Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_041750295.1 BBTA_RS03370 AtzE family amidohydrolase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000015165.1:WP_041750295.1 Length = 466 Score = 259 bits (663), Expect = 1e-73 Identities = 181/476 (38%), Positives = 251/476 (52%), Gaps = 39/476 (8%) Query: 7 LTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAAG 66 +T + +A ++S+ E T+A L+RIAA + + AF V A ARA+A DA AAG Sbjct: 1 MTASAIAAAVATRKLSAKEATEAALSRIAARDGVLNAFTDVTAERARAKAAEIDAAIAAG 60 Query: 67 DA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVY-DATAVARLKAAGAVILGKLNC 124 + PL G+P +K++ +GL T SK+ + P DAT +AR++AAGAV++G LN Sbjct: 61 KSVGPLAGVPFAVKNLFDVEGLPTRAGSKINRDRAPAARDATLIARMEAAGAVLVGALNM 120 Query: 125 DEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAA 184 E+A + EN +RNP + R+ GGSSGGS +AV G P ALG+DT GSIR P++ Sbjct: 121 GEYAYDFTGENVHDGPSRNPHDPTRMSGGSSGGSGSAVGGGLVPIALGSDTNGSIRVPSS 180 Query: 185 LCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDYP 244 CGI GLKPTYGR+SR F SLD +GP AR+V D A+ + G DP DA CT P Sbjct: 181 FCGIFGLKPTYGRLSRARSFPFVMSLDHLGPFARSVEDLALAYDAMQGPDPDDAACTTRP 240 Query: 245 APDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTPY 304 A L+ ++ GLRIG+ +F + P+ AV L+ EV E+ P Sbjct: 241 AEPVSGLLSQELDGLRIGLAGGHFQTNLFPEAAEAVARVAAALKV--TEVIEV--PEAAR 296 Query: 305 ALPVYYLIAPAE-ASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLGTY 363 A Y+I+ E AS +L R RTR F P VR R++ G Sbjct: 297 ARAAAYVISTTEGASLHLDRL-------------------RTRPHDFDPAVRDRLIAGA- 336 Query: 364 ALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHT------DDP 417 + A D RAQ+ R R + F VDV+ AP TP +A K+G T + P Sbjct: 337 MIPAPLVD----RAQKFRRWYRAKVLELFTSVDVLIAPATPCIAPKLGQATFMLDGVELP 392 Query: 418 LAMYLEDVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGDAYQR 473 + + + T P++ GLP + VP E +PIG+Q+I + E LRV A Q+ Sbjct: 393 VRANI-GIHTQPISFIGLPVVAVPIPL-EPMPIGVQIIAAPWCEHVALRVAHALQQ 446 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: 530 Number of extensions: 29 Number of successful extensions: 6 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: 466 Length adjustment: 34 Effective length of query: 456 Effective length of database: 432 Effective search space: 196992 Effective search space used: 196992 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