Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate AO356_09120 AO356_09120 amidase
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09120 Length = 453 Score = 170 bits (431), Expect = 8e-47 Identities = 152/475 (32%), Positives = 218/475 (45%), Gaps = 48/475 (10%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAG 61 L A L F +G V++ E AL + A+ E F+++ A+ AR +AG Sbjct: 7 LDAIALAEAFASGRTDPVQVLEQALEQAARAEHV---FVSLTEARARREAQASAARWRAG 63 Query: 62 DTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPF-DATVVERLRAAGAMIIGKAN 120 L GVP+A KD +G TT A+ + + DA V L AG + +GK N Sbjct: 64 QP-LSGFDGVPMAWKDLFDVAGSVTTAAAAVRRNAPPALLDAASVSLLSRAGMVCLGKTN 122 Query: 121 MDEFAMGSSGESSAFGVTRNPWD--LERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQ 178 + EFA G + FG NP+ R+PGGSSSGSA AVAAG P+A+GTDT GSIR Sbjct: 123 LSEFAYSGLGLNPHFGTPVNPFSDAQPRIPGGSSSGSAVAVAAGIVPIAMGTDTAGSIRV 182 Query: 179 PAAFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNA 238 PAAF +VG + + +R GV A S+D +GP+ R V D + E++ G D R A Sbjct: 183 PAAFNALVGFRASSRRHNRDGVFPLAHSIDSIGPLTRSVRDAWMIDELLQGRDPRQA--- 239 Query: 239 GRTPPALKFGGEPSLSGVRLGVPKELLGPG-IDPGVKARVEEAIAQLEELGATVEECSLP 297 PP SL+G R V + +L ++ V+A V + L GA VE LP Sbjct: 240 ---PPV------RSLAGQRFWVEQAVLEDARVEAAVRANVLAGVQALRTAGALVEIRPLP 290 Query: 298 STEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHE-MYSKTRGEGFGTEVKRRI 356 + +AS L R G AA+A LHE + E V+RR+ Sbjct: 291 A-------------FQASLALIRDHG---WLGAAEAFALHEALLDSADAERLDPRVRRRL 334 Query: 357 MLGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDDPV 416 + ++ Y R+ R L V + + A L+TPT A + D Sbjct: 335 EAARPMTASQVLKLYDARSTLQRQL-VEELDGA-----VLITPTVAHVAPPLAPLEADDE 388 Query: 417 SMYLGDICTI----PVNLAGLPAVSVPCG-FVDGLPVGMQLIGKPFADTQILQIA 466 ++ T+ P +L +P V++P G GLP G+ L D ++L++A Sbjct: 389 LFARTNLATLSLTMPGSLLDMPGVNLPSGRDSQGLPTGLLLSVPQGEDARLLRVA 443 Lambda K H 0.318 0.135 0.391 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: 525 Number of extensions: 41 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: 488 Length of database: 453 Length adjustment: 33 Effective length of query: 455 Effective length of database: 420 Effective search space: 191100 Effective search space used: 191100 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 (21.7 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