Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011427974.1 RHE_RS24625 allophanate hydrolase
Query= curated2:Q1J0C2 (483 letters) >NCBI__GCF_000092045.1:WP_011427974.1 Length = 603 Score = 187 bits (476), Expect = 7e-52 Identities = 164/484 (33%), Positives = 226/484 (46%), Gaps = 49/484 (10%) Query: 12 RAVQARETTPQALLEAARRRAEAARDLNALISLNDRADE----QAARVQVRLDAGETLPL 67 RA TP ++E R A D I + DE +A + R +LPL Sbjct: 12 RAAYEAGKTPLDIIEIVIARRNDATD--PAIFITPAPDEALRGEARALMERAPDPNSLPL 69 Query: 68 AGVPIVVKDNLNVIGTRTTCGSRILANYVSPYDATAVERLTGAGAVIIGKANMDEFAMGS 127 G+P VKDN++V G TT + Y DAT V RL AGA++IGK N+D+FA G Sbjct: 70 WGIPFAVKDNIDVAGLPTTAACPTFS-YRPEKDATVVARLRAAGAIVIGKTNLDQFATGL 128 Query: 128 STESSAWGPTLNPWDRERVPGGSSGGSAVAVAANLTPVALGSDTGGSVRQPAAFTGIYGL 187 + S +G + +D+ V GGSS GSAVAVA+ L ALG+DT GS R PAAF + G+ Sbjct: 129 NGTRSPYGAPRSVFDKNYVSGGSSSGSAVAVASGLASFALGTDTAGSGRVPAAFNNLVGI 188 Query: 188 KPTYGRVSRYGLVAYASSLDQIGPFARSAADLALLMNVLAGHDPRDATSLDAPPAFRPGT 247 KPT G V G+V S+D + FA + D + V+ G+D D S A P+ P + Sbjct: 189 KPTPGLVPNVGVVPACRSVDVVTVFAATVGDGVTIRKVMEGYDAADPFSRKAVPSSLPAS 248 Query: 248 PDDLQGLRVGVIREA---LEGNTPGVEAALNATLDALRGAGATVREVSVPSVQHAIAAYY 304 GLR+GV+ A GN VEA +A ++ R GAT I A+ Sbjct: 249 -----GLRIGVLDGAEREFFGNRQ-VEALYDAAIERARDLGAT------------IVAFD 290 Query: 305 LIATPEASSNLARYDGMVYGERVSAPDAVSSMTLTREQGFGREVKRRIMLGTYALSSGYY 364 +A+ L Y+G ER++ AV T F V R I+ G A Y Sbjct: 291 YAPFRQAAELL--YNGPWVAERLA---AVKDFLATNATDFEPTV-RTIIEGAKA-----Y 339 Query: 365 DAYYSKAMKVR-RLIAQDFARAFGNVDVLVTPTSPFPAFRRGEKTQDPLAMYA-ADVDTV 422 DA + + + + Q + + D+L+ PTSP + E DP+ T Sbjct: 340 DAVAAFEGRYKLEALRQKTGKEWEKADLLMLPTSP-TTYTVEEMLADPIVKNGHFGRYTN 398 Query: 423 AINLAGLPALSVPAGFERVDGVRLPVGVQLIAPPLQDERLVALAGGLE-----GIGAVRM 477 +NL A++VPAGF+ DG LP GV LI P D+ L A + G+G R+ Sbjct: 399 FVNLLDCAAIAVPAGFD-ADG-HLPAGVTLIGPAFTDDALARFADAMHRTANAGMGKDRL 456 Query: 478 EVAP 481 P Sbjct: 457 SAIP 460 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: 761 Number of extensions: 47 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: 603 Length adjustment: 35 Effective length of query: 448 Effective length of database: 568 Effective search space: 254464 Effective search space used: 254464 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