Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate HSERO_RS02850 HSERO_RS02850 glutamyl-tRNA(Gln) amidotransferase
Query= curated2:Q2LXM9 (485 letters) >FitnessBrowser__HerbieS:HSERO_RS02850 Length = 651 Score = 214 bits (545), Expect = 7e-60 Identities = 162/480 (33%), Positives = 243/480 (50%), Gaps = 19/480 (3%) Query: 3 LYQLTIHELQNKIRQGGVTSTAIVNSVFGRIDAVEENVHSY--ITLMRESALEEAQKADE 60 +++ +I LQ+ G TS ++V + RI A ++ S I + ALEEA + D Sbjct: 49 VFEASITHLQSAQDAGRATSRSLVLAYLARIRAYDQQGPSLNAIVTLNPKALEEADQLDR 108 Query: 61 QIR-TGEINALTGIPVALKDIYCTRGVRTTCGSLILDNFIPPYDATVVVKLREAGAVFTG 119 + R +G L GIP+ +KD Y T + TT G+L L DA V +LREAGAV G Sbjct: 109 ERRQSGPRGPLHGIPILVKDNYDTVDMPTTGGTLALATLQAQADAFQVKRLREAGAVILG 168 Query: 120 KTNMDEFAMGSSTETSYYGFTRNPWDLERIPGGSSGGSAAAVAADECIAALGSDTGGSIR 179 KT M E A G +T +S GFTRNP+D R PGGSSGG+ AAVAA A +GSDT GSIR Sbjct: 169 KTTMHELAAGVTTVSSLTGFTRNPYDPRRAPGGSSGGTGAAVAASFAAAGMGSDTCGSIR 228 Query: 180 QPAALCGVVGMKPTYGRVSRFGLIAFASSLDQIGPFTKDVEDCAILLNVIAGYDLRDSTS 239 PAA + G++ T G SR G++ +S+ D P + VED AI+L+ G D +DS++ Sbjct: 229 IPAAHQNLFGLRTTRGLASRSGVMPLSSTQDVAAPLARSVEDLAIMLDATVGSDPQDSST 288 Query: 240 VPVD--VP-DYRDYLNR-GIEGWTVGIPKEYF-IEGIDPEVRGAIEQAIRTVEGLGARCR 294 V + +P YRD L ++G +G+ + F D EV AI +A++ ++ GA Sbjct: 289 VDANGHIPKSYRDGLRADSLQGARIGVLRALFGAAPEDAEVSAAINKALQQLKDQGAIVT 348 Query: 295 EISLPHTDYCVAVYYIIAPAEASSNLARYDGVKYGFRAADCRDLLDMYKKTRSAGFGTEV 354 ++++P D ++ II P E +L Y G ++L + G + Sbjct: 349 DVTIPELDGLLSGSSII-PYEFKYDLGAYLQSHPGAPVGSLGEILARGMEHELLEAGLRL 407 Query: 355 KRRVMLGTYSLSSGYYDAYYKKASQVRGLIKRDFEEALKDCNVILTPTTPTPAFTIGEKT 414 + V L + K S ++ L+ ++ + ++ PT A IGE Sbjct: 408 RNSVDLQN-PKDKEELEKVMLKRSALKSLMTDVMQK--NHLDTLVYPTIQRKAALIGEPQ 464 Query: 415 DDPMQMYLSDIFTISANLAGIPGISVPCGYTQSGLPVGIQFLAGHFEEGKLLQIASAYER 474 M LS G+P +++P G+T+ GLPV ++ LA F E LL +A +E+ Sbjct: 465 GGAMNCQLS-------ATTGLPALALPVGFTEDGLPVSLELLAPEFAEPALLGLAYGWEQ 517 Lambda K H 0.319 0.137 0.402 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: 654 Number of extensions: 27 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: 485 Length of database: 651 Length adjustment: 36 Effective length of query: 449 Effective length of database: 615 Effective search space: 276135 Effective search space used: 276135 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 (21.7 bits) S2: 53 (25.0 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