Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011766088.1 AZO_RS11895 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000061505.1:WP_011766088.1 Length = 497 Score = 201 bits (511), Expect = 5e-56 Identities = 160/494 (32%), Positives = 230/494 (46%), Gaps = 54/494 (10%) Query: 7 LTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAAG 66 LT AQA L G S+ +L A RI P + A + ++ GA A AR AD R A G Sbjct: 9 LTAAQAVRDLRAGRYSAEQLVLACQARIDRFNPTLNALVTLNREGALAAARGADRRLAQG 68 Query: 67 DASP-LLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCD 125 +P LLG+P+ IKD +T+ + TT + + L Y P DAT VAR + AGAV++GK N Sbjct: 69 GLAPALLGVPVSIKDAFATRDMLTTASHRPLAAYRPGADATVVARWREAGAVLMGKSNLP 128 Query: 126 EFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPAAL 185 E A + F TRNPWN PGGSSGG+A AVAAG + +G+D GSIR PAA Sbjct: 129 ELAGAPHCWSPLFGLTRNPWNPALTPGGSSGGAAVAVAAGFSLLDIGSDIAGSIRIPAAY 188 Query: 186 CGITGLKPTYGRVSRYGLVAFAS-----------SLDQIGPMARTVRDCAIVLRVIAGAD 234 CGI GLK T R+ R G + + G +AR+V D + ++AG D Sbjct: 189 CGIAGLKATENRIPRTGHIPHLPPEFGGPGRSVWHMLAFGVLARSVEDLQLGYGLLAGPD 248 Query: 235 PFDATCTDY-PAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAE 293 D T + P P + +RI + ++ + P + ++ LR G E Sbjct: 249 GVDCTVPPFLPEPPSLPTTARAVAPMRIALWDDFAGMPLCPRIRRGLQNMAGKLRASGHE 308 Query: 294 VCEISLPHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPE 353 V + P + + A + L G GL +PG +R P Sbjct: 309 VVRCA--------PADFDVGAAWHAFGL--IGGAEIGLGMPG------WQRRLFLALRPL 352 Query: 354 VRRRIMLGTYALSAGY-YD-AYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIG 411 + R ++ T A++AG +D Y +A R + R ++ + D + P PT G Sbjct: 353 LPRDHVI-TRAVAAGMRFDLRRYNQALNQREGLIRSLERFVGEWDAVICPVAPT-----G 406 Query: 412 AHTDDPL---------------AMYLED--VCTLPLNLAGLPGLVVPCGFAEGLPIGLQL 454 + +P+ YLE T P +L G P L +P G +GLP+G+Q+ Sbjct: 407 PYPGEPMPPTRKPPRLNVGEATLPYLEATIAMTAPFSLTGSPVLSLPVGIEDGLPVGVQV 466 Query: 455 IGRAFDEESLLRVG 468 IG+ + E +LL G Sbjct: 467 IGKRWQEHALLETG 480 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: 607 Number of extensions: 34 Number of successful extensions: 4 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: 497 Length adjustment: 34 Effective length of query: 456 Effective length of database: 463 Effective search space: 211128 Effective search space used: 211128 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 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