Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate HSERO_RS21870 HSERO_RS21870 amidase
Query= SwissProt::O06491 (485 letters) >FitnessBrowser__HerbieS:HSERO_RS21870 Length = 506 Score = 197 bits (500), Expect = 9e-55 Identities = 152/484 (31%), Positives = 228/484 (47%), Gaps = 40/484 (8%) Query: 3 LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62 L + EL+QLI K++ +L++ RI+ ++ + A A ERAR A+ ++AV Sbjct: 5 LVEKSAVELRQLIGSKQLSPVELLEACIARIEDINPHINAVTATCFERARGEARAAEQAV 64 Query: 63 DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122 GLL G+PIG+KD T+GL TT S + P D +V RL+ A A+ GK Sbjct: 65 IDGKPLGLLHGLPIGIKDLEETEGLLTTYGSPLYRGNIPARDNALVARLRAAGAIVAGKT 124 Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 N+ E G+++ N+ + T NP+N GGSSGGSAAA+A +P GSDTGGS+R P Sbjct: 125 NVPEMGAGANSRNAVWGATGNPFNPLLNAGGSSGGSAAALATDLLPLCSGSDTGGSLRIP 184 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 A+ CGVVG +P+ G V + + + +GP+ R V D L+A G+ D Sbjct: 185 AAKCGVVGFRPSPGLVPSERKLLGWTPISVVGPMGRDVADTVLQLRATLGLHASDPLGYA 244 Query: 243 VDVPDFLSSLTGDIKGLKIAVPKEY----LGEGVGKEARESVLAALKVLEGLGATWEEVS 298 V +F S D+ L+I +++ + G+ + R+ + A ++ ++ Sbjct: 245 VSDSEFASLPQVDLSQLRIGYTEDFGVCDVDNGIRQVFRDKMAAIAPYVKLCEPVDVDMG 304 Query: 299 LPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRR 358 H + + A A +A FD YR D A G + Sbjct: 305 EAHRAFDVI--------RAEAFVAGFDA---AYRRDPA-------------SLGPNTRAN 340 Query: 359 IMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGE----- 413 +G + D + AQ +T I + F+ ++E+YD+I+ PTTP F E Sbjct: 341 YEMGA---AMSLLDCAW--AQSEQTRIFRRFQQLYERYDLILSPTTPVSPFPWSELYLKE 395 Query: 414 -NTKDPLTMYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHA 471 N Y LT V LA P IS+PCG G+P GLQ+ G ++ V A A Sbjct: 396 VNGVALENYYRWLALTYVVTLATNPAISLPCGRDHRGMPFGLQVTGPFRGDARVLACAAA 455 Query: 472 FEQA 475 EQA Sbjct: 456 LEQA 459 Lambda K H 0.315 0.134 0.381 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: 533 Number of extensions: 30 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: 485 Length of database: 506 Length adjustment: 34 Effective length of query: 451 Effective length of database: 472 Effective search space: 212872 Effective search space used: 212872 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 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