Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012044479.1 BBTA_RS20770 amidase
Query= curated2:Q46E35 (475 letters) >NCBI__GCF_000015165.1:WP_012044479.1 Length = 504 Score = 253 bits (645), Expect = 1e-71 Identities = 154/441 (34%), Positives = 240/441 (54%), Gaps = 33/441 (7%) Query: 49 AKKIDVEG-HNGPLAGVPIAIKDNISVVGLPNSCGSKILEDYIPPFNAYVIEKLLAAGAV 107 A K +V+G +G LAG + +KDN+++ G+P GS LE +IP +A ++ ++L AG Sbjct: 75 AIKTEVKGASSGKLAGRTVVLKDNVALAGVPMMNGSTTLEGFIPAADATIVSRILDAGGT 134 Query: 108 ILGKTNMDEFAMGSSTETSYFGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGG 167 I+GK + F + + TS P NPW + GGSS GSAA+VAAGE ++G D GG Sbjct: 135 IVGKAVCEHFCLSGGSHTSDPAPVHNPWKMGYSAGGSSSGSAALVAAGEVDMSIGGDQGG 194 Query: 168 SVRCPAAFCGVVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVTDIAVLMDVIAGYDRKD 227 S+R PA++CG+ G+K T+G V GV+ ++++ GP+ NV D A+L++V+AG D D Sbjct: 195 SIRIPASYCGIYGMKATHGLVPYTGVMPIESTIDHTGPMTANVKDNALLLEVLAGADGLD 254 Query: 228 STSIDSK-TEYQKALIEDVKGLKIGVPKEFFGEGIHPDVEKAVWNAI----HKCEDLGAS 282 K + Y +AL + VKGLKIGV KE F P++E+ V + + + LGAS Sbjct: 255 PRQYAPKVSAYTEALGKGVKGLKIGVLKEGFSA---PNMEEGVVSKVKAGAERFAKLGAS 311 Query: 283 WEEVSMPHIKYALASYYIIAMSEASSNLARFDGTRYGYRASGENWHAMVS---------- 332 EVS+P +ALA++ I + + +G G NW + Sbjct: 312 VSEVSIPEHMHALAAWNPITLEGFLVQMMLGNG-------MGFNWKGLYDVGLLDAHSGW 364 Query: 333 KTRAEGFGTEVKRRILLGTYALSAGYHDKYYLKALKVRTLVKQDFDKALSKVDVLMAPTM 392 +TRA+ +K +L+G + L Y +YY K+ + K +D D+L+ PT+ Sbjct: 365 RTRADDLSVTLKLTMLVGQWGLE-HYRGRYYAKSRNIAIQAKAAYDAMFGSYDLLLMPTL 423 Query: 393 PNPAFKIGEKIEDPLT-----LYLSDVNTCPINLAGVPSLSVPCGFTDGLPIGLQIMGKP 447 P A I K + PL + T P ++ G P++++PCG +DGLP+GL ++GK Sbjct: 424 PCVATPIPAK-DAPLAEVVQRAFEMTATTSPFDVTGHPAMTLPCGLSDGLPVGLMLIGKD 482 Query: 448 FDEPAVLRAAYTFEQNTDYHT 468 + E + +AA FE + D+ T Sbjct: 483 YAESTIYQAAAAFEADGDWKT 503 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: 596 Number of extensions: 35 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: 475 Length of database: 504 Length adjustment: 34 Effective length of query: 441 Effective length of database: 470 Effective search space: 207270 Effective search space used: 207270 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