Align glutaminase (EC 3.5.1.2) (characterized)
to candidate HSERO_RS04140 HSERO_RS04140 glutaminase
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__HerbieS:HSERO_RS04140 Length = 305 Score = 266 bits (679), Expect = 6e-76 Identities = 135/286 (47%), Positives = 195/286 (68%), Gaps = 1/286 (0%) Query: 23 QGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQSISKVLSLVVAMRHYSE 82 +GKVADYIPALA V + G+A+ T+DG + GD + RFSIQSISKV L +A Y E Sbjct: 20 EGKVADYIPALACVAPDQFGMAVATIDGGVHCVGDGETRFSIQSISKVFLLTMAYGSYGE 79 Query: 83 EEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCDMLQGRLSAPRQRMLEVV 142 + +W+RVG+ PS +PFNSL++LE+E+G+PRNPF+N GAL V D L R + M+ ++ Sbjct: 80 D-LWKRVGQHPSTNPFNSLIELELERGVPRNPFLNPGALAVADALLSRHTHLESAMVSLM 138 Query: 143 RGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDVTTVLQNYFHYCALKMSC 202 R LSG +D++YD+ V SE S+R+ A A+LM+S GNF ++V V++ Y CA++ SC Sbjct: 139 RELSGSADLNYDSEVFNSELRSSSRHHAAAYLMQSHGNFSNEVGEVVRAYCASCAIEASC 198 Query: 203 VELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQNAGEFAWRVGLPAKSGV 262 VELAR +FLAN G+ I +++ +A+++ ALM T+G Y+ +G A+ +GLP KSGV Sbjct: 199 VELARAGLFLANGGRDIASGRQLLSAREAQRVCALMLTTGTYEYSGMTAFAIGLPTKSGV 258 Query: 263 GGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGRSVY 308 GGG++A++P I WSP LD GNS+ + LE ++ G SV+ Sbjct: 259 GGGVLAVIPGRGCICAWSPRLDPRGNSVRAMKALELVSNTAGLSVF 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: 268 Number of extensions: 12 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: 305 Length adjustment: 27 Effective length of query: 281 Effective length of database: 278 Effective search space: 78118 Effective search space used: 78118 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