Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate RR42_RS12610 RR42_RS12610 glutaminase
Query= curated2:Q8TV84 (458 letters) >FitnessBrowser__Cup4G11:RR42_RS12610 Length = 332 Score = 105 bits (263), Expect = 2e-27 Identities = 98/297 (32%), Positives = 136/297 (45%), Gaps = 29/297 (9%) Query: 96 LPNVSVMSTGGTIACRVDYETGAVK---PAFTAEELVGAVPELLDVINIVDARAVLDLLS 152 LP V V++TGGTIA + K L+ AVP L V I +A + + S Sbjct: 4 LPRVVVLATGGTIAGSSSNPASSAKYQAATVPVTALLDAVPALGAVARI-EAEQLAQVDS 62 Query: 153 ENMEPKHWMKIAEEVVDALSDPDVEGVVIGHGTDTMAFTAAALSFVIEGLNGPVVLVGAQ 212 ++M W ++ E V + PDV G+VI HGTDT+ TA L G PVVL A Sbjct: 63 KDMSFALWSRLVERVAFWSAQPDVSGIVITHGTDTLEETAMLLHLACVG-TVPVVLTAAM 121 Query: 213 RSSDRPSSDAASNLIAACAFAGDGEVGEVTVCMHGWTSDEVCLV-----HRGVRVRKMHT 267 R S S+D NL+ A A D G T+ V LV H G V K HT Sbjct: 122 RPSTSLSADGPLNLLDAVRVAADA----------GATAKGVLLVINQEIHAGRDVMKAHT 171 Query: 268 SRRDAFRSVESIPIAKVDVKDLRNPKIEFLRSDYRRPEDGEPEISGGFEEKVALVKFA-P 326 S +AF S S PI V ++ + F+R+ R P P + G + + + +A P Sbjct: 172 SAVNAFVSPVSGPIGFV-----QDNLVRFVRTPSRLPAKAWP-VPGAWPQVEIVASYAEP 225 Query: 327 GMDPEVLDFYVDRGYRGIVLEGTGLGHVSEQWLESIERAVDDGIAVVMTSQCLYGRV 383 G V+D G G+V+ G G V + +E++ A G+AVV +S+ G V Sbjct: 226 GR--IVVDALAQAGVSGLVVAAAGNGSVHQSLVEALTDAAGAGVAVVRSSRTGAGHV 280 Lambda K H 0.318 0.139 0.404 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: 304 Number of extensions: 21 Number of successful extensions: 5 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: 458 Length of database: 332 Length adjustment: 30 Effective length of query: 428 Effective length of database: 302 Effective search space: 129256 Effective search space used: 129256 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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