Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate SMa2363 SMa2363 amidase
Query= curated2:Q7UT33 (499 letters) >FitnessBrowser__Smeli:SMa2363 Length = 471 Score = 131 bits (329), Expect = 6e-35 Identities = 138/483 (28%), Positives = 205/483 (42%), Gaps = 59/483 (12%) Query: 1 MLHSASEILKQLDSGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRK 60 M A+ + + + G +TA E + SLAA T A HV AAE DA + Sbjct: 1 MAGDATSLGQAIQMGRLTASEAMEASLAAACQLAET-GAIVHVDPTLGRTAAENADARLR 59 Query: 61 ---AGKTLGPLAGLPVAIKDVLCT-SDMPTTCSSKMLEGFVP-PYDATVVARLKSAGAIV 115 G + P G+P KD+ + + S MLE D+ + RL+ G Sbjct: 60 HLPGGGRIPPFLGVPSLAKDLGGPFAGLSVAAGSNMLERRAAVAEDSDLAERLRGTGLCF 119 Query: 116 VGKTNMDEFAMGASTETSAMGVTGNPWDTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGS 175 G T + E + ++E +A + NP D +TPGGSSGGAAAAVAAG V ++ TD GGS Sbjct: 120 FGLTTVPEMGLSLASEPAAGPICRNPLDAGRTPGGSSGGAAAAVAAGIVAIAHATDAGGS 179 Query: 176 IRQPAAFCGITGLKPTYGRVS---RYG--LVAFASSLDQAGPMGWSVDDVAIGLQAMAGY 230 +R PAA CG+ GLK + G ++ +G L AS L + SV D+A+ A AG Sbjct: 180 MRVPAACCGLFGLKASRGAIAAGPSFGNHLGGIASEL----ALCRSVRDLAVIFNAAAG- 234 Query: 231 DPRDSTSVNAEVPDFTPAMAAEDVRGMRIGVLREGLDQDGISPAVRDALATAESVFREQG 290 A P P A +R+G+L E DQ PA +A+ A G Sbjct: 235 --------RARGPFADPWFAPSPPGPLRVGLLLETGDQYPTEPARSEAVEEAARALEADG 286 Query: 291 AEIVEVELPHSKYWVPTYYVIAPCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAMYS 350 +V + YW + + + L + V A + A S L + Sbjct: 287 HSVVPM------YW--DAFAASVATSGRALRDIIAVNLANFVVSAGLDAGRSERLTQAFI 338 Query: 351 LSRAGGFGSEVKRRIMVGTYALSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGPVT 410 GS+++ + T L + + ++ +L F +VD +L P+ Sbjct: 339 -----NHGSQLEATALWAT--LGDAVHASHAVWSL-------------FDRVDCILTPML 378 Query: 411 PSPAFALN----EKTDDPIAMYLCDLF---TVGANLAGVPAISLPGGFDAVGLPVGVQLQ 463 S + + D + + F AN G PA++LP G D GLP+ VQ+ Sbjct: 379 ASAPLPIGSFPFDHDDIDLQIRRMTAFAPLAALANATGFPALTLPFGADDAGLPLPVQIL 438 Query: 464 APV 466 AP+ Sbjct: 439 APM 441 Lambda K H 0.316 0.132 0.381 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: 531 Number of extensions: 24 Number of successful extensions: 3 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: 499 Length of database: 471 Length adjustment: 34 Effective length of query: 465 Effective length of database: 437 Effective search space: 203205 Effective search space used: 203205 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