Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf1N1B4_3300 Allophanate hydrolase (EC 3.5.1.54)
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3300 Length = 592 Score = 153 bits (387), Expect = 1e-41 Identities = 156/476 (32%), Positives = 220/476 (46%), Gaps = 48/476 (10%) Query: 7 LNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTELG 66 L + G+++ ++ + + A + P FI + + +E + A D Sbjct: 10 LRNAYHQGQITPRQLLLNLREKAAALNPDYHLFIHLLS---VEELEPYLAALDGRDPGSL 66 Query: 67 PLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDEFAM 126 PL GVP A+KDNI +G+ TT A YV ATVVE+L A GA+ +GK N+D+FA Sbjct: 67 PLYGVPFAIKDNIDLAGIPTTAACPAF-AYVPERSATVVEQLLALGAIPLGKTNLDQFAT 125 Query: 127 GSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIV 186 G +G S +G N E GGSS+GS+ AVA G A +LGTDT GS R PAA +V Sbjct: 126 GLNGSRSPYGACPNSVLPEYPSGGSSAGSSLAVALGVASFSLGTDTAGSGRVPAALNNLV 185 Query: 187 GLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRTPPALK 246 GLK + G +S GVV +LD V + ++L + A D RD R+ P Sbjct: 186 GLKASKGLISTAGVVPACRTLDCVTTFTATAREASQLLALTAHLDPRD--EYSRSNPLWN 243 Query: 247 FG---GEPSLSGVRLGVPK--ELLGPGIDPGVKARVEEAIAQLEELGATVEECSL-PSTE 300 G G P +R GVP+ +L G G +AI QL+ +G E L P E Sbjct: 244 DGSAFGTP--RPLRFGVPRAQDLAFFGCPEG-PLLFGDAIDQLKAMGGEAVELDLSPFLE 300 Query: 301 YALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGT 360 A Y VAE R + AG L E + + ++ + Sbjct: 301 AARLLYEGPWVAE---------------RYSVAGELMEQHP----QAVLPVIRAVLDKAP 341 Query: 361 YVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPT--TPFTAWKIGEKVDDPV-- 416 V + A Y R Q ++ L ++A E D +VTPT P T E +PV Sbjct: 342 AVTGVQTFRAQY-RLQALKALC----DKALEGLDCVVTPTIGRPVTR---AELAAEPVLR 393 Query: 417 SMYLGDICTIPVNLAGLPAVSVPCGFV-DGLPVGMQLIGKPFADTQILQIAWAYQK 471 + LG T +NL AV+VP GF+ +GLP G+ L G+ F D +L +A Q+ Sbjct: 394 NSELG-YYTNFMNLLDYAAVAVPSGFMGNGLPWGVTLFGRVFTDQYLLSVADTLQR 448 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: 697 Number of extensions: 35 Number of successful extensions: 3 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: 592 Length adjustment: 35 Effective length of query: 453 Effective length of database: 557 Effective search space: 252321 Effective search space used: 252321 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 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