Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011444266.1 SARO_RS03015 allophanate hydrolase
Query= curated2:Q1J0C2 (483 letters) >NCBI__GCF_000013325.1:WP_011444266.1 Length = 589 Score = 177 bits (449), Expect = 9e-49 Identities = 165/468 (35%), Positives = 223/468 (47%), Gaps = 42/468 (8%) Query: 6 TATDLARAVQARETTPQALLEAARRRAEAARDLNALISLNDRADEQ----AARVQVRLDA 61 TA +A AV + +TT A+ EA R A + I ++ + E A + VRL A Sbjct: 8 TARAIAAAVNSGQTTALAVAEATLLRLAAYDAVQPQIWISRASPEALLAAARAIDVRLAA 67 Query: 62 GETLPLAGVPIVVKDNLNVIGTRTTCGSRILANYVSPYDATAVERLTGAGAVIIGKANMD 121 GE LPLAGVP VKDN++V G TT A Y AT VERL AGA+ +GK N+D Sbjct: 68 GEDLPLAGVPFAVKDNIDVAGFHTTAACPAFA-YRPATSATVVERLLAAGALCVGKTNLD 126 Query: 122 EFAMGSSTESSAWGPTLNPWDRERVPGGSSGGSAVAVAANLTPVALGSDTGGSVRQPAAF 181 +FA G + S +G N + V GGSS GSA AVAA L ALG+DT GS R PAAF Sbjct: 127 QFATGLNGTRSPYGAPRNAHNLAYVSGGSSSGSASAVAAGLVAFALGTDTAGSGRVPAAF 186 Query: 182 TGIYGLKPTYGRVSRYGLVAYASSLDQIGPFARSAADLALLMNVLAGHDPRDATSLDAPP 241 + G KP+ GR S GLV +LD I FA AD ++ ++AG DP DA S P Sbjct: 187 QHLVGFKPSKGRWSNRGLVPACRTLDCITVFAHDTADARIVDGIVAGFDPADAFS--KPL 244 Query: 242 AFRPGTPDDLQGLRVGVIREALEGNTPGVEA--ALNATLDALRGAGATVREVSVPSVQHA 299 A RP + +GV R VEA + LD L G V E+ +Q Sbjct: 245 ADRP-----RKMRAIGVPRRDQRAFFGDVEAEHLYDRALDRLSTLGRIV-EIDYAPLQE- 297 Query: 300 IAAYYLIATPEASSNLARYDGMVYGERVSAPDAVSSMTLTREQGFGREVKRRIMLGTYAL 359 AA L P + A G++ PDA+ T+ G+++ G L Sbjct: 298 -AAQLLYGGPWVAERTAALAGLL----ADNPDALDP-TVREVVAPGQDI------GAVDL 345 Query: 360 SSGYYDAYYSKAMKVRRLIAQDFARAFGNVDVLVTPTSPFPAFRRGEKTQDPLAMYAA-D 418 +G Y + +++R + ++D+L PT+ +R E P+A+ +A Sbjct: 346 FNGIY-----RLAELKR----HADTLWESIDLLAFPTTG-TTYRVAELLAAPIALNSALG 395 Query: 419 VDTVAINLAGLPALSVPAGFERVDGVRLPVGVQLIAPPLQDERLVALA 466 T +NL + AL+VPAG R + GV LI P D L+ A Sbjct: 396 YYTNFVNLLDMAALAVPAG-SRANATGF--GVTLIGPADTDLALLDAA 440 Lambda K H 0.316 0.132 0.375 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: 652 Number of extensions: 31 Number of successful extensions: 4 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: 483 Length of database: 589 Length adjustment: 35 Effective length of query: 448 Effective length of database: 554 Effective search space: 248192 Effective search space used: 248192 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 (21.6 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