Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013090166.1 BC1002_RS11280 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000092885.1:WP_013090166.1 Length = 459 Score = 221 bits (564), Expect = 3e-62 Identities = 170/488 (34%), Positives = 234/488 (47%), Gaps = 66/488 (13%) Query: 9 VAQAREMLARGEISSLELTDALLTRIAAVEPKVRA-FLVVDAAGARAQARAADARRAAGD 67 +AQ LA G +S L + L RIA + A F+ VDA ARA A A D RAAG Sbjct: 11 LAQLAADLAAGRTTSRALVETALDRIADPAGQGAAVFMHVDADAARAAADAHDRLRAAGT 70 Query: 68 A-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVY-DATAVARLKAAGAVILGKLNCD 125 SPL GIP+ +KD+ +G +T S +L + P DA AVARLK AGAVI+G+ N Sbjct: 71 VLSPLAGIPVSVKDLFDIEGQQTRAGSVVLADAPPAKADAVAVARLKRAGAVIVGRTNMS 130 Query: 126 EFAMGSSTENSAFQQTRNPWNL-----ERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIR 180 EFA N + +P+ ERV GGSS G+AA+VA G A ALGTDTGGSIR Sbjct: 131 EFAFSGLGLNPHYGHPLSPYRRGVKGDERVSGGSSSGAAASVADGMAAVALGTDTGGSIR 190 Query: 181 QPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATC 240 PAALCG+TG KPT R+ + G V +S+LD GP+ +V CA+V R++AG +P Sbjct: 191 IPAALCGLTGFKPTAARIPKQGGVPLSSTLDSFGPIGVSVACCALVDRMLAGLEP----- 245 Query: 241 TDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLP 300 + G+R+GV + G++P+V A+ TA++ L GA V E+ Sbjct: 246 --------RIPAARPLEGVRLGVLTNFVTDGVEPEVARAIDTALKHLEAAGAIVSEVR-- 295 Query: 301 HTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIML 360 AP + A + RF + ++ L + P V RIM Sbjct: 296 -----------FAPLDRLAEINRFG----FSPIEAYAWHRPLLDKHREQYDPRVLVRIMK 340 Query: 361 GTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIG--------- 411 G A + Y D +RA + R +Q + D + APT P V ++ Sbjct: 341 GQPATAVDYLDLLAERAAMLDEAARTLWQ----RFDAVVAPTVPVVPPRLADLLTDDDTF 396 Query: 412 AHTD-----DPLAMYLEDVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLR 466 HT+ +P A D C L L PC P+GL + G +++LL Sbjct: 397 GHTNALILRNPSAFNFLDSCALSL----------PCHLRGDAPVGLMMAGAPHADDALLA 446 Query: 467 VGDAYQRV 474 +G A + V Sbjct: 447 IGRAAEAV 454 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: 508 Number of extensions: 32 Number of successful extensions: 6 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: 459 Length adjustment: 33 Effective length of query: 457 Effective length of database: 426 Effective search space: 194682 Effective search space used: 194682 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: 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