Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Ga0059261_1617 Ga0059261_1617 Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit and related amidases
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__Korea:Ga0059261_1617 Length = 533 Score = 224 bits (572), Expect = 4e-63 Identities = 179/505 (35%), Positives = 246/505 (48%), Gaps = 69/505 (13%) Query: 8 TVAQAREMLARGEISSLELTDALLTRIAAVE---PKVRAFLVVDAAGARAQARAADARRA 64 ++ Q + MLA G I+S +LT A L RI ++ PK+R+ + ++ A+AQAR AD R Sbjct: 39 SIEQLQAMLASGRITSAQLTQAYLDRIRVLDRAGPKLRSVIALNPQ-AKAQARRADRNRQ 97 Query: 65 AGDAS-PLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLN 123 G A PL GIP+ +KD I T TT S L++ DA VARL+AAGA+ILGK N Sbjct: 98 LGIAEGPLFGIPVLVKDNIDTAENATTAGSLALKDNFTKRDAPLVARLRAAGAIILGKTN 157 Query: 124 CDEFA-MGSSTENSAFQQT----RNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGS 178 E+A + S S + RNP+ L+R GSS G+ AA+AA A +GT+T GS Sbjct: 158 LSEWANIRDSDSMSGWSAVGGLVRNPYALDRSACGSSSGTGAAIAASLAAVGVGTETDGS 217 Query: 179 IRQPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDA 238 I P+++ G+ GLKPT G VSR +V +SS D GPMAR+V+D A + + G+D DA Sbjct: 218 IVCPSSMTGLVGLKPTLGAVSRTHVVPISSSQDTAGPMARSVKDAAALFAAMIGSDSADA 277 Query: 239 TCTDYPAPDYEAALTGD-----IRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAE 293 D A AALT D ++G+RIGV R AG+ A + VLR GAE Sbjct: 278 ATVD--ADARRAALTPDWRRASLKGVRIGVVRPEMRAGL----AALYDAQLAVLRNAGAE 331 Query: 294 VCEISLPHTPYALPVYYLIAPAEASANLARF--------------DGVRYGLRVP----- 334 + E+ L P + + + E ++LA + D + + P Sbjct: 332 LVEVKLAPPPTLRGLEFKLLQMELKSDLAAYLATTPSSVKVRTLADAIAFNRGSPAELAY 391 Query: 335 -GESYFDELERTRGAGFGPEVRRRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFE 393 G+S F+ E+T G + R L+AG D R Sbjct: 392 FGQSIFEMAEKTGGTADPAYAKTRD--DARRLAAGTLDTVLTR----------------N 433 Query: 394 QVDVIAAPTTPTVAFKIGAHTDD---PLAMYLEDVCTLPLNLAGLPGLVVPCGFAEGLPI 450 ++ V+ APTT T H D P A L V AG P L VP G GLP Sbjct: 434 RIAVLVAPTTGTAWLSDPVHGDQGSGPSASQLPAV-------AGYPHLTVPMGLTSGLPA 486 Query: 451 GLQLIGRAFDEESLLRVGDAYQRVT 475 GL IG + E LL +G AY++ + Sbjct: 487 GLSFIGAKWSEGRLLELGHAYEQAS 511 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: 533 Number of extensions: 22 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: 490 Length of database: 533 Length adjustment: 35 Effective length of query: 455 Effective length of database: 498 Effective search space: 226590 Effective search space used: 226590 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 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