Align glutaminase (EC 3.5.1.2) (characterized)
to candidate 202473 SO3365 glutaminase A (NCBI ptt file)
Query= BRENDA::P0A6W0 (308 letters) >FitnessBrowser__MR1:202473 Length = 304 Score = 390 bits (1002), Expect = e-113 Identities = 188/303 (62%), Positives = 245/303 (80%), Gaps = 1/303 (0%) Query: 6 DNAILENILRQVRPLIGQGKVADYIPALATVDGSRLGIAICTVDGQLFQAGDAQERFSIQ 65 + A+LE ++ +VRPL+GQGKVA+YIPALA +D +LGIA+ T+DG+ AGD E FSIQ Sbjct: 3 ETALLEEVVDRVRPLLGQGKVANYIPALANIDPGKLGIAVTTIDGETIGAGDYLEPFSIQ 62 Query: 66 SISKVLSLVVAMRHYSEEEIWQRVGKDPSGSPFNSLVQLEMEQGIPRNPFINAGALVVCD 125 SISKV SL +A+ Y E EIW RVGK+PSG FNSLVQ+E+E+G PRNPFINAGALV+ D Sbjct: 63 SISKVFSLTLALTLYEETEIWSRVGKEPSGHSFNSLVQVELERGKPRNPFINAGALVIAD 122 Query: 126 MLQGRLSAPRQRMLEVVRGLSGVSDISYDTVVARSEFEHSARNAAIAWLMKSFGNFHHDV 185 +LQ RL AP+ RMLE+VR LS + +D VA SE++HSARNAAIA+LMKSFGNF DV Sbjct: 123 LLQSRLGAPKHRMLELVRALSQNDKVCFDKQVADSEYQHSARNAAIAYLMKSFGNFQGDV 182 Query: 186 TTVLQNYFHYCALKMSCVELARTFVFLANQGKAIHIDEPVVTPMQARQINALMATSGMYQ 245 TVL+ YFHYCALKM+C +L++ ++LAN+GK + E +++ +Q RQ+NAL+ATSG+Y Sbjct: 183 DTVLRTYFHYCALKMNCADLSKAMLYLANRGKTLDGTE-LISQVQTRQLNALLATSGLYD 241 Query: 246 NAGEFAWRVGLPAKSGVGGGIVAIVPHEMAIAVWSPELDDAGNSLAGIAVLEQLTKQLGR 305 AGEFA+RVG+P KSGVGGGI+A++P E+++ VWSPELD GNSLAG A+LEQL+++LGR Sbjct: 242 GAGEFAYRVGMPGKSGVGGGIIAVIPGELSVCVWSPELDTQGNSLAGTAMLEQLSQRLGR 301 Query: 306 SVY 308 S++ Sbjct: 302 SIF 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: 334 Number of extensions: 8 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