Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011883775.1 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000016205.1:WP_011883775.1 Length = 458 Score = 218 bits (554), Expect = 5e-61 Identities = 174/490 (35%), Positives = 231/490 (47%), Gaps = 70/490 (14%) Query: 9 VAQAREMLARGEISSLELTDALLTRIAAVEPK-VRAFLVVDAAGARAQARAADARRAAGD 67 +AQ + LA G +S L D L RIA + F VDA AR A A D RAAG Sbjct: 10 LAQLADDLAAGRTTSRALVDIALERIADPSGQGAVVFTEVDADHARTAADAHDRLRAAGT 69 Query: 68 A-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVY-DATAVARLKAAGAVILGKLNCD 125 SPL GIP+ +KD+ G T S++L+ P DA AVARL+ AGAV++G+ N Sbjct: 70 VLSPLAGIPVSVKDLFDVAGQVTRAGSRVLDGAPPAQADAAAVARLRRAGAVLVGRTNMS 129 Query: 126 EFAMGSSTENSAFQQTRNPWNLE-----RVPGGSSGGSAAAVAAGEAPAALGTDTGGSIR 180 EFA N F R+P+ + R+ GGSS G+AA+VA G A ALGTDTGGSIR Sbjct: 130 EFAFSGLGLNPHFGTPRSPYRRDVPGDARIAGGSSSGAAASVADGMAAVALGTDTGGSIR 189 Query: 181 QPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATC 240 PAALCG+TG KPT R+ G V +++LD GP+ TV CA+V RV+AG +P Sbjct: 190 IPAALCGLTGFKPTASRIPTGGAVPLSTTLDSFGPIGLTVACCALVDRVLAGLEPH---- 245 Query: 241 TDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLP 300 PA + G+R+GV Y G+ DV AA+ +++ L GA V ++ P Sbjct: 246 --VPA-------ARPLEGVRLGVLTNYVTDGVDADVAAALDASLKHLEAAGAIVSDVRFP 296 Query: 301 HTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESY--FDELERTRGAGFGPEVRRRI 358 LP D R+G P E+Y L + P V RI Sbjct: 297 ALD-TLP-----------------DVNRFGFS-PIEAYAWHRPLLAQHRDRYDPRVLARI 337 Query: 359 MLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIG------- 411 + G A +A Y D RA + R + + D + APT P V +I Sbjct: 338 LKGEPASAADYLDLLAARAAMLDEAART----VWSRFDALVAPTVPIVPPRIADLEADDA 393 Query: 412 --AHTD-----DPLAMYLEDVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESL 464 AHT+ +P A D C L L PC P+GL L +++L Sbjct: 394 AFAHTNALVLRNPAAFNFLDACALSL----------PCQPRGAAPVGLMLAAAPHRDDAL 443 Query: 465 LRVGDAYQRV 474 L +G A + V Sbjct: 444 LAIGQAVEAV 453 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: 529 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 490 Length of database: 458 Length adjustment: 33 Effective length of query: 457 Effective length of database: 425 Effective search space: 194225 Effective search space used: 194225 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