Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 6937567 Sama_1722 cytoplasmic asparaginase I (RefSeq)
Query= curated2:O59132 (438 letters) >FitnessBrowser__SB2B:6937567 Length = 337 Score = 150 bits (378), Expect = 8e-41 Identities = 106/345 (30%), Positives = 171/345 (49%), Gaps = 21/345 (6%) Query: 92 PDVTIIGTGGTIASRIDYETGAVYPAFTAEELAKAVPEIFEIANIKPKLLFN-----IFS 146 P + + TGGTI + A F + +++PE + P+ + + I S Sbjct: 4 PSIYVAYTGGTIGMQKTANGFAPVAGFLTQ-CVQSMPEFYH--EEMPEFVIHEYDPLIDS 60 Query: 147 EDMKPKHWIKIAHEVAKSLNSGDSGVVVAHGTDTMGYTAAALSFMLRDLGKPVILVGAQR 206 +M P HW IA ++ + D G V+ HGTDTM YTA+ALSFML+ LGKPVI+ G+Q Sbjct: 61 SNMSPAHWQMIADDIRNNYGKYD-GFVILHGTDTMAYTASALSFMLQGLGKPVIVTGSQI 119 Query: 207 SSDRPSSDAAMNLICSVRMSTS-DVAEVMVVMHGETGDTYCLAHRGTKVRKMHTSRRDAF 265 + SD NL+ ++ ++ VAEV + + + RG + K H DAF Sbjct: 120 PLAQLRSDGQTNLLNALYIAARYPVAEVCLFFNNKL-------FRGNRTTKAHADGFDAF 172 Query: 266 RSINDVPIAKVWPNGKIEFLRDDYRRRSDSEVWVDDKLEEKVALVKVYPGISSEIIEFFI 325 S N + + I R + ++ V + V +V +YPGIS++I + Sbjct: 173 ASPNFPLLLEAGIT--INLKAGKITREATGQLEVACISPQPVGVVTLYPGISTDIFINVL 230 Query: 326 DKGYRGIVIEGTGLGHTPND--IIPSIQRATEEGIAVCMTSQCIYGRVNLNVYATGRRLL 383 + + +++ G+G+ P D ++ +++ A E G+ + +QC G+VN+ YATG L Sbjct: 231 QQPVKALILLTFGVGNAPQDPALLNTLKEADERGVVLVNLTQCFQGKVNMGGYATGNALA 290 Query: 384 KAGVIPCEDMLPETAYVKLMWVLGHTQDLEEVRRMMLTNYAGEIT 428 +AGVI DM E KL ++L +++ M TN GE+T Sbjct: 291 RAGVISGADMTIEACLAKLHFLLSKNLPPADIKAAMQTNLVGELT 335 Lambda K H 0.320 0.138 0.403 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: 355 Number of extensions: 15 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: 438 Length of database: 337 Length adjustment: 30 Effective length of query: 408 Effective length of database: 307 Effective search space: 125256 Effective search space used: 125256 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