Align glutaminase (EC 3.5.1.2) (characterized)
to candidate 6938368 Sama_2487 glutaminase (RefSeq)
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__SB2B:6938368 Length = 304 Score = 396 bits (1018), Expect = e-115 Identities = 194/304 (63%), Positives = 247/304 (81%), Gaps = 1/304 (0%) Query: 5 MDNAILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSI 64 ++ A+L++++ +VRPL+GQGKVADYIPALA V +LGIA+ T+DG AGD QE FSI Sbjct: 2 LEQALLDDLVAKVRPLLGQGKVADYIPALARVSPYKLGIAVTTIDGTTLGAGDWQEAFSI 61 Query: 65 QSISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVC 124 QSISKV SL AM Y E EIW RVGK+PSG FNSLVQ+E+E+GIPRNPFINAGALV+ Sbjct: 62 QSISKVFSLTGAMMLYEEREIWSRVGKEPSGHSFNSLVQVELERGIPRNPFINAGALVIA 121 Query: 125 DMLQGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHD 184 D+LQ RL AP+QRMLE+VR LS + YD VVA SE++HSARNAAIA+LMKSFGNFH+D Sbjct: 122 DLLQSRLGAPKQRMLEIVRMLSQNHKVCYDKVVADSEYQHSARNAAIAFLMKSFGNFHND 181 Query: 185 VTTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMY 244 V VL++YFHYC+L MSC +L+R V+LANQG ++ +E VV+P Q R++NAL+ATSG+Y Sbjct: 182 VDKVLRSYFHYCSLSMSCADLSRAMVYLANQGVSLDGNE-VVSPTQTRRLNALLATSGLY 240 Query: 245 QNAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLG 304 AGEFA+RVG+P KSGVGGGI+A++P +M++ VWSP LD +GNSLAG +LE L ++LG Sbjct: 241 DGAGEFAYRVGMPGKSGVGGGIIAVIPGDMSVCVWSPALDASGNSLAGTRLLELLAQELG 300 Query: 305 RSVY 308 RS++ Sbjct: 301 RSIF 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: 331 Number of extensions: 10 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