Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate BPHYT_RS21005 BPHYT_RS21005 asparaginase
Query= curated2:O29380 (418 letters) >FitnessBrowser__BFirm:BPHYT_RS21005 Length = 330 Score = 99.8 bits (247), Expect = 1e-25 Identities = 100/324 (30%), Positives = 148/324 (45%), Gaps = 36/324 (11%) Query: 82 DVKIISTGGTIAS--KVDYRTGA-VTSQFTAEEIASEVPELTEICNVDAELLYNILSENM 138 ++ +I TGGTIA K T + S +EI +P E+ N+ AE L SEN Sbjct: 6 NIVVIGTGGTIAGQGKASVNTSTYMCSVLGIDEILGSIPHAGELANLRAEQLLQTGSENF 65 Query: 139 KPENWIELARHVYKAL--KDHEGVIITHGTDTMHFSAAALSFMLSTPKPVVFVGAQRSSD 196 + + + V + L D +GV+ITHGTDT+ +A L L + KPVV VG+ R Sbjct: 66 NNTHLLAIGNRVAELLARNDVDGVVITHGTDTIEETAYFLHLTLKSAKPVVVVGSMRPPS 125 Query: 197 RPSSDAAMNLLCAAKAAT----EDIGEVVVCMHGSTSDDYCLVHRGVKVRKNHTSRRDAF 252 SSDAA+NL A AT +G +VV + +H V K+++ + DAF Sbjct: 126 AMSSDAALNLYDALAVATHPSSRGLGTLVVANNE--------IHTARDVVKSNSFKLDAF 177 Query: 253 QSVNAKPIGRIDYPSLSVEWLSWRYRRGERELKL-------TDRLERKVVLIKFFPGLSS 305 +S P G + Y +E YRR R L T R KV ++ + L Sbjct: 178 RS----PYGALGY---VIEGAPRYYRRPARAHTLDTPWSITTLRSLPKVDIVYAYGALEP 230 Query: 306 DILEYYHSKGYRGFVIEGTGLGHVSTDWIDTLRRVCEDSV-VVMTSQCLWGRVCDRVYDT 364 + + RG + GTG G+V++ ID LR V VV S+ G V +++ Sbjct: 231 GAISAITANA-RGLIYVGTGNGNVASHLIDPLRDAARRGVHVVRASRTGSGIV---LHNG 286 Query: 365 GRDILRAGVIEGEDMLPEVALIKL 388 + G + +D +P+ A I L Sbjct: 287 AQPDHEYGWLTVDDQIPQKARILL 310 Lambda K H 0.319 0.136 0.406 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: 269 Number of extensions: 17 Number of successful extensions: 3 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: 418 Length of database: 330 Length adjustment: 30 Effective length of query: 388 Effective length of database: 300 Effective search space: 116400 Effective search space used: 116400 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 (21.7 bits) S2: 49 (23.5 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