Align glutaminase (EC 3.5.1.2) (characterized)
to candidate WP_079648661.1 B5X82_RS13450 glutaminase
Query= BRENDA::P0A6W0 (308 letters) >NCBI__GCF_900167915.1:WP_079648661.1 Length = 318 Score = 285 bits (730), Expect = 8e-82 Identities = 159/312 (50%), Positives = 209/312 (66%), Gaps = 6/312 (1%) Query: 1 MAVAMD-NAILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQ 59 + VA D AI++ I ++ +GKVADYIP LA VD GIA+ T DG++F AGDA Sbjct: 3 VTVAPDLQAIVDRIAAEMAGREERGKVADYIPGLARVDPKHFGIAVATHDGRMFAAGDAD 62 Query: 60 ERFSIQSISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAG 119 FSIQS+SKV +L +A+ + +W+RVG++PSG+ FNS+VQLE EQGIPRNPFINAG Sbjct: 63 AAFSIQSVSKVFALTIALGKVGDA-LWKRVGREPSGNAFNSIVQLEAEQGIPRNPFINAG 121 Query: 120 ALVVCDMLQGRLSAPRQRMLEV---VRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMK 176 A+VV D++ AP++ + E+ VR L+G I D VA+ E + RNAA+A M+ Sbjct: 122 AIVVSDVVLAG-HAPKEAIGEILRFVRDLAGDDGIVIDDEVAQGEADTGFRNAALANYMR 180 Query: 177 SFGNFHHDVTTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINA 236 SFGN HH V VL YFH CAL MSC +LAR FL ++G+ +V+PM+AR+INA Sbjct: 181 SFGNIHHPVDQVLGVYFHQCALAMSCRQLARAGRFLMHEGQHPDTGFNIVSPMRARRINA 240 Query: 237 LMATSGMYQNAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVL 296 LM G Y +GEFA+RVG+P KSGVGGGI+ +VP +IAVWSP L++ GNS G L Sbjct: 241 LMMLCGHYDGSGEFAFRVGIPGKSGVGGGILCVVPGIASIAVWSPGLNERGNSTLGSLAL 300 Query: 297 EQLTKQLGRSVY 308 E+L G SV+ Sbjct: 301 ERLAAATGWSVF 312 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: 288 Number of extensions: 10 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: 318 Length adjustment: 27 Effective length of query: 281 Effective length of database: 291 Effective search space: 81771 Effective search space used: 81771 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 24 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