Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_051347134.1 B076_RS0102630 allophanate hydrolase
Query= curated2:O66610 (478 letters) >NCBI__GCF_000483485.1:WP_051347134.1 Length = 606 Score = 167 bits (423), Expect = 9e-46 Identities = 147/482 (30%), Positives = 229/482 (47%), Gaps = 47/482 (9%) Query: 6 SLSELRELLKRGEVSPKEVVESFYDRY-NQTEEKVKAYITPLYGKALKQAESLKEREL-- 62 ++ ++ RG+VSP+ + E + + + E + + PL K E+L E +L Sbjct: 14 NIEQIHGYYARGDVSPEVLFEFLHQQAESMAEYNIWIELLPLQ-KIRGYLENLGEFDLDS 72 Query: 63 -PLFGIPIAVKDNILVEGEKTTCASKILENFVAPYDATVIERLKKAGALIVGKTNLDEFA 121 PL+GIP AVKDNI + G T+ A + DA V+ L +AGA+ +GKTNLD+FA Sbjct: 73 KPLWGIPFAVKDNIDLAGVPTSAACPSYA-YTPQEDAEVVRLLIEAGAVPLGKTNLDQFA 131 Query: 122 MGSSTEYSAFFPTKNPWDLERVPGGSSGGSAASVAVLSAPVSLGSDTGGSIRQPASFCGV 181 G S + N +D E + GGSS GSA SVA+ SLG+DT GS R PA+F + Sbjct: 132 TGLVGTRSPYGVCHNSFDFETISGGSSSGSAVSVAMGLCSFSLGTDTAGSGRVPAAFNNL 191 Query: 182 IGIKPTYGRVSRYGLVAFASSLDQIGVFGRRTEDVALVLEVISGWDEKDSTSAK---VPV 238 IG+KP+ G +S G+V S D + +F + D V +V++ D D+ S K + V Sbjct: 192 IGLKPSKGILSTRGVVPAVRSQDVVSIFALDSVDAEKVFDVVAKQDPDDAFSRKQSELNV 251 Query: 239 PEWSEEVKKEVKGLKIGLPKE---FFEYELQPQVKEAFENFIKELEKEGFEIKEVSLPHV 295 P W E+ IG+P E F + Q Q FE + +L++ G+E+KE+ Sbjct: 252 PAWGEKP-------VIGIPDEAGRMFYGDAQAQAN--FEKSVAQLQEMGYEVKELDFS-- 300 Query: 296 KYSIPTYYIIAPSEASSNLARYDGVRYGYRAKEYKDIFEMYARTRDEGFGPEVKRRIMLG 355 A E + L Y G + A+ Y I E + + + P V+ I Sbjct: 301 ----------AWLETAKLL--YGG---AWVAERYAAIAE-FIESTPKDMDPTVEGIIRSA 344 Query: 356 TFALSAGYYDAYYLKAQKVRRLITNDFLKAFEEVDVIASPTTPTLPFKFGERLENPIEMY 415 T + Y Y +R+ + ++EVD +PTTP++ FK E + P+ + Sbjct: 345 TDLSAVDAYRGAYQLQDAIRQTES-----IWQEVDCFVTPTTPSI-FKIAEVEKEPVALN 398 Query: 416 LS-DILTVPANLAGLPAISIPIAWK-DGLPVGGQLIGKHWDETTLLQISYLWEQKFKHYE 473 + T NL A+++P ++ DG P G L + LL ++ W KF + Sbjct: 399 SALGTYTNFMNLLDYSAVAMPSGFREDGRPCGITLFAPAGSDCKLLNLTKQWHPKFVEFA 458 Query: 474 KI 475 + Sbjct: 459 AV 460 Lambda K H 0.316 0.136 0.394 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: 660 Number of extensions: 41 Number of successful extensions: 5 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: 478 Length of database: 606 Length adjustment: 35 Effective length of query: 443 Effective length of database: 571 Effective search space: 252953 Effective search space used: 252953 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