Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_052668729.1 NITAL_RS23625 amidase family protein
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000969705.1:WP_052668729.1 Length = 456 Score = 205 bits (522), Expect = 2e-57 Identities = 162/495 (32%), Positives = 228/495 (46%), Gaps = 72/495 (14%) Query: 1 MTPLYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAAD 60 MT L L + ++ +++S E+ +A L R AV+P+V A +V A A A A AAD Sbjct: 1 MTELIGLPALELASLVRERQVTSREIVEAFLARTEAVDPEVNAVTLVLADEALAAADAAD 60 Query: 61 ARRAAGDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILG 120 G PL G+P+ +K+ I G TT L + P DA V R++AAGA+ Sbjct: 61 RTEPTG---PLHGVPISVKENIDLTGTPTTHGLPALADAMPEEDAPIVTRMRAAGAIPFL 117 Query: 121 KLNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIR 180 + N EF + T+N +TRNPW+ R PGGSSGG AAA+AA +P LG D GGS+R Sbjct: 118 RTNLPEFGLRLDTDNPLRGRTRNPWDPSRTPGGSSGGEAAAIAARMSPLGLGNDIGGSLR 177 Query: 181 QPAALCGITGLKPTYGRVSRYGLVAFASSLDQI------------GPMARTVRDCAIVLR 228 PA CGI G +PT GR V ASSL + GPM R V D + + Sbjct: 178 NPAFCCGIVGFRPTTGR------VPMASSLPPVDGPLSEQLMATDGPMGRRVDDVSAAMA 231 Query: 229 VIAGADPFDATCTDY----PAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAI 284 ++ GADP D D P+P + A GV +QP V AAV A Sbjct: 232 ILNGADPSDPRSVDVPLDRPSPAHRVA----------GVVTTGSDGPLQPAVAAAVGRAA 281 Query: 285 EVLREQGAEVCEISLPHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELER 344 E L E G E+ E++LP V+ I + +PG L Sbjct: 282 EALAEAGWELEEVTLPELALVNEVWMRIMSED----------------IPG------LVE 319 Query: 345 TRGAGFGPEVRRRIMLGTYALSAGYYD----AYYKRAQQVRTLIRRDYQQAFEQVDVIAA 400 G+ P +R ++ YYD + R L+RR + + F++ V+ Sbjct: 320 AMGSLLTPRLREVLL-----DHVTYYDPDRIPRGALLPERRRLMRR-WTEMFQRTPVVIG 373 Query: 401 PTTPTVAFKIGA---HTDDPLAMYLEDVCTLPLNLAGLPGLVVPCGFAEGLPIGLQLIGR 457 P P AF GA H +A +L+ V P L GLP L VP G ++G+P+G+Q+ Sbjct: 374 PVWPEQAFVGGADMEHGIGFVARFLQFVTPAP--LLGLPALAVPTGTSDGVPVGVQIHAD 431 Query: 458 AFDEESLLRVGDAYQ 472 +++ G A + Sbjct: 432 RWNDAWCFEAGRAIE 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: 556 Number of extensions: 33 Number of successful extensions: 4 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: 456 Length adjustment: 33 Effective length of query: 457 Effective length of database: 423 Effective search space: 193311 Effective search space used: 193311 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 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