Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_019864744.1 METMI_RS0103000 allophanate hydrolase
Query= curated2:Q46E35 (475 letters) >NCBI__GCF_000384075.1:WP_019864744.1 Length = 592 Score = 172 bits (435), Expect = 4e-47 Identities = 134/421 (31%), Positives = 207/421 (49%), Gaps = 38/421 (9%) Query: 46 LEQAKKI-DVEGHNGPLAGVPIAIKDNISVVGLPNSCGSKILEDYIPPFNAYVIEKLLAA 104 + QAKK+ D++ H+ PL G+P A+KDNI VGLP + Y+P +A+V++KL+ A Sbjct: 56 MAQAKKLEDLDPHDLPLYGIPFAVKDNIDCVGLPTTAACPGFS-YLPAKSAFVVQKLIDA 114 Query: 105 GAVILGKTNMDEFAMGSSTETSY--FGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALG 162 GAV++GKTNMD+FA G + S +G N + + + GGSS GSA VA F+LG Sbjct: 115 GAVLIGKTNMDQFATGLTGTRSPEPYGICKNSINPDYISGGSSSGSAVAVALNIVSFSLG 174 Query: 163 SDTGGSVRCPAAFCGVVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVTDIAVLMDVIAG 222 +DT GS R PA F +VGLKPT G +S GVV SL+ V + + + L D++ Sbjct: 175 TDTAGSGRVPAGFNNIVGLKPTRGLLSCSGVVPACKSLDCVSIFSQTIAEAEYLFDIVNA 234 Query: 223 YDRKDSTSIDSKTEYQKALIEDVKGLKIGVPK----EFFGEGIHPDVEKAVWNAIHKCED 278 YD DS + + + ++ K L+ GVPK ++FG P+ E I K + Sbjct: 235 YDTNDSYARNDRQGLDASMTATAK-LRFGVPKPEQLQYFGA---PEGEALFAQTITKLQT 290 Query: 279 LGASWEEVSMPHIKYALASYYIIAMSEASSNLARFDGTRYGYRASGENWHAMVSKTRAEG 338 LG E P ++ A Y E R+ G R E H ++ + A Sbjct: 291 LGEVVEIDFQPFLEAAALLY------EGPWLAERYAGIRAFIENHPEQLHPVIMEVLA-- 342 Query: 339 FGTEVKRRILLGTYALSAGYHDKYYLKALKVRTLVKQDFDKALSKVDVLMAPTMPNPAFK 398 G + K I A + + L+ L K+D L + ++ PT P ++ Sbjct: 343 -GAKDKNAI--------AAFDALHRLQQL------KRDTATLLQSLSCVVVPTAPR-IYR 386 Query: 399 IGEKIEDPLTLYLS-DVNTCPINLAGVPSLSVPCGF-TDGLPIGLQIMGKPFDEPAVLRA 456 I E + +P+ L + T +NL + +L++P GF ++ LP G+ + + +L Sbjct: 387 IDEVLAEPIRLNSNLGYYTNYMNLLDLSALAIPAGFYSNQLPFGITLFSTALADARLLAI 446 Query: 457 A 457 A Sbjct: 447 A 447 Lambda K H 0.315 0.133 0.391 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: 619 Number of extensions: 30 Number of successful extensions: 3 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: 475 Length of database: 592 Length adjustment: 35 Effective length of query: 440 Effective length of database: 557 Effective search space: 245080 Effective search space used: 245080 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: 42 (22.0 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