Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_041550504.1 SARO_RS15510 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000013325.1:WP_041550504.1 Length = 489 Score = 188 bits (477), Expect = 4e-52 Identities = 167/497 (33%), Positives = 235/497 (47%), Gaps = 45/497 (9%) Query: 15 MLARGEISSLELTDALLTRIAAVE---PKVRAFLVVDAAGARAQARAADARRAAGDASPL 71 ++A ++ + A L RIA ++ P++ A + ++ + + A R PL Sbjct: 14 LVAASPATASQGVSADLDRIARIDDSGPRLNAVVTINPDARKMEEAARKVR------GPL 67 Query: 72 LGIPMGIKDVISTQG-LRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCDEFA-M 129 G + IKD I T + TT S L++ DA VARL++AG VILGK N E+A + Sbjct: 68 AGRTLLIKDNIETADPMATTAGSLALKDNVTGRDAPLVARLRSAGVVILGKTNLSEWANI 127 Query: 130 GSSTENSAFQ----QTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAAL 185 SS +S + QT+NP L+R P GSS GS AAVAAG A A+GT+T GSI PA++ Sbjct: 128 RSSASSSGWSAVGGQTKNPHALDRSPCGSSSGSGAAVAAGLAWGAIGTETDGSITCPASV 187 Query: 186 CGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATC--TDY 243 GI G KPT G VSR +V + S D GPM R+VRD A+++ + G+DP DA D Sbjct: 188 NGIVGFKPTVGMVSRTHVVPISHSQDTAGPMTRSVRDAALLMNALVGSDPQDAATAEADR 247 Query: 244 PAPDYEAAL-TGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHT 302 D+ A L T + G+RIGV R+ AG P V A+ L GA + EI Sbjct: 248 RKVDFSAGLETASLNGVRIGVLRKQ--AGAHPGVVTLFDNALADLARAGARLVEIDYSPP 305 Query: 303 PY----ALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAG-----FGPE 353 P L V + A L G P S D + + G FG + Sbjct: 306 PEMGRDELTVLLFELREDLGAYLRSLPG-----EPPVRSLADVIAFNKANGAELRWFGQD 360 Query: 354 VRRRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDV--IAAPTTPTVAFKIG 411 + T A Y A RA +R + ++ DV + APT A+ I Sbjct: 361 TFEQAEATTD--RAAYETA---RANSLRLAGAEGIDRLLKENDVAFLVAPTAGP-AWPID 414 Query: 412 AHTDDPLAMYLEDVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGDAY 471 T D +L+ +AG P L VP G EGLP+GL ++G +D+ +L+ G AY Sbjct: 415 LVTGD---HFLDVGAGSLAAIAGYPHLSVPMGAVEGLPVGLSIMGAKWDDARVLKAGAAY 471 Query: 472 QRVTDWHTRMPEVREDG 488 +R P ++ G Sbjct: 472 ERARSVAVPTPRLKRWG 488 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: 496 Number of extensions: 27 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: 490 Length of database: 489 Length adjustment: 34 Effective length of query: 456 Effective length of database: 455 Effective search space: 207480 Effective search space used: 207480 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: 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