Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011801148.1 PNAP_RS08795 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000015505.1:WP_011801148.1 Length = 450 Score = 179 bits (454), Expect = 2e-49 Identities = 134/412 (32%), Positives = 196/412 (47%), Gaps = 43/412 (10%) Query: 68 LAGVPIAVKDNICTSGMETTCASRILKGYV-SPFDATVVERLRAAGAMIIGKANMDEFAM 126 L G+P++VKD +G TT S +L G + DA V RLRAAGA+++G++NM EFA Sbjct: 70 LTGIPVSVKDLFDVAGQVTTAGSTVLAGAAPASTDAVAVARLRAAGAVLVGRSNMVEFAF 129 Query: 127 GSSGESSAFGVTRNPWD--LERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTG 184 G + +G NP D +ER+PGGSSSG+A +VA G A + LG+DTGGSIR PAA G Sbjct: 130 SGVGINPHYGTPVNPADASIERIPGGSSSGAAVSVATGAALVGLGSDTGGSIRIPAALCG 189 Query: 185 IVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRTPPA 244 IVG K T V G V ++SLD V + R V D + EV++ RR Sbjct: 190 IVGFKSTARLVPATGAVPLSTSLDTVCAVTRSVHDAVTVHEVLSA--RR----------- 236 Query: 245 LKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEYALS 304 ++ G+P LS R+ V + L+ G+D V E ++ L + GA +E E AL Sbjct: 237 VQLAGKP-LSSCRIAVARTLMQDGLDSTVAQAFEHSLRVLRQAGARIE-------EIALE 288 Query: 305 AYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTYVLS 364 ++ AS L+ AA++ H + V RI+ G + + Sbjct: 289 EIGELSAINASGGLS----------AAESHAWHRKLIAEHEAQYDPRVALRILRGARMSA 338 Query: 365 AGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPVSMYLGDIC 424 A + D R + + E +DA+++PT P A I +D + + Sbjct: 339 ADYIDLLAARQNWISRM-----EARLSHFDAVLSPTVPIVAPSIASVLDHDDEFFRINAL 393 Query: 425 ----TIPVNLAGLPAVSVPCGFVDGLPVGMQLIGKPFADTQILQIAWAYQKV 472 T N+ A+S+PC LPVG+ L D +L +A + V Sbjct: 394 LLRNTSVANMLDGCAISIPCQTPGQLPVGLMLWHAALHDDNVLDLALQVEAV 445 Lambda K H 0.318 0.135 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: 535 Number of extensions: 24 Number of successful extensions: 7 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: 488 Length of database: 450 Length adjustment: 33 Effective length of query: 455 Effective length of database: 417 Effective search space: 189735 Effective search space used: 189735 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 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