Align glutaminase (EC 3.5.1.2) (characterized)
to candidate 5208617 Shew_1126 glutaminase (RefSeq)
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__PV4:5208617 Length = 304 Score = 403 bits (1035), Expect = e-117 Identities = 196/300 (65%), Positives = 247/300 (82%), Gaps = 1/300 (0%) Query: 9 ILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQSIS 68 +LE I+ QVRPL+G+GKVADYIPALA VD ++LGIA+ T+DGQ AGD E FSIQSIS Sbjct: 6 LLETIIEQVRPLLGKGKVADYIPALAEVDPTKLGIAVTTIDGQTIGAGDYLEPFSIQSIS 65 Query: 69 KVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCDMLQ 128 KV SL VA+ Y E EIW RVGK+PSG FNSLVQ+E+E+G+PRNPFINAGAL++ D+LQ Sbjct: 66 KVFSLTVALTLYEEAEIWSRVGKEPSGQSFNSLVQIELERGVPRNPFINAGALIIADLLQ 125 Query: 129 GRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDVTTV 188 RL AP+ RMLEVVR LS + YD VA SE+EHSARNAAIA+LMKSFGNF++DV V Sbjct: 126 SRLGAPKHRMLEVVRKLSANPHVIYDKRVAASEYEHSARNAAIAYLMKSFGNFNNDVDRV 185 Query: 189 LQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQNAG 248 L+NYFHYCALKMSC +L++ ++LAN+G+++ E VV+P+Q R++NAL+ATSG+Y AG Sbjct: 186 LRNYFHYCALKMSCADLSKAMLYLANRGQSLSA-EQVVSPIQTRKLNALLATSGLYDGAG 244 Query: 249 EFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGRSVY 308 EFA+RVG+P KSGVGGGI+A++P +M+I VWSPELD GNSLAG A LE+L++ LGRS++ Sbjct: 245 EFAYRVGMPGKSGVGGGIIAVIPGDMSICVWSPELDKNGNSLAGTAALEKLSQALGRSIF 304 Lambda K H 0.321 0.135 0.395 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: 316 Number of extensions: 7 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: 308 Length of database: 304 Length adjustment: 27 Effective length of query: 281 Effective length of database: 277 Effective search space: 77837 Effective search space used: 77837 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: 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