Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate RR42_RS28435 RR42_RS28435 amidase
Query= curated2:B8HY89 (482 letters) >FitnessBrowser__Cup4G11:RR42_RS28435 Length = 508 Score = 211 bits (537), Expect = 5e-59 Identities = 148/478 (30%), Positives = 236/478 (49%), Gaps = 43/478 (8%) Query: 7 LHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGTEIGL 66 L + + SKE S E+ + + +I+ + P ++A E+A +A ++ + G +GL Sbjct: 15 LRRLIGSKEISPVELLEACIARIEAVNPFINAITATCYERAREEARAAERAVLDGAPLGL 74 Query: 67 LAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLDEFAMG 126 L G+P+ +KD T G+ TT GS + + +P ++ + +RL AAGA++ GKTN+ E G Sbjct: 75 LHGLPLGVKDLEATAGLLTTYGSPLYRDNVPSADNVLVARLRAAGAIVTGKTNIPEMGAG 134 Query: 127 SSTENSAYQLTANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPASFCGVVG 186 +++ N+ + T NP++ GGSSGGSAAA+A + GSDTGGS+R PA+ CGVVG Sbjct: 135 ANSRNAVWGATGNPFNPNLNAGGSSGGSAAALATDMLPVCTGSDTGGSLRIPAAKCGVVG 194 Query: 187 LKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNVPIPDYTQ 246 +P+ G+V + + + +GP V DA L L A AG D + + D Sbjct: 195 FRPSPGVVPSSRKLLGWTPISVVGPMGRTVADACLQLAASAGVSASDPLTYAL---DPMS 251 Query: 247 FLIP---DLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFRYGLP 303 FL+P DL ++G ++ +D Q+ QV I + L EI Sbjct: 252 FLLPANVDLGSLRVGWTEDFGVCAVDNQIRQVFRDKIAAMRHLFRSCDEIQ--------- 302 Query: 304 TYYIIAPSEASANLARYDGVKYGFRSP---DPENLLSMYTRTRAEGFGPEVKRRIMIGTY 360 + + + ++ R + G R DP++L GP + +G Sbjct: 303 --FDLGDAHRCFDVLRAESFVAGTREAYQRDPQSL------------GPNTRANYEMGA- 347 Query: 361 ALSAGYYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAPTTAFAAGAKTADPL----- 415 A+S D+ + +A++ R L + F+AAFE DV++ PT P + F A+ + Sbjct: 348 AMSLS--DSAWAQAEQTRILGR--FQAAFEDYDVILSPTTPVSPFPWTNLYAETINGEKQ 403 Query: 416 -SMYLSDLMTIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQA 472 + Y T V L P +SLPCG D G+P GLQ++G + VA+A EQA Sbjct: 404 ENYYRWLAPTYVVTLTTHPAISLPCGLDHAGMPFGLQVVGRFRADHHTLGVAHAMEQA 461 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: 552 Number of extensions: 20 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: 482 Length of database: 508 Length adjustment: 34 Effective length of query: 448 Effective length of database: 474 Effective search space: 212352 Effective search space used: 212352 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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