Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate N515DRAFT_0701 N515DRAFT_0701 amidase
Query= curated2:B8HY89 (482 letters) >FitnessBrowser__Dyella79:N515DRAFT_0701 Length = 541 Score = 199 bits (506), Expect = 2e-55 Identities = 166/499 (33%), Positives = 258/499 (51%), Gaps = 40/499 (8%) Query: 2 ASIRELHQQLVSKERSAKEITQDALEKIQQLE---PKVHAFLTLTAEQALAQAERVDQQI 58 ASI+EL Q++ + + ++ + + LE+IQ+++ P + A L T AL A ++D+Q Sbjct: 32 ASIKELQQRMDAGQLRSEALARLFLERIQRIDRDGPALRAVLE-TNPDALKLAAQIDRQK 90 Query: 59 ATGTEIGLLAGIPIAIKDNLCTKG-IPTTCGSKILQGFIP-PYESTVTSRLAAAGAVMVG 116 G L GIP+ +KDN+ T + TT GS L P P ++ + +RL GA+++G Sbjct: 91 PKGA----LRGIPVLLKDNIDTGDRMLTTAGSLALADAPPAPRDAGLVARLRKNGALILG 146 Query: 117 KTNLDEFA-MGSSTENSAYQL----TANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDT 171 KTNL E+A M S+ +S + T NP+ L R P GSS GS AAVAAG +A+GS+T Sbjct: 147 KTNLSEWANMRSNHASSGWSARGGQTRNPYALDRNPCGSSAGSGAAVAAGLATVAIGSET 206 Query: 172 GGSIRQPASFCGVVGLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDP 231 GSI PA+ G+VG+KPT GLVSR G+V + + D GP A V DAA +LGAIAG DP Sbjct: 207 DGSIICPAAANGIVGIKPTVGLVSRSGIVPISHNQDTAGPMARTVADAAAVLGAIAGSDP 266 Query: 232 QDSTSLNVP--IPDYTQFLIPD-LKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGA 288 +D + DYT+FL P+ LKGK+IG+++ G +P +++ ++I ++ GA Sbjct: 267 RDPATAEADKHATDYTRFLDPNGLKGKRIGVVRGL--AGAEPNADRILEQSIALMKAQGA 324 Query: 289 EVRE-ISCPRFR-YGLPTYYIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAE- 345 + + + P + G P ++ + ++ Y + G +L++ + + AE Sbjct: 325 VIVDPVELPHLKELGDPELTVLL-YDLKQDMQAYLATRTGTSMKTLADLIA-FNKREAER 382 Query: 346 ---GFGPEVKRRIMIGTYALSAGYYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPT-AP 401 FG E+ + Y +A KA++ D A + +D L+ P+ P Sbjct: 383 EMPWFGQELFEQAQAKGPLTDKDYVEA-QAKAKRFAGPEGIDVALAKDHLDALLAPSWGP 441 Query: 402 T----TAFAAGAKTADPLSMYLSDLMTIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVL 457 T + DP S P +AG P +++P GF LP+G+ G Sbjct: 442 TFVTDPVLGDHVVSGDPTVGGASQ----PAAVAGYPSITVPAGF-AHDLPVGIVFFGAKW 496 Query: 458 REDLVFQVAYAYEQ-ATPW 475 E + +AY YEQ A W Sbjct: 497 SEPTLITIAYGYEQHAQAW 515 Lambda K H 0.317 0.134 0.388 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: 594 Number of extensions: 35 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: 482 Length of database: 541 Length adjustment: 35 Effective length of query: 447 Effective length of database: 506 Effective search space: 226182 Effective search space used: 226182 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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