Align glutaminase (EC 3.5.1.2) (characterized)
to candidate GFF4008 Psest_4081 glutaminase A
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__psRCH2:GFF4008 Length = 302 Score = 374 bits (959), Expect = e-108 Identities = 182/301 (60%), Positives = 234/301 (77%), Gaps = 1/301 (0%) Query: 8 AILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQSI 67 A+L+ IL +VRPL+GQG+VA YIPALA V +LGIA+C+ DG++F+AGDAQ FSIQSI Sbjct: 3 ALLQEILDEVRPLLGQGRVASYIPALADVPAEQLGIAVCSADGEVFEAGDAQTPFSIQSI 62 Query: 68 SKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCDML 127 SKV SLV A+ H E +W+R+G +PSG PFNSLVQLE E+G PRNPFINAGALV+CD+ Sbjct: 63 SKVFSLVQAIGHRGES-LWERLGHEPSGQPFNSLVQLEFERGRPRNPFINAGALVICDVN 121 Query: 128 QGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDVTT 187 Q R + P M + VR LSG I DT VA SE++H ARNAA+A+LM++FGNFH+DV Sbjct: 122 QSRFATPELSMRDFVRHLSGNRQIVSDTRVAESEYQHRARNAAMAYLMQAFGNFHNDVEA 181 Query: 188 VLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQNA 247 VL++YFH+CAL+M+C++LAR F FLA +G E ++ P QA+Q+NA+MATSG+Y A Sbjct: 182 VLRSYFHHCALRMNCIDLARAFAFLAREGSCPQSGEVILAPRQAKQVNAIMATSGLYDEA 241 Query: 248 GEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGRSV 307 G FA+RVGLP KSGVGGGIVA+VP + VWSPEL+ AGNSL G+A LE L++++G SV Sbjct: 242 GNFAYRVGLPGKSGVGGGIVAVVPGRFTVCVWSPELNAAGNSLIGMAALEALSQRIGWSV 301 Query: 308 Y 308 + Sbjct: 302 F 302 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: 324 Number of extensions: 9 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: 302 Length adjustment: 27 Effective length of query: 281 Effective length of database: 275 Effective search space: 77275 Effective search space used: 77275 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