Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_057508933.1 ABB28_RS12410 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_001431535.1:WP_057508933.1 Length = 535 Score = 212 bits (539), Expect = 3e-59 Identities = 179/497 (36%), Positives = 259/497 (52%), Gaps = 43/497 (8%) Query: 7 LNRLFLAGELSAVEIAESALSRIAQVE---PAVGAFITVAADHVIERAKKLDARRKAGDT 63 L LAGEL++ + + L+RIA ++ P + A I + D + E A++ D R++G Sbjct: 58 LQARMLAGELTSTTLTTAYLARIAALDRAGPRLRAVIELNPDALKEAAQR-DRERRSGRV 116 Query: 64 ELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDE 123 GPL G+P+ +KDNI + M TT S L G+ P DA +V RLR AGA+I+GK+N+ E Sbjct: 117 R-GPLHGIPVLLKDNINAAPMSTTAGSLALAGFRPP-DAFLVRRLREAGAVILGKSNLSE 174 Query: 124 FAM-----GSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQ 178 +A SG S+ G TRNP+ L P GSSSGSA AV+A A +++GT+T GSI Sbjct: 175 WANYRGEDSISGWSARGGQTRNPYRLGYSPCGSSSGSAVAVSANLAAVSIGTETDGSIVC 234 Query: 179 PAAFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRD---A 235 PAA G+VGLKPT G VSR G++ + S D GP+ R V D A + IAG D D A Sbjct: 235 PAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPITRTVADAAAVLTAIAGRDDADPATA 294 Query: 236 TNAGRTPPALKFGGEP-SLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEEC 294 T GR P L G R+GV L PG+ ++ A+ +L GATV + Sbjct: 295 TLPGRAVYDYTARLNPDGLRGARIGVMDSPLTQ--RPGIGTLMQHAVDELRRAGATVVKV 352 Query: 295 -SLPSTEYALSAYYVIAVAEASSNLARFDGVRYGYRA-----AQAGGLHEMYSKTRGEGF 348 L T++A A + E S L R+ +R+ ++A Q + ++ F Sbjct: 353 PELDPTQWA-EAEQTVLRFEFKSGLERY--LRH-WKAPLRTLPQLIAFNTRHAAQELPLF 408 Query: 349 GTE-VKRRIMLGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERY--DALVTPTTPFTA 405 G E ++ +GT + AG+ A R+Q R + + + DALV PT TA Sbjct: 409 GQELLEASAQVGT-LGDAGYIQA---RSQARRIAGEQGIDALLRAHQLDALVAPTMG-TA 463 Query: 406 WKIGEKVDD--PVSMYLGDICTIPVNLAGLPAVSVPCGFVDGLPVGMQLIGKPFADTQIL 463 W I D P Y +AG P++SVP G VDGLPVG+ +G +A+ +++ Sbjct: 464 WPITRSGGDTSPGGSYGA------AAVAGYPSLSVPMGHVDGLPVGLLFMGTAWAEPRLI 517 Query: 464 QIAWAYQKVTKHHEARP 480 ++ +AY++ T P Sbjct: 518 ELGYAYEQRTMARRPPP 534 Lambda K H 0.318 0.135 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: 675 Number of extensions: 38 Number of successful extensions: 6 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: 488 Length of database: 535 Length adjustment: 35 Effective length of query: 453 Effective length of database: 500 Effective search space: 226500 Effective search space used: 226500 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 (21.7 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