Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_078428416.1 BK574_RS09330 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= curated2:B0KBN4 (488 letters) >NCBI__GCF_002019605.1:WP_078428416.1 Length = 466 Score = 358 bits (919), Expect = e-103 Identities = 203/479 (42%), Positives = 299/479 (62%), Gaps = 32/479 (6%) Query: 2 ELYSLTIHELRELLKKREVSALEVTKSYLERIKEVEPKIDALITITEDFALQRAKEADEK 61 EL TI +L L++ +E+S +E+T++ L+R KE P I+A I I E+ AL+ AK A+ + Sbjct: 3 ELAKKTIADLAPLVESKELSPVEITEAVLKRTKEYNPTINAYIDINEETALEAAKAAEVE 62 Query: 62 IKNGE-DTALTGIPVIIKDNISTEGIKTTCSSKMLENYIPPYNATVVEKLLEEGVIILGK 120 I NG L GIP+ +KD ++ +G T SK+ ++++P ++ATVV KL E G + GK Sbjct: 63 ISNGNYKGVLHGIPLALKDILNFKGETVTYGSKIHKDFVPDFDATVVTKLKEAGSVFTGK 122 Query: 121 SNLDEFAMGSSTENSAFKTTKNPWDLSRVPGGSSGGSAAAIAADEAAFALGSDTGGSIRQ 180 N+ E+A G++T+N F +NPWDL R P GSSGGS AA+AAD +LG+DTGGSIR Sbjct: 123 LNMHEYAWGATTDNPHFGACRNPWDLQRNPMGSSGGSGAAVAADMTIASLGTDTGGSIRM 182 Query: 181 PASLCGVVGMKPTYGLVSRYGLVAFASSLDQIGPFTKDVTDCAIVLNTIIGHDPKDSTSL 240 PA+ CG+VG+KPT+G VS+YG + SLD IGP TK V D AI+L I G+D KD T++ Sbjct: 183 PAAACGIVGLKPTHGRVSKYGCFPLSWSLDHIGPMTKTVEDAAILLEYIAGYDEKDPTTI 242 Query: 241 KIDKPDYTSYLKEDIKGLRIGVAKEFFGEGIEEGVKETVQESIKVLQDLGAEIIDISIPY 300 + +Y++YL DIKG IG+ +++F + I+ G+++TV++ IK L+ +GA + I +P Sbjct: 243 EKPIENYSNYLTGDIKGKVIGIIEDYFFQEIDNGIEKTVRDGIKQLESMGATVEVIKVPS 302 Query: 301 VEYALPAYYIIASAEASSNLARYDGIRYGHIAGKYEDLIDMYMVTRSEGFGKEVKRRIML 360 ++YA+ A YI AE+++ AR I R FG++V+ + L Sbjct: 303 LKYAMFAEYITILAESTTIHARNIKI-------------------RPNDFGEDVRLNLKL 343 Query: 361 GTYALSSGYYDAYYKKALKVRTLIKNDFEKAFEKCDVIIGPTSPTVAFKIG-ERANDPLA 419 G + SG Y +A ++R +I +F +AFEK DVIIGP+ P IG + + + Sbjct: 344 G--MVPSG---VDYLQAQQIRRMIDLEFVRAFEKVDVIIGPSLPVAPPTIGIDTTSQGVR 398 Query: 420 MYLADIYTVSVNIAGLPGISIPCGLSDGLPVGLQIIGRHFDEGKILNVAYAFEQANKFN 478 + + N+ GLP IS+PCG+S+GLPVG+QIIG F E +ILN AYA E+ N N Sbjct: 399 L------SCPANLTGLPSISVPCGISEGLPVGMQIIGPAFKETEILNFAYALEKTNPLN 451 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: 578 Number of extensions: 26 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: 488 Length of database: 466 Length adjustment: 33 Effective length of query: 455 Effective length of database: 433 Effective search space: 197015 Effective search space used: 197015 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: 51 (24.3 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