Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf6N2E2_878 Amidase clustered with urea ABC transporter and nitrile hydratase functions
Query= curated2:Q46E35 (475 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_878 Length = 504 Score = 249 bits (637), Expect = 1e-70 Identities = 151/427 (35%), Positives = 233/427 (54%), Gaps = 24/427 (5%) Query: 58 NGPLAGVPIAIKDNISVVGLPNSCGSKILEDYIPPFNAYVIEKLLAAGAVILGKTNMDEF 117 +G L+G +A+KDNIS+ G+P G+ LE ++P F+A V+ +LL AGA ILGK + + Sbjct: 85 SGKLSGKTVALKDNISLAGVPMMNGAAPLEGFVPSFDATVVTRLLDAGATILGKATCEHY 144 Query: 118 AMGSSTETSYFGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSVRCPAAFCG 177 + + TS P NP+ GGSS GSAA+VA G A+G D GGS+R PAA+CG Sbjct: 145 CLSGGSHTSDPAPVHNPFRHGYTTGGSSSGSAALVATGAVDLAIGGDQGGSIRIPAAWCG 204 Query: 178 VVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVTDIAVLMDVIAGYDRKDSTSIDSKTE- 236 + G+KPT+G V GV+A ++ + VGP+ +NV D A++++V+AG D D K + Sbjct: 205 IYGMKPTWGLVPYTGVMAIESTFDHVGPMTSNVRDNALMLEVMAGADGLDPRQAAPKVDA 264 Query: 237 YQKALIEDVKGLKIGVPKEFFG-EGIHPDVEKAVWNAIHKCEDLGASWEEVSMPHIKYAL 295 Y L V GL+IGV +E F P + + V +AI + E LGA EEVS+P A Sbjct: 265 YCDYLERGVTGLRIGVLQEGFQLANQDPRIAEKVRSAIARLEALGARVEEVSVPEHNLAG 324 Query: 296 ASYYIIAMSEASSNLARFDGTRYGYRASGENWHAMVS----------KTRAEGFGTEVKR 345 + + I + + +G +G NW + + +A +K Sbjct: 325 SLWSPIGCEGLTMQMMHGNG-------AGFNWKGLYDVGLLDKQAGWRDQANALSPSLKL 377 Query: 346 RILLGTYALSAGYHDKYYLKALKVRTLVKQDFDKALSKVDVLMAPTMP---NPAFKIGEK 402 + +G + L Y+ +YY KA + + +DKAL D+L+ PT+P P + G Sbjct: 378 CMFVGQFGLER-YNGRYYAKAQNIARFARAAYDKALDTYDLLVMPTVPITAQPLPEPGSS 436 Query: 403 IEDPLTLYLSDV-NTCPINLAGVPSLSVPCGFTDGLPIGLQIMGKPFDEPAVLRAAYTFE 461 I + +T L + NT ++ G P++S+PCG DGLP+GL ++G+ + E + +AA FE Sbjct: 437 ITETVTRALEMLGNTAAQDITGHPAMSIPCGLVDGLPVGLMLVGRHYAEGTLYQAAAAFE 496 Query: 462 QNTDYHT 468 + D+ T Sbjct: 497 ASVDWRT 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: 630 Number of extensions: 39 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: 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 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