Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_019556639.1 F612_RS0104900 allophanate hydrolase
Query= curated2:Q1J0C2 (483 letters) >NCBI__GCF_000381085.1:WP_019556639.1 Length = 598 Score = 179 bits (454), Expect = 2e-49 Identities = 156/472 (33%), Positives = 225/472 (47%), Gaps = 47/472 (9%) Query: 10 LARAVQARETTPQALLEAARRRAEAARDLNALISLNDRADEQAARVQVRLDAGETLPLAG 69 L A + E TP+ ++ ++ AE D N I + + + + LPL G Sbjct: 8 LKAAYASGELTPRKVISHIKQAAENYDDHNIFIHVLSDTELEPYLAALEKTERNNLPLWG 67 Query: 70 VPIVVKDNLNVIGTRTTCGSRILANYVSPYDATAVERLTGAGAVIIGKANMDEFAMGSST 129 +P V+KDN+++IG TT G A Y AT V L AGA+ IGKANMD+FA G Sbjct: 68 IPYVIKDNIDLIGIPTTAGCPEYA-YTPTESATVVRLLIEAGAIPIGKANMDQFATGLVG 126 Query: 130 ESSAWGPTLNPWDRERVPGGSSGGSAVAVAANLTPVALGSDTGGSVRQPAAFTGIYGLKP 189 S +G N +D + + GGSS GSAV++A NL +LG+DT GS R PAAF + GLKP Sbjct: 127 TRSPYGVCHNSFDFDMISGGSSSGSAVSLALNLCSFSLGTDTAGSGRVPAAFNNLIGLKP 186 Query: 190 TYGRVSRYGLVAYASSLDQIGPFARSAADLALLMNVLAGHDPRDATSLD----APPAF-- 243 + G +S G+V S D I FA +A D + +V A D RD S D PPA+ Sbjct: 187 SKGLLSTSGVVPAVRSQDVISIFALNAQDAYQVFDVAAQVDARDEYSRDENALMPPAWGA 246 Query: 244 RP--GTPDDLQGLRVGVIREALEGNTPGVEAALNATLDALRGAGATVREVSVPSVQHAIA 301 +P G PD+ + E + AT+ L+ G ++E +P + Sbjct: 247 KPILGIPDE---------TSLFFNDDKKAEISFFATIHQLKQMGYEIKE--IPFKRWLDT 295 Query: 302 AYYLIATPEASSNLARYDGMVYGERVSAPDAVSSMTLTREQGFGREVKRRIMLGTYALSS 361 A L Y G ER A + L R + R I+ G +LS+ Sbjct: 296 AKLL------------YGGAWVAERYVAIEDF----LNRHEDKIDPTVRTIIAGARSLSA 339 Query: 362 GYYDAYY-SKAMKVRRLIAQDFARAFGNVDVLVTPTSPFPAFRRGEKTQDPLAMYA-ADV 419 DAY S A++ + QD + +VD ++TPT+P F + + +DP+ + Sbjct: 340 A--DAYKGSYALQKAQSETQDL---WQSVDCMITPTTP-SIFSQAQLEKDPIGFNSILGT 393 Query: 420 DTVAINLAGLPALSVPAGFERVDGVRLPVGVQLIAPPLQDERLVALAGGLEG 471 T +NL AL++P GF + D LP G+ L AP D +L+ LA L+G Sbjct: 394 YTNFMNLLDYAALALPTGFRKDD---LPTGITLFAPAGSDRQLLQLADQLQG 442 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: 615 Number of extensions: 26 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: 598 Length adjustment: 35 Effective length of query: 448 Effective length of database: 563 Effective search space: 252224 Effective search space used: 252224 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 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