Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_043458298.1 H537_RS0106090 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000430725.1:WP_043458298.1 Length = 474 Score = 219 bits (557), Expect = 2e-61 Identities = 167/476 (35%), Positives = 229/476 (48%), Gaps = 37/476 (7%) Query: 1 MTPLYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAAD 60 M PL+Q T + E+L R E+S++E+ DA+ R+ A++P++ A D RA+A AD Sbjct: 1 MDPLFQATATELAELLRRREVSAVEVFDAVAERVHALDPQLNALPGFDPGPGRAEAAEAD 60 Query: 61 ARRAAGDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILG 120 R AGD +PLLG+P +K + G R T S ++ DA AVA+L+ AGAV+LG Sbjct: 61 RRLRAGDTAPLLGVPFSVKHNLWVAGRRVTQGSARFASFVAPQDAFAVAQLRRAGAVVLG 120 Query: 121 KLNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIR 180 NC EFA T N TRNPW+L R PGGSSGG+AAAVAAG P AL TD GGS R Sbjct: 121 MSNCSEFACKGVTTNPLHGTTRNPWDLARTPGGSSGGAAAAVAAGLGPLALCTDGGGSTR 180 Query: 181 QPAALCGITGLKPTYGRVSRYGLVAFASSL---DQIGPMARTVRDCAIVLRVIAGADPFD 237 +PAA CG+ G+KP+ G V V FA + +G MAR V D A++L +A D Sbjct: 181 RPAAHCGLVGMKPSAGLVPH--PVGFAEPVFGNAVVGQMARRVADVALMLDALAQPGLSD 238 Query: 238 ATCTDYPAPDYEAALTGDI-RGLRIG-VPREYFVAGMQPDVEAAVRTAIEVLREQGAEVC 295 P AAL + R+ PR + DV AA A+ L + G V Sbjct: 239 PQGLPLPVWPGAAALDEALPPAPRLAWSPRLGLDVPVDEDVAAACEAAVRRLADAGCRV- 297 Query: 296 EISLPHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVR 355 E + P P EA+ + G+ Y D L + P++ Sbjct: 298 ERADPAWPE--------GAGEAALMPLQLAGL-------AALYGDALGQWEA---DPDIA 339 Query: 356 RRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTD 415 +I G A A + R R L R F +++ PTTP A+++G + Sbjct: 340 AQIEAGRRTTGAEVARALFAREALYRALDR-----FFGSHELLVTPTTPCTAWELGRNGP 394 Query: 416 DPLAMYL-----EDVCTLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLL 465 + + V T N LP VPCG GLP+GLQ++G F + +L Sbjct: 395 ERIGGQAVGPRGHAVFTPIFNHCYLPACSVPCGLDRRGLPVGLQIVGPRFSDARVL 450 Lambda K H 0.320 0.136 0.398 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: 571 Number of extensions: 35 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: 490 Length of database: 474 Length adjustment: 34 Effective length of query: 456 Effective length of database: 440 Effective search space: 200640 Effective search space used: 200640 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: 52 (24.6 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