Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate AO356_11100 AO356_11100 asparaginase
Query= curated2:A1RX40 (451 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_11100 Length = 334 Score = 103 bits (258), Expect = 6e-27 Identities = 92/294 (31%), Positives = 135/294 (45%), Gaps = 31/294 (10%) Query: 151 IFSEDMTPSHWQQLASKIGEIFRRESDVKG---VVVAHGTDTLHYSAAAMAFAVQEAPGP 207 I S +MTP++WQQL + + DV+G V++ HGTDTL YSAAAM+F + Sbjct: 64 IDSANMTPAYWQQLREAVVDAV----DVQGCDSVLILHGTDTLAYSAAAMSFQLLGLHAR 119 Query: 208 IVFVGAQRSSDRPSSDAALNVIGATVVAVHAPFAESV-IAMHGSVNDDTILVHRGVRARK 266 + F G+ + SDA N+ GA +VA+ A V + HG + T R K Sbjct: 120 VCFTGSMLPAGVTDSDAWENLSGA-LVALGQGLAPGVHLYFHGELLAPT-------RCAK 171 Query: 267 MHTSRRDAFMSINSKPIAEVDPLRGSLKLSTSTYKGRGDDVVVQASFSDKVALVKFYPGM 326 + + R F + + P L T + + +A + +PG+ Sbjct: 172 VRSFGRHPFKRLERQGGGTPAPT-----LPTQLNYNQPKQLT-------NIAALPLFPGI 219 Query: 327 SPDIFDFYLEKGFKGLVIE--GTGLGHVST-ALIDSVRRLVREGVFVAMASQCIFGRVNM 383 S I D L G +GLV+E G+G G A + S+ R GV V +QC G V + Sbjct: 220 SAQILDGLLGSGIQGLVLECYGSGTGPSDNPAFLASLERARDSGVVVVAVTQCHEGGVEL 279 Query: 384 NVYRTGVELIKAGVVPAGDMIPETAYVKLSWILGQTEDPEEIQRLFTANLAFEI 437 +VY G L GV+ G M E A KL ++G EE++RL +L E+ Sbjct: 280 DVYEAGSRLRGVGVLSGGGMTREAALGKLQALIGAGLPVEEVRRLVELDLCGEL 333 Lambda K H 0.319 0.136 0.391 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: 386 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 451 Length of database: 334 Length adjustment: 30 Effective length of query: 421 Effective length of database: 304 Effective search space: 127984 Effective search space used: 127984 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 (21.8 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