Align Glutamyl-tRNA(Gln) amidotransferase subunit D; Glu-ADT subunit D; EC 6.3.5.- (uncharacterized)
to candidate 201565 SO2421 L-asparaginase I (NCBI ptt file)
Query= curated2:O59132 (438 letters) >FitnessBrowser__MR1:201565 Length = 337 Score = 154 bits (388), Expect = 5e-42 Identities = 110/339 (32%), Positives = 175/339 (51%), Gaps = 21/339 (6%) Query: 99 TGGTIASRIDYETGAVYPAFTAEELAKAVPEIFEIANIKPKLLFN-----IFSEDMKPKH 153 TGGTI + + G A + +++PE + P+ + + I S +M P Sbjct: 11 TGGTIGMQ-KTDNGFAPVAGFLTQCVQSMPEFYHAE--MPEFVIHEYCPLIDSSNMAPTD 67 Query: 154 WIKIAHEVAKSLNSGDSGVVVAHGTDTMGYTAAALSFMLRDLGKPVILVGAQRSSDRPSS 213 W IA ++ + + D G V+ HGTDTM YTA+ALSFML+ L KPVI+ G+Q + S Sbjct: 68 WQMIADDINANYDKYD-GFVILHGTDTMAYTASALSFMLQGLSKPVIVTGSQIPLAQLRS 126 Query: 214 DAAMNLICSVRMSTS-DVAEVMVVMHGETGDTYCLAHRGTKVRKMHTSRRDAFRSINDVP 272 D NL+ S+ ++ + VAEV + + + RG + K H DAF S N Sbjct: 127 DGQTNLLNSLYIAANYPVAEVCLFFNNKL-------FRGNRSTKAHADGFDAFASPNFPL 179 Query: 273 IAKVWPNGKIEFLRDDYRRRSDSEVWVDDKLEEKVALVKVYPGISSEIIEFFIDKGYRGI 332 + + KI S++ + V + + V +V +YPGIS++I E + + + + Sbjct: 180 LLEA--GIKINLRAGKIATPSNNPLEVANISPQPVGVVTLYPGISTQIFENILQQPVKAL 237 Query: 333 VIEGTGLGHTPNDI--IPSIQRATEEGIAVCMTSQCIYGRVNLNVYATGRRLLKAGVIPC 390 ++ G+G+ P D+ + ++++A E GI + +QC G+VN+ YATG L KAGVI Sbjct: 238 ILLTFGVGNAPQDVALLRTLKQADERGIVLVNLTQCFQGKVNMGGYATGNALAKAGVISG 297 Query: 391 EDMLPETAYVKLMWVLGHTQDLEEVRRMMLTNYAGEITP 429 DM E A KL ++L E++ ML N GE++P Sbjct: 298 ADMTIEAALAKLHYLLSKNLKPIEIKTAMLQNLVGELSP 336 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: 333 Number of extensions: 13 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: 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