Align D-glucosaminate dehydratase (EC 4.3.1.9) (characterized)
to candidate AZOBR_RS26420 AZOBR_RS26420 amino acid deaminase
Query= reanno::pseudo3_N2E3:AO353_21740 (405 letters) >FitnessBrowser__azobra:AZOBR_RS26420 Length = 432 Score = 202 bits (513), Expect = 2e-56 Identities = 140/378 (37%), Positives = 182/378 (48%), Gaps = 23/378 (6%) Query: 24 DVSLPALVLHREALEHNIHWMQAFVSHSGAELAPHGKTSMTPSLFRRQLEAGAWGITLAT 83 D++LP L L +A N + A+ G LAPH KT M P + +EAGAWG T+A Sbjct: 43 DMALPVLTLDEDAFAANRDLIFAYARRHGVALAPHAKTPMAPQIASALVEAGAWGATVAN 102 Query: 84 VVQTRAAYAHGVRRVLMANQLVGAPNMALIAELLAD-PSFDFYCMVDHPDNVADLGVFFA 142 + Q GV R+++AN++ G + + LLA P D D P V L Sbjct: 103 LQQAAVLLRAGVTRLILANEIGGRASGERLGALLASHPDADLRAFADSPAAVETLAAAAR 162 Query: 143 ARG----LRLNVMIEYGVVGGRCGCRSEAEVLALAEAIKAQPG-LALTGIEGYEGVIHGD 197 A G L V++E G GR G R A V A+ A+ PG L L GI YEG + Sbjct: 163 AAGRPPERPLPVLVEVG--AGRAGARDRAAVDAILAAVVRHPGLLVLDGIATYEGAVATA 220 Query: 198 QAVSGIREFAASLVRLAVQLQDSGAFAISKP-IITASGSAWYDLIAESFEAQNA-GGRFL 255 AA + R A A A +P ++TA GSA++D++ A G Sbjct: 221 DPAETAANIAALMRRTAEAFALVRALAPERPLLLTAGGSAFFDMVVAGLAPVAATDGNAT 280 Query: 256 SVLRPGSYVAHDHGIYKEAQCCVLDRRSDLHEG------LRPALEVWAHVQSLPEPGFAV 309 VLR G+ HDHG+Y+ A LD R G RPAL +WA V + PEP A+ Sbjct: 281 LVLRSGAIFFHDHGVYERA-LGALDARQGFACGGATAADFRPALRLWAEVLTRPEPELAI 339 Query: 310 IALGKRDVAYDAGLPVPLLRYRAG-VLPAVGDDVSACTVTAVMDQHAFMTVAPGVQLRVG 368 G RD ++D GLP PL +R G L A G VT + DQHAF+ V G L VG Sbjct: 340 CGFGMRDASFDQGLPRPLRVHRDGTALSAEG-----LRVTRLNDQHAFVAVPAGHDLAVG 394 Query: 369 DIISFGTSHPCLTFDKWR 386 DI+ G SHPC D+WR Sbjct: 395 DIVELGISHPCTCIDRWR 412 Lambda K H 0.322 0.136 0.413 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: 483 Number of extensions: 21 Number of successful extensions: 7 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: 405 Length of database: 432 Length adjustment: 32 Effective length of query: 373 Effective length of database: 400 Effective search space: 149200 Effective search space used: 149200 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 (21.9 bits) S2: 50 (23.9 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