Align glutaminase (EC 3.5.1.2) (characterized)
to candidate WP_086509908.1 BZY95_RS10685 glutaminase A
Query= BRENDA::P0A6W0 (308 letters) >NCBI__GCF_002151265.1:WP_086509908.1 Length = 310 Score = 171 bits (433), Expect = 2e-47 Identities = 104/303 (34%), Positives = 168/303 (55%), Gaps = 5/303 (1%) Query: 8 AILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQSI 67 A L+ ++ Q R + ++A + + D +GIA+ + + QAG A++RF ++S+ Sbjct: 10 AFLQEVVEQEREYRHESEMASFGES-GEEDQELVGIALMGAESDVAQAGSAEQRFPLESV 68 Query: 68 SKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEM-EQGIPRNPFINAGALVVCDM 126 SK L+L +A+ E ++ RVG +PSG P++S+ LE E GIP NP INAGA+V M Sbjct: 69 SKALTLALALEDVGAEALFARVGMEPSGDPYHSIATLEEGEMGIPSNPMINAGAIVTTAM 128 Query: 127 LQGRLSAPR-QRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDV 185 ++GR R +R+ + R LS ++ Y+ A E E N A+ + M+S Sbjct: 129 IRGRDGKDRFERLRDFFRRLSANPELDYNR--AMFEAEDQDLNRALFYYMRSHDVLVGSE 186 Query: 186 TTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQ 245 +L Y +++M+C EL+R LAN+G E ++ R + LM T+GMY Sbjct: 187 EDLLVPYLKQTSIEMNCRELSRIAAVLANRGCDPVSGERLIGEETVRIVLTLMFTTGMYD 246 Query: 246 NAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGR 305 +G +A VG+P+KSGV G I+A+ P + V P L++ GNS+AG+ +LE L+ + Sbjct: 247 QSGRYAVEVGMPSKSGVSGAILAVAPGRLGCGVIGPALNEHGNSVAGLRLLEALSNRWRL 306 Query: 306 SVY 308 V+ Sbjct: 307 GVF 309 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: 211 Number of extensions: 7 Number of successful extensions: 3 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: 310 Length adjustment: 27 Effective length of query: 281 Effective length of database: 283 Effective search space: 79523 Effective search space used: 79523 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 Apr 09 2024. 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