Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 3606629 Dshi_0061 Amidase (RefSeq)
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__Dino:3606629 Length = 443 Score = 172 bits (437), Expect = 2e-47 Identities = 149/467 (31%), Positives = 218/467 (46%), Gaps = 47/467 (10%) Query: 10 AQAREMLARGEISSLELTDALLTRIA--AVEPKVRAFLVVDAAGARAQARAADARRAAGD 67 AQ R +A G + + LT+A L +IA A P++ A D A + A A A D R+ Sbjct: 12 AQGRA-IAEGTLDPVALTEAYLDKIASRAESPRIYARTTPDRALSEAMA-AHDRARSQTR 69 Query: 68 ASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCDEF 127 PL G+P+ KD+ T G+ T + +L+ TP DA +A AAG V LGK + E Sbjct: 70 HGPLDGVPISWKDLFDTAGVATESGTALLKGRTPDRDAEVLANATAAGLVCLGKTHLSEL 129 Query: 128 AMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAALCG 187 A N N + VPGGSS G+AA+VA G A A +G+DTGGS+R P+A Sbjct: 130 AFSGLGLNPITATPPNINDPGAVPGGSSSGAAASVAFGLAAAGIGSDTGGSVRIPSAWND 189 Query: 188 ITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDYPAPD 247 + GLK T G +S G V AS+ D +GP+ RTV D A++L + G APD Sbjct: 190 LVGLKTTSGLLSLEGAVPLASAFDTVGPLTRTVEDAALLLGALGGT----------KAPD 239 Query: 248 YEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTPYALP 307 A + G + V R ++P+ E A A+ L E GA++ E+ P AL Sbjct: 240 LRGA---TLTGTHLAVLRTGAFEDIRPEPEQAFAAAVARLAEAGAQITELHAPEVDEALA 296 Query: 308 VYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLGTYALSA 367 + ++ EA YG+ + D +E F P + R G A Sbjct: 297 LSGVLFATEA-----------YGI------WKDVIEAAPEKMFPPILDR--FRGGRDYDA 337 Query: 368 GYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTDDPLAMYLEDVCT 427 Y A +++ ++R + D +AF D + PT PT+ + + E++ Sbjct: 338 PAYVAGWRKLVELRA-VWADRTRAF---DGVLLPTAPTLPPNVDRLLSEKAYFVEENLLA 393 Query: 428 LPL----NLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGDA 470 L NL G+ L +P G GL ++G+ F E +LLR+G A Sbjct: 394 LRNTRIGNLMGVCALNLPTGTPS---CGLSIMGQPFGEAALLRLGAA 437 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: 489 Number of extensions: 34 Number of successful extensions: 2 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: 443 Length adjustment: 33 Effective length of query: 457 Effective length of database: 410 Effective search space: 187370 Effective search space used: 187370 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