVKKIE-GTSVSNGICWSQDNRTLYYIDSFLYHIKAFDYDLATGNISNERIVVEITEPNT 193 Query: 192 VYPDGSVVDSEGYLWTALWGGFGAVRFSP-QGDAVTRIELPAPNVTKPCFGGPDLKTLYF 250 V DG +DSEG LW A+WGG R++P G + +IE+ APNVT FGG + + Sbjct: 194 V-ADGMCIDSEGMLWVAIWGGACVNRYNPLTGACIGKIEINAPNVTSCAFGGKLMNQMLI 252 Query: 251 TTARKGLSDETLAQYPLAGGVFAVPVDVAGQP 282 TTA+ GLS + L +YP +G +F V + V G P Sbjct: 253 TTAKDGLSADELKKYPHSGSLFMVKLKVTGLP 284 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: 281 Number of extensions: 21 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: 291 Length adjustment: 26 Effective length of query: 263 Effective length of database: 265 Effective search space: 69695 Effective search space used: 69695 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