Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 6938403 Sama_2522 amidase (RefSeq)
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__SB2B:6938403 Length = 567 Score = 122 bits (306), Expect = 3e-32 Identities = 103/340 (30%), Positives = 148/340 (43%), Gaps = 47/340 (13%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRI-----AQVEPAVGAFITVAADHVIERAKKLDA 56 +S A L +G +AVE+ ++ L+RI A + + A + D ++ A+ DA Sbjct: 7 VSIAELRGALESGRTTAVELVKAYLARIEAYDGADTDTKLNAVVVHNPD-ALKEAEASDA 65 Query: 57 RRKAGDTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMII 116 RR G+T LGPL G+P KD+ G+ S K V+ DA VERLRA GA+ + Sbjct: 66 RRARGET-LGPLDGIPYTAKDSYLVKGLTAASGSPAFKDLVAQRDAFTVERLRANGAICL 124 Query: 117 GKANMDEFAMGSSGESSAFGVTRNPWDLERV----PGGSSSGSAAAVAAGEAPLALGTDT 172 GK NM A G + +G +P++ + GSS+G+ A AA L +T Sbjct: 125 GKTNMPPMANGGM-QRGVYGRAESPYNAAYLTAPFASGSSNGAGTATAASFCAFGLAEET 183 Query: 173 GGSIRQPAAFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDR 232 S R PA+ G+ P+ G +S G ++D V P R + D+ + +V+ D Sbjct: 184 WSSGRGPASNNGLCAYTPSRGVISVRGNWPLTPTMDVVVPYARTMADLLEVLDVVVADDS 243 Query: 233 RDATNAGRTPPALKFG---------------GEPSLSGVRLGVPK------ELLGPGIDP 271 + R P ++ G SL G R GVPK EL G +P Sbjct: 244 ETRGDLWRMQPWVQIPKASEVRPESYIALACGADSLKGKRFGVPKMFINKDELAGTSENP 303 Query: 272 G--------------VKARVEEAIAQLEELGATVEECSLP 297 G V A E+A A LE GA V E P Sbjct: 304 GIGGPTGQRIHTRDSVIALWEQARAALEAAGAEVIEVDFP 343 Score = 37.4 bits (85), Expect = 1e-06 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 12/86 (13%) Query: 394 DALVTPTTPFTAWKIGEKVDDPVSMYLGDICTIPVNLAGLPAVSVPCGFVD--GLPVGMQ 451 DA V P + AW G V + + + G+P V+VP G + G+PVG+ Sbjct: 482 DADVNPASADIAWSNGVWVANG---------NLAIRHLGVPTVTVPMGIMADIGMPVGLT 532 Query: 452 LIGKPFADTQILQIAWAYQKV-TKHH 476 G+ + D +L +A A++ K H Sbjct: 533 FAGRAYDDNALLSLASAFESTGNKRH 558 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: 660 Number of extensions: 30 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: 488 Length of database: 567 Length adjustment: 35 Effective length of query: 453 Effective length of database: 532 Effective search space: 240996 Effective search space used: 240996 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