Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AZOBR_RS31530 AZOBR_RS31530 glutamyl-tRNA amidotransferase subunit A
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__azobra:AZOBR_RS31530 Length = 462 Score = 283 bits (724), Expect = 9e-81 Identities = 183/494 (37%), Positives = 254/494 (51%), Gaps = 44/494 (8%) Query: 1 MTPLYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAAD 60 MT LT+ +A + G + + L DA L RIA + P + AFL V+ A A ARAAD Sbjct: 1 MTDPTSLTLTEAARAVRDGTLRAEALADACLDRIARLNPTLNAFLSVEPEEALAAARAAD 60 Query: 61 ARRAAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLE-NYTPVYDATAVARLKAAGAVI 118 A AG PL G+P+ KD+ G R TC S + ++ P AT + RL AGAV Sbjct: 61 AEVRAGRLRGPLHGVPLAHKDMFHRAGKRCTCGSPTIRGDFRPERTATVLERLDTAGAVT 120 Query: 119 LGKLNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGS 178 LG L+ EFAMG + N+ + RNPW+ +R+ GGSS GS AAVA A +LG+DTGGS Sbjct: 121 LGTLHMAEFAMGPTGHNAHLGRCRNPWDPDRITGGSSSGSGAAVAGRLAFGSLGSDTGGS 180 Query: 179 IRQPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDA 238 +R PAALCG+ GLKPT G G++ + SLD +GP+AR+ D A + VI G Sbjct: 181 VRLPAALCGVVGLKPTQGATPMDGVMPLSESLDCVGPLARSAEDAATLFSVITG------ 234 Query: 239 TCTDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEIS 298 D AA+ + GLR+G+PR+++ G+ P V AA+ A VL GA V ++ Sbjct: 235 ------RTDAVAAIGQGVEGLRLGIPRQFYYDGLDPAVAAALERARAVLERAGARVVDVD 288 Query: 299 LP-HTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRR 357 +P H PY + P A+ + R R +GP+VR R Sbjct: 289 IPDHEPYGDLANLVFTPEAAAVHAPWL-------------------RERPQDYGPQVRAR 329 Query: 358 IMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPT----TPTVA-FKIGA 412 ++ G +A Y A RA +R +I F + D + P PT A +GA Sbjct: 330 LLQGLMVPAASYLQAKQLRALHLRAMI----DGPFARCDALFVPALRSRVPTAAQTDVGA 385 Query: 413 HTDDPLAMYLEDVCTLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLLRVGDAY 471 + T P++ GLP LV P GF +G+PI +QLI R E +LLR+ DAY Sbjct: 386 GPAMAAVVAGVAALTRPVSYLGLPALVTPAGFDPDGMPIAMQLIARPQAEATLLRIADAY 445 Query: 472 QRVTDWHTRMPEVR 485 +R W +R+P+ + Sbjct: 446 ERAAGWLSRVPQTQ 459 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: 560 Number of extensions: 36 Number of successful extensions: 7 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: 462 Length adjustment: 33 Effective length of query: 457 Effective length of database: 429 Effective search space: 196053 Effective search space used: 196053 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