Align glutaminase (EC 3.5.1.2) (characterized)
to candidate GFF939 PGA1_c09550 glutaminase A
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__Phaeo:GFF939 Length = 304 Score = 252 bits (644), Expect = 7e-72 Identities = 143/304 (47%), Positives = 194/304 (63%), Gaps = 11/304 (3%) Query: 9 ILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQSIS 68 +L+ I +Q+R G+VA YIP L V + I++ T DG LF AGD Q RFS QSI+ Sbjct: 8 VLDEISQQMRASTDWGEVASYIPELGEVRPDQFAISVATADGGLFSAGDFQTRFSAQSIT 67 Query: 69 KVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCD-ML 127 KV +L +A+ + +++W RVG++PSG+ FNS+VQLE EQG PRNPF+NAGA+V D +L Sbjct: 68 KVFTLAIALGR-AGDQLWHRVGREPSGTAFNSIVQLEHEQGRPRNPFVNAGAIVTTDEVL 126 Query: 128 QGRLSAPRQRMLEV---VRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHD 184 GR PR+ + E VR + DI + VARSE H RNAA A + SFGN + Sbjct: 127 AGR--EPREALAEFLGFVRAAAEDDDIHINADVARSETAHGHRNAAHAHFLASFGNLKNP 184 Query: 185 VTTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMY 244 VL YFH+CA +M+ +LA+ FL G + V+ + R++NALM T G Y Sbjct: 185 PEKVLGTYFHHCATEMTTQQLAKAGRFLIGTGSYPRM----VSLDRVRRLNALMLTCGHY 240 Query: 245 QNAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLG 304 +GEFA+RVGLPAKSGVGGGI+ +VP + +IAVWSP L+ GNS G +EQL +++ Sbjct: 241 DGSGEFAYRVGLPAKSGVGGGILGVVPGQASIAVWSPGLNRNGNSKLGTEAMEQLAREMD 300 Query: 305 RSVY 308 SV+ Sbjct: 301 WSVF 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: 256 Number of extensions: 12 Number of successful extensions: 4 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