Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate H281DRAFT_01685 H281DRAFT_01685 aspartyl-tRNA(Asn)/glutamyl-tRNA(Gln) amidotransferase subunit A
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__Burk376:H281DRAFT_01685 Length = 469 Score = 233 bits (593), Expect = 1e-65 Identities = 177/494 (35%), Positives = 249/494 (50%), Gaps = 49/494 (9%) Query: 4 AARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDT 63 A RL L E+S VE+ ++ L RI ++P V A +TVA D V++ A+ +A AG T Sbjct: 10 ATRLAELIRKREISPVEVMQAHLDRIEAIDPKVNAIVTVA-DDVMKAAQAAEAAVLAGQT 68 Query: 64 ELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDE 123 LGPL GVP KD+I T+G+ T S I KG V DA V RL+ AG +++ K N+ E Sbjct: 69 -LGPLHGVPFTAKDSIDTAGVPTQRGSPIFKGRVPDADAVSVARLKKAGGILLAKTNLPE 127 Query: 124 FAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFT 183 F+ ++ G + NPWDL+ PGGSS G +AA+AAG +PL LGTD S+R PAA T Sbjct: 128 FSYWIESDNLLSGRSNNPWDLDLTPGGSSGGESAAIAAGMSPLGLGTDLAISVRGPAAQT 187 Query: 184 GIVGLKPTYGYVSRYGVVAFA-SSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRTP 242 GIV LK T+G V G+ A VGPM R + D+A F +AGPD +DA + Sbjct: 188 GIVSLKATHGRVPMTGIWPRAPRRFWHVGPMARSIRDLALAFSQLAGPDGQDAFASS--- 244 Query: 243 PALKFGGEPSLSGVRLGVPKELLGPG---IDPGVKARVEEAIAQLEELGATVEECSLPST 299 ++F S R ++GPG +DP V A V+ A L +G VE S+P+ Sbjct: 245 -TVQFDAGVVRSDDRPLRVGWMVGPGFGPVDPEVAATVQSAAEALRSVGCIVEPVSIPAL 303 Query: 300 E--YALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIM 357 E +AL + + V E ++ + A AG + K R M Sbjct: 304 ERDFALDVFNRLHVME----------MKPAFAEATAGHAQDELYK----------MARTM 343 Query: 358 LGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWK--------IG 409 L S Y + A+++R + F RYDAL+T P A K G Sbjct: 344 LALPDTSMKDYIDAEQAAERLRD----GYAEYFTRYDALITHVLPIPAHKHGVDTFTING 399 Query: 410 EKVDDPVSMYLGDICTIPVNLAGLPAVSVPCG-FVDGLPVGMQLIGKPFADTQILQIAWA 468 E VD + YL T+P+N+ GLP VS+ G D LP+ +Q++G A++ IL IA Sbjct: 400 ETVD---ARYLQG-ATVPLNVTGLPGVSMRFGTSKDALPINVQIVGSWQAESTILHIASL 455 Query: 469 YQKVTKHHEARPAL 482 + V+ + P + Sbjct: 456 LESVSPVRDQHPKI 469 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: 551 Number of extensions: 43 Number of successful extensions: 7 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: 488 Length of database: 469 Length adjustment: 34 Effective length of query: 454 Effective length of database: 435 Effective search space: 197490 Effective search space used: 197490 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: 51 (24.3 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