Align glutaminase (EC 3.5.1.2) (characterized)
to candidate RR42_RS27580 RR42_RS27580 glutaminase
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__Cup4G11:RR42_RS27580 Length = 304 Score = 283 bits (725), Expect = 3e-81 Identities = 155/305 (50%), Positives = 199/305 (65%), Gaps = 2/305 (0%) Query: 5 MDNA-ILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFS 63 MD A IL+ I R + PL+ QG+VADYIP L V + G+A+ DG+ GDA FS Sbjct: 1 MDYAHILQRIHRDIAPLLTQGRVADYIPELGKVPATHFGMALVFADGRSHCVGDAAVPFS 60 Query: 64 IQSISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVV 123 IQSISK+ + +A + E+ +WQRVG++PSG+ FNSLVQLE EQG PRNPFINAGALVV Sbjct: 61 IQSISKLFACTLAFQLLGED-LWQRVGREPSGNAFNSLVQLEYEQGKPRNPFINAGALVV 119 Query: 124 CDMLQGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHH 183 D+L R M++ +R LSG I YD VA+SE EH+ RN A+A+ MK FG Sbjct: 120 TDVLCSRFVQAETAMVQFLRRLSGNPAIDYDPRVAQSEREHADRNRAMAYFMKDFGRLEM 179 Query: 184 DVTTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGM 243 V V+ Y CA+ MSC +LAR +FLA+ G E V+ ++++ALM T G Sbjct: 180 PVDKVIDAYCRQCAITMSCEDLARAALFLAHGGVVPWSGERVLDASPTKRLSALMLTCGT 239 Query: 244 YQNAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQL 303 Y AG+F +RVGLPAKSGVGGGIVA++P A+ VWSP LD +GNSLAG+ LE LT Sbjct: 240 YDAAGDFVYRVGLPAKSGVGGGIVAVLPGRWAVCVWSPGLDHSGNSLAGVQALEWLTTLS 299 Query: 304 GRSVY 308 G S++ Sbjct: 300 GHSIF 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: 272 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