Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012404708.1 BPHY_RS27340 amidase
Query= curated2:B0KBN4 (488 letters) >NCBI__GCF_000020045.1:WP_012404708.1 Length = 508 Score = 220 bits (561), Expect = 8e-62 Identities = 153/484 (31%), Positives = 243/484 (50%), Gaps = 39/484 (8%) Query: 2 ELYSLTIHELRELLKKREVSALEVTKSYLERIKEVEPKIDALITITEDFALQRAKEADEK 61 +L S ELR ++ +E+S +E+ + +ERI+ P ++A+ D A + AK A+ K Sbjct: 6 DLVSRNAVELRRMIGAKEISPVELLDACIERIEAANPAVNAITATCYDAARKAAKAAERK 65 Query: 62 IKNGEDTALT-GIPVIIKDNISTEGIKTTCSSKMLENYIPPYNATVVEKLLEEGVIILGK 120 + +GE L G+P+ +KD T G+ TT S M ++P + +VE+L G I++GK Sbjct: 66 VLDGEPLGLLHGLPLGVKDLEDTAGLLTTYGSPMSRGHVPSRDVVLVERLRAAGAILVGK 125 Query: 121 SNLDEFAMGSSTENSAFKTTKNPWDLSRVPGGSSGGSAAAIAADEAAFALGSDTGGSIRQ 180 +N+ E G++T N + T +P+D GGSSGGSAAA+A D GSDTGGS+R Sbjct: 126 TNVPELGAGANTRNPVWGATGDPFDPELNAGGSSGGSAAALACDMLPVCTGSDTGGSLRI 185 Query: 181 PASLCGVVGMKPTYGLVSRYGLVAFASSLDQIGPFTKDVTDCAIVLNTIIGHDPKDSTSL 240 PAS CGVVG +P+ GLV + + + +GP +DV + A+ L G +D S Sbjct: 186 PASKCGVVGFRPSPGLVPNSRRLLGWTPISVVGPMGRDVDETALQLAATAGLSTRDPLSY 245 Query: 241 KIDKPDYTSYLKEDIKGLRIGVAKEFFGEGIEEGVKETVQESIKVLQDLGAEIIDISIPY 300 +D P + + D+ LR+G ++F +++ ++ + + L P Sbjct: 246 DVDAPGFATLPAFDLSTLRVGYTEDFGCCDVDDDIRALFRARMAAL-----------APL 294 Query: 301 VEYALPAYYIIASAEASSNLARYDGIRYGHIAGKYEDLIDMYMVTRSEG-FGKEVKRRIM 359 V P + + A ++ R + +AG L D Y R G G + Sbjct: 295 VHTCEPVAFDLGDAHRCFDVIRAESF----VAG----LCDAY--ARDPGALGPNTRANYE 344 Query: 360 LGTYALSSGYYDAYYKKALKVRTLIKNDFEKAFEKCDVIIGPTSPTVAF--------KIG 411 +G + D+ + +A + R I F+ AFE+CDVI+ PT+P F +I Sbjct: 345 MGA---AMTLADSAWAQAEQTR--IFRRFQSAFERCDVILSPTTPVSPFPWRELYAAQID 399 Query: 412 ERANDPLAMYLADIYTVSVNIAGLPGISIPCGLS-DGLPVGLQIIGRHFDEGKILNVAYA 470 RA + +LA Y V++ P +S+PCG+ G+P GLQI+G + K L VA A Sbjct: 400 GRAQENYYRWLALTYVVTLTTH--PALSLPCGVDRAGMPFGLQIVGPFHGDLKTLAVARA 457 Query: 471 FEQA 474 E+A Sbjct: 458 MEKA 461 Lambda K H 0.316 0.136 0.380 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: 502 Number of extensions: 27 Number of successful extensions: 5 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: 508 Length adjustment: 34 Effective length of query: 454 Effective length of database: 474 Effective search space: 215196 Effective search space used: 215196 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 10 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