Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate SMc02881 SMc02881 hypothetical protein
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__Smeli:SMc02881 Length = 453 Score = 186 bits (471), Expect = 2e-51 Identities = 156/473 (32%), Positives = 217/473 (45%), Gaps = 45/473 (9%) Query: 5 ARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTE 64 A L L +G+L V + L+RI P F+ + + AK AR K G + Sbjct: 8 ASLAVLVQSGKLDPVALVAETLTRIED-HPDRSIFVALTQERAAREAKAASARIKTGRS- 65 Query: 65 LGPLAGVPIAVKDNICTSGMETTCASRIL-KGYVSPFDATVVERLRAAGAMIIGKANMDE 123 LG L G+P+A KD +G TT S +L +G + DATV+ L +AG + IG+ NM E Sbjct: 66 LGLLDGLPVAWKDLFDLAGSITTAGSVVLAEGSPAAADATVIADLGSAGMVSIGRTNMSE 125 Query: 124 FAMGSSGESSAFGVTRNPW--DLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAA 181 FA G + +G RNP D+ R+PGGSSSGSAAAVAAG PLA+GTDTGGS+R PAA Sbjct: 126 FAFSGLGINPHYGTPRNPRSADVHRIPGGSSSGSAAAVAAGLVPLAIGTDTGGSVRIPAA 185 Query: 182 FTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRT 241 TGIVG K T G + GV A SLD +GP+ + V+D DA G T Sbjct: 186 MTGIVGYKATRGRYAMKGVFPLAQSLDSLGPLCQTVQDAV----------WADAAMHGLT 235 Query: 242 PPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEY 301 P ++ ++ + + VP+ ++ + V A EEAI +LE GA V + PS Sbjct: 236 APVIR---RAEIADLSIVVPETIVFDDAEAEVVAAFEEAIKRLEAAGAKVRRQAFPS--- 289 Query: 302 ALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLH-EMYSKTRGEGFGTEVKRRIMLGT 360 AE AR + A+A LH E + E V R LG Sbjct: 290 ---------FAEIFELTARHGAL----VTAEAYALHRERLAGPEAERMDPRVVARTRLGE 336 Query: 361 YVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPVSMYL 420 + + Y R ++ + + + + PT P A + + D + Sbjct: 337 KITVSD-----YIALLDARDRLIHETIETLKAGELIAHPTLPHVAPPLDPLLADDDLFFK 391 Query: 421 GDICTIP----VNLAGLPAVSVPCGF-VDGLPVGMQLIGKPFADTQILQIAWA 468 + T+ N VS+PCG G+P G QL D ++L A A Sbjct: 392 VNARTLRNTSIGNFLDFCGVSIPCGTGAAGMPAGFQLAAPHHQDDRLLSAALA 444 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: 489 Number of extensions: 31 Number of successful extensions: 4 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: 453 Length adjustment: 33 Effective length of query: 455 Effective length of database: 420 Effective search space: 191100 Effective search space used: 191100 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