Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_010529587.1 ON01_RS03315 amidase
Query= curated2:B3DWT4 (494 letters) >NCBI__GCF_000224785.1:WP_010529587.1 Length = 498 Score = 155 bits (391), Expect = 4e-42 Identities = 137/509 (26%), Positives = 230/509 (45%), Gaps = 67/509 (13%) Query: 5 ELSVKELRRLLVQKEVSPLEVVENLLCRIAEVDPKIFAYIYLNHERALEASKKADISLPL 64 +L ++ L+ KE++P E + R+ +V+P + A ++ +R + + + Sbjct: 8 QLDAVDIAELIRMKEMTPDEFLNLAFQRLEQVNPALNAVVHTRKDRVMAEVESLGVERSF 67 Query: 65 GGVPVAIKDNINVL-GEPCRCASRILEGYLAPYDSTVIEKLKKAGAILLGRTNMDEFAMG 123 GVP+ +K+ L EP +S++++ ++ DS + KL+ AG + +G TN EF + Sbjct: 68 SGVPMLLKNLSQSLENEPITSSSKLMKDHIGRQDSNYVSKLRAAGFLFMGHTNTPEFGLK 127 Query: 124 SSTENSSVGITRNPWNTERVPGGSSGGSAAAVAAHEAFCALGSDTGGSIRQPAAFCGCVG 183 + TE G+TRNPWNT GGSSGG+AAAVA+ A SD GGSIR PA+F G G Sbjct: 128 NITEPEVHGLTRNPWNTNYASGGSSGGAAAAVASGVVPAAGASDGGGSIRIPASFTGLFG 187 Query: 184 LKPTYGRV---SRYGLTAFASSLDQIGPITKTVEDAALLLEVISGFDPFDNTSEKLPVPR 240 LKPT GR G +S+D ++++V D+A LL+++ P P Sbjct: 188 LKPTRGRTPVGPGAGRQWQGASID--FALSRSVRDSAALLDILQVVQP----EAAFQTPA 241 Query: 241 FSELLENRPLKDFVLGIPKEYFIEG-----IDGEVRQALSQVIGHYEKLGVKIEEVSLPH 295 F + F + Y E + + R+A+ + + EK G +EE H Sbjct: 242 FPGSYKTDMAVPFKGQLRIAYTTESPVGTPVSDDAREAVVKTVCWLEKSGHIVEEQD--H 299 Query: 296 TPYAV---ATYYILATAEASANLARFDGIRYGKRAKNYNDL-IDYYGKTRDEGFGSEVKR 351 V YY++ + E SA AR + R +R D+ I+ + + S + Sbjct: 300 DVDGVRIMQDYYLMNSGEISAVTARLE--RLLERELTPEDVEIETWLLHKAGKSVSAAEF 357 Query: 352 RILLGTYVLSSGYYDAYYLRALKVKEKIKQDFSLAFQKCQALLTPTSPFCAFRIGE--KT 409 L ++ +++ +A++ DF +TP + + A +GE + Sbjct: 358 SASLASWDMAAAQMEAFHR---------TYDF---------FITPAAAYTAPEVGELSHS 399 Query: 410 SDPLQMYLADI------------------------FTIAVNLAGICALSIPCGRSTEGLP 445 S Q++ + + FT NL G A+S+P S EGLP Sbjct: 400 SGEQQLWRSKMETANKAEQQAIIWDIFLPSLTYTPFTQLANLTGQPAMSVPVHLSKEGLP 459 Query: 446 IGFQLIGPAWKEETILALGYIYQKTTGWV 474 +G Q++ +E +L L Y +++ WV Sbjct: 460 LGVQVMASKGREYMLLKLAYQLEQSDIWV 488 Lambda K H 0.319 0.139 0.410 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: 435 Number of extensions: 16 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: 494 Length of database: 498 Length adjustment: 34 Effective length of query: 460 Effective length of database: 464 Effective search space: 213440 Effective search space used: 213440 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: 52 (24.6 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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