Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf6N2E2_3403 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= curated2:B8HY89 (482 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3403 Length = 475 Score = 251 bits (642), Expect = 3e-71 Identities = 173/482 (35%), Positives = 244/482 (50%), Gaps = 32/482 (6%) Query: 3 SIRELHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGT 62 SI +L Q L S +++ + LE+I++ +++A++ ++AL A D+Q A G Sbjct: 11 SIGQLRQALESGTLTSESLVGAQLERIERFNGQLNAYVEAYPQRALGAAIAADRQRAAGV 70 Query: 63 EIGLLAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLDE 122 +G L GIPIAIKD G T GS I +T RL AGA+++GKT+ E Sbjct: 71 HLGPLHGIPIAIKDLFEIDGKAITGGSLAQTPRISRLTATAVQRLERAGAIIMGKTHTVE 130 Query: 123 FAMGSSTENSAYQLTANPWD--LQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPAS 180 FA G N+ NPWD + R PGGSS GSA AVA G ALG+DTGGS+R PA Sbjct: 131 FAFGGWGTNAVMGTPWNPWDHEVHRAPGGSSSGSAVAVAGGLASAALGTDTGGSVRIPAG 190 Query: 181 FCGVVGLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNVP 240 CG+VGLK T GLVSR+GL+ SLD +GP VEDAA +L A+ G DP D S P Sbjct: 191 MCGLVGLKTTRGLVSRHGLIELCPSLDSVGPITHTVEDAAWMLDALLGPDPLDPVSAKSP 250 Query: 241 IPDYTQFLIPDLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFRY 300 + L + G +I ++ +T E + P V + ++QL LG + E P Sbjct: 251 VFSAAAGLNLPVAGLRIWVLPQTEREHIAPGVLAAYDQGLEQLAALGMHLVEQPLPT--- 307 Query: 301 GLPTYYIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAEGFGPEVKRRIMIGTY 360 L +A SA G+ S L S++ R F P V+RR++ G Sbjct: 308 SLEQCMRVAGGLMSAE---------GYAS-----LGSLFERDDLR-FDPHVQRRVLSGR- 351 Query: 361 ALSAGYYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAPTTAFAAGAKTADPLSMYLS 420 A+ A A Y+ R +Q + A QVD PT A G+ + Y + Sbjct: 352 AIDA----AAYIHLHNQRRAARQAMDEAMSQVDACAFPTN-----AIGSVPLSQVDEYGT 402 Query: 421 DLMTIP--VNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQATPWHDR 478 L + NL L ++LP GFD+Q +P+ +Q++G E LV ++A+AY+Q + WH R Sbjct: 403 PLALLGRFANLLNLCSVALPVGFDEQRMPVSMQIVGRAFAEPLVLRIAHAYQQVSDWHQR 462 Query: 479 HP 480 P Sbjct: 463 RP 464 Lambda K H 0.317 0.134 0.388 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: 575 Number of extensions: 24 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: 482 Length of database: 475 Length adjustment: 34 Effective length of query: 448 Effective length of database: 441 Effective search space: 197568 Effective search space used: 197568 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 (21.6 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