Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 3610038 Dshi_3419 Amidase (RefSeq)
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__Dino:3610038 Length = 441 Score = 191 bits (485), Expect = 4e-53 Identities = 160/465 (34%), Positives = 216/465 (46%), Gaps = 46/465 (9%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 L L++ Q L GE+++L L DA L RIAA +P V+A+ +D ARAQA A DA + Sbjct: 7 LPDLSLQQMSAALRTGEVTALALLDAHLDRIAARDPSVKAWAWLDPDQARAQAIALDAAQ 66 Query: 64 AAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKL 122 A G A PL GIP+G+KDVI T + T + P DA ARL+A GAVI+GK Sbjct: 67 AEGKALGPLHGIPVGLKDVIDTADMPTENGTPPDAGRQPDQDAWITARLRAVGAVIVGKT 126 Query: 123 NCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQP 182 E A + TE T NP N PGGSS GSAA+VAAG P A+GT TGGS+ +P Sbjct: 127 TTTELAFLNPTE------TLNPHNPNHTPGGSSAGSAASVAAGMVPLAVGTQTGGSVIRP 180 Query: 183 AALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTD 242 AA CG+ G+KPT+G + R G+ + +LD +G R D A L + D D+ Sbjct: 181 AAFCGVVGVKPTFGAIPRQGVTMQSHTLDTLGVFTRDAEDAAFALTCM--MDTEDSDPAT 238 Query: 243 YPAPDYEAALTGDIRGLRIGVPREYFVAGMQPD-VEAAVRTAIEVLREQGAEVCEISLPH 301 P D A+ G R G FV + D A + A+E L Q +SLP Sbjct: 239 LPPQDAHPAIAGATRPPVFG-----FVRPPEWDRASAETKAALEKL-AQALGAIPLSLPE 292 Query: 302 TPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLG 361 + + +A A N A R G +D L R + G Sbjct: 293 S------FEQVADLRARINFAEMAWHYSRYRTAG---WDALSAA--------TRDAMEAG 335 Query: 362 TYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTDDPLAMY 421 + Y A +R +L F QVD + P+ A + + T D + Sbjct: 336 AACAAVDYLAALMQREPLYASL-----DPLFSQVDCLLCPSALGAAPEGLSSTGDAIFNG 390 Query: 422 LEDVCTLPLNLAGLPGLVVPCGFAE-GLPIGLQLIGRAFDEESLL 465 L G P + +P E GLPIG+QL+GR ++ +LL Sbjct: 391 L-------WTFMGTPCVTLPLPETEKGLPIGVQLVGRRGEDRALL 428 Lambda K H 0.320 0.136 0.398 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: 30 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: 490 Length of database: 441 Length adjustment: 33 Effective length of query: 457 Effective length of database: 408 Effective search space: 186456 Effective search space used: 186456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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