Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011384077.1 AMB_RS08440 amidase
Query= curated2:Q9HR43 (423 letters) >NCBI__GCF_000009985.1:WP_011384077.1 Length = 391 Score = 150 bits (380), Expect = 5e-41 Identities = 132/428 (30%), Positives = 196/428 (45%), Gaps = 58/428 (13%) Query: 3 LNAFIT--ETTIQGAADGPLDGTTVAVKDNISTKGVPTTCGSKMLADYEPP--YNATVVE 58 LNAF + + GA GPL G T A KD G T G+ P + A + Sbjct: 5 LNAFALGGDVYLNGAETGPLAGLTFAAKDVFDVAGYVTGAGNPDWRRLAEPAKHTAWAIG 64 Query: 59 DLLAAGGTIVGKTNMDEFGMGTTTETSYFGPTKNPVDETRVPGGSSGGSAAAVANGDADL 118 LL +G +VGKT+ DE G + S++G NP VPGGSS GSAAAVA G + Sbjct: 65 TLLESGARLVGKTHTDELTRGIFGDNSHYGTPDNPRAPGHVPGGSSSGSAAAVAGGLCSM 124 Query: 119 ALGSDTGGSVRAPAAYCGVVGLKPTYGLVSRYGLVAYANSLEQIGPIAPTVEGAAELLDV 178 ALG+DT GS R PA++CGV GL+PT G + G+++ +N+ + +G +A E A++ + Sbjct: 125 ALGTDTAGSTRVPASFCGVFGLRPTLGTIPMDGVLSQSNTFDTVGLLADDPEILAKMGEA 184 Query: 179 IAGPDEHDGTTRDAGADADYASAATGDVDGLTIGVPQELTDGADDRVVERFEAALADLRA 238 + D TR A + V ++ + +D V EAAL ++ Sbjct: 185 LLRKKIKD--TRPA-----------------QVVVLEDALEASDPAVAAAIEAALPRIKE 225 Query: 239 EGATTVD----VALPSCEYAVAAYYVIAMSEASSNLARFDGVRYGTGGGFDGNWNETFAD 294 A V +P ++ V I EA + T G + N N F Sbjct: 226 AVAPIVRGRKLSPVPLADW-VEHQNAIQGREA-----------WETFGEWINNSNPRFGF 273 Query: 295 ARADGF--GDEVTRRILLGTYALSAGYHDKYYKQAQEARAWVKQDFDETFADVDVVASPT 352 AD F G +V++R T + + G+ A+ WV+ E ++ PT Sbjct: 274 EVADNFLRGSKVSQR----TLSAARGFR-------LRAKRWVQ----EALEGNAMLVLPT 318 Query: 353 MPVLPPKLGESLDDPVQM-YLADANTTPANLANLPAISVPAGDADGLPVGVQLVGPKFGE 411 PV P + ++ + + TT A +A P IS+P DGLPVG+ L+GP+ G Sbjct: 319 TPVTAPPVHSPRSVMWEIRHRIVSLTTIAGMAGCPQISLPLCKVDGLPVGLSLIGPR-GS 377 Query: 412 ETIINAAA 419 + ++ AAA Sbjct: 378 DALLLAAA 385 Lambda K H 0.312 0.132 0.381 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: 434 Number of extensions: 24 Number of successful extensions: 3 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: 423 Length of database: 391 Length adjustment: 31 Effective length of query: 392 Effective length of database: 360 Effective search space: 141120 Effective search space used: 141120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 50 (23.9 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