Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate AZOBR_RS25530 AZOBR_RS25530 sugar aminotransferase
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__azobra:AZOBR_RS25530 Length = 346 Score = 305 bits (781), Expect = 1e-87 Identities = 173/341 (50%), Positives = 214/341 (62%), Gaps = 7/341 (2%) Query: 29 MFREAGEAARVAAVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFARYLIETK 88 M +EA A L ++ + ALA RLRA PP +T ARGSSDHAA +ARYL ET Sbjct: 7 MMQEAVTAPAAVRRLLDSDTAAVAALADRLRAVPPPFAMTIARGSSDHAAGYARYLFETA 66 Query: 89 AGVLTSSAGPSVSSVYDASPNLEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVNVV 148 G++T+SA PSV + Y A ++ A LAISQSG+SPDLL +AA+A GA ALVN Sbjct: 67 LGLVTASAAPSVVTAYGADLRVKDAFVLAISQSGQSPDLLCVAEAARAGGAVTAALVNAE 126 Query: 149 DSPLAALADEVIPLHAGPELSVAATKSYIAALVAVTQLIAAWTEDAELTAALQDLPTALA 208 D+PLA +PLHAGPELSVAATKS++A+L A+ +L A W +D L AL LP L Sbjct: 127 DAPLAERVAHPLPLHAGPELSVAATKSFVASLAAIARLTAVWMDDRTLLDALPRLPFWLE 186 Query: 209 AAWTLDWSLAVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPM 268 A DWS A+ L+ S+L ++ RG + +A E ALKFKET HAE FSAAEV+HGPM Sbjct: 187 RAGAADWSAALPVLEAVSSLLIVARGRSYPIAQEMALKFKETAAAHAEPFSAAEVMHGPM 246 Query: 269 ALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGGG------GDAPDALPTLAS 322 ALV+ GFP LV A DE+ V + A L+ GA +L+A D P LP Sbjct: 247 ALVEPGFPVLVVAVRDETLDGVLDTARALKEAGAHLLVASAEERALALADTPLLLPP-PL 305 Query: 323 HPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNKVTETI 363 HPVL+PI IQ+FY L+VARG+DPD P HL KVT TI Sbjct: 306 HPVLDPIAAIQAFYPFMARLAVARGFDPDRPRHLRKVTRTI 346 Lambda K H 0.315 0.128 0.360 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: 392 Number of extensions: 11 Number of successful extensions: 2 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: 363 Length of database: 346 Length adjustment: 29 Effective length of query: 334 Effective length of database: 317 Effective search space: 105878 Effective search space used: 105878 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