Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011765689.1 AZO_RS09885 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000061505.1:WP_011765689.1 Length = 465 Score = 273 bits (698), Expect = 9e-78 Identities = 191/485 (39%), Positives = 252/485 (51%), Gaps = 35/485 (7%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 L+ L +A+ +L G+IS L LT +L RI A++ ++ A+ V A A A A A+A Sbjct: 8 LHYLEIAELAPLLRAGDISPLALTRHMLARIDALDSRLHAYARVTADEALAAAAQAEADI 67 Query: 64 AAGD-ASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKL 122 AAG PL G+P+ +KD+ T+G T C + +L ++ P DAT V RL+ AGAVILGKL Sbjct: 68 AAGRYRGPLHGVPVAVKDLFWTRGTVTACGTTVLADFVPDEDATVVRRLREAGAVILGKL 127 Query: 123 NCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQP 182 E A +T + NPW + G SS GS A AAG AALGTDTGGSIR P Sbjct: 128 QMTEGAF--ATPHPDLAAPLNPWGADHWTGASSSGSGVATAAGLCFAALGTDTGGSIRFP 185 Query: 183 AALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTD 242 AA G++GLKP +GRVSR+G+ A +LD +GPMAR+VRD A++ + IAG DP D T D Sbjct: 186 AAANGLSGLKPGWGRVSRHGVFPLAPTLDHVGPMARSVRDVALMYQAIAGPDPLDPTSLD 245 Query: 243 YPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHT 302 AP AA + GLR+G+ + G +V A E L GAE+ E+ LP + Sbjct: 246 -DAP--RAAGHSGLAGLRVGIDAAWNARGSDAEVLAGCARLREALVAGGAEIVELELPES 302 Query: 303 -PYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLG 361 P A L A A+ A + R A +GP + R I +G Sbjct: 303 WPIAGAWELLCGVQTAVAHAATYP-------------------ARAADYGPALARLIEVG 343 Query: 362 TYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVA---FKIGAHTDDPL 418 +AG D Y RAQ ++A VD++ AP P A ++G P Sbjct: 344 R---AAGAMD--YHRAQLAALDFGGRLERALAGVDLLLAPVQPFAAPTHARLGELAQSPE 398 Query: 419 AMYLEDVCTLPLNLAGLPGLVVPCG-FAEGLPIGLQLIGRAFDEESLLRVGDAYQRVTDW 477 T PLN++G P L +PCG A GLP+G QLI R E +LL G A Q VT W Sbjct: 399 LNQRLIQFTAPLNISGSPSLALPCGSTAAGLPVGCQLIARKGGEATLLAAGAALQAVTHW 458 Query: 478 HTRMP 482 H P Sbjct: 459 HRAHP 463 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: 537 Number of extensions: 22 Number of successful extensions: 5 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: 465 Length adjustment: 34 Effective length of query: 456 Effective length of database: 431 Effective search space: 196536 Effective search space used: 196536 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 Apr 10 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