Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_015926975.1 MNOD_RS01070 amidase
Query= curated2:Q2IH94 (492 letters) >NCBI__GCF_000022085.1:WP_015926975.1 Length = 469 Score = 222 bits (565), Expect = 2e-62 Identities = 176/477 (36%), Positives = 228/477 (47%), Gaps = 34/477 (7%) Query: 23 KAISSTELVEASLARIQATDGKLGAFLAVCADRARAAAKAADARAARGERRSELDGVPVA 82 +++S E+V L+R A + + AF+ + A AAA A++AR A G LDG+PV Sbjct: 19 RSLSPREVVADVLSRTAAQEPAVNAFILADGEAALAAAAASEARWAAGAPCGPLDGLPVT 78 Query: 83 VKDLFVTKGVPTTAGSRILEGYLPPYDATVVERLEAAGAVIVGKLNMDEFAMGSSNENSA 142 +KD G P GSR+ +A V+RL AGA+ VGK M EF +++ Sbjct: 79 IKDNIAWAGHPMRRGSRVSPETPLSENAPAVDRLLEAGAIPVGKTTMPEFGWKGLGDSTL 138 Query: 143 YKPCHNPWDLSRTPGGSSGGSAASVAAGQVHASLGTDTGGSIREPAAFCGVVGVKPTYGR 202 NPWDLSRT GGSS G+AA+ A A LGTD GSIR PAAFCGV G+KP+YGR Sbjct: 139 TGITRNPWDLSRTTGGSSAGAAAAAALDLGLAHLGTDGAGSIRIPAAFCGVFGLKPSYGR 198 Query: 203 VSRYGVVAFASSLDQVGPLAREVGDAALVLRTIAGHDPRDMTSSTRPVDDYLGPLEEGAR 262 V Y F + +GPLAR VGDAAL++R IA D RDM + DY LE G R Sbjct: 199 VPAYPPSPF-GPVAHLGPLARRVGDAALMMRAIARPDARDMAAWLSEPPDYSAGLETGLR 257 Query: 263 GLRVG-VPREWLSGGLDAGVEAAIRAALDTYRRLGATLVDVSLPHSKYGIGAYYLIAPAE 321 GLRV PR + +D V A A + LGA + E Sbjct: 258 GLRVAWSPRLGFARQVDPEVAALTAKAAAAFADLGAIV--------------------EE 297 Query: 322 ASSNLARYDGVRYGLRAEGAKGLKEMYAESREQGLGAEPKRRIMLGTYALSSGYYDAYYL 381 A A G+ GA + E R + + G+ + + A Sbjct: 298 ADPGFADPVETLNGIWLVGAWSVLRALPEDRRPEVEPALRAAAERGSRIAAPDFLAALNA 357 Query: 382 RAQKVRTLIRRDFDEAFRGCDVIAGPVTPSVAFALGERT---GDPLQMYLA-DIFTITCN 437 RA + R F + D++ P T AFA G T G + +LA F+ N Sbjct: 358 RAAVYTAMAR--FHARY---DLLLTPSTAVAAFAAGHLTPPDGSYGEDWLAWTPFSYPFN 412 Query: 438 LAALPGLSVPCGLEAASGLPVGLQLVGRPFDEATLFRAARALE--RELGPLPAPPEP 492 L P SVPCGL A GLPVGLQ+VG ++A + AARA E R L AP +P Sbjct: 413 LTGQPAASVPCGLTRA-GLPVGLQIVGPMGEDARVLAAARAFEAARPWPVLDAPRQP 468 Lambda K H 0.317 0.135 0.393 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: 683 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 492 Length of database: 469 Length adjustment: 34 Effective length of query: 458 Effective length of database: 435 Effective search space: 199230 Effective search space used: 199230 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: 51 (24.3 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