Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_013420214.1 RVAN_RS13195 amidase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000166055.1:WP_013420214.1 Length = 490 Score = 170 bits (431), Expect = 9e-47 Identities = 161/501 (32%), Positives = 214/501 (42%), Gaps = 80/501 (15%) Query: 15 ELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTELGPLAGVPIA 74 E+SA E+ A +R V PA+ A + E A++ DA A D PLAGVP Sbjct: 23 EVSAGELLAEARARADAVNPALNAIVY---RRDAEAAREADA--VAPDA---PLAGVPFL 74 Query: 75 VKD-NICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANMDEFAMGSSGESS 133 VKD +G TC S++ YV D +V+R + AG + GK N+ EF + E Sbjct: 75 VKDLGSPLAGAPLTCGSKLFANYVPDHDGEIVKRFKRAGLIAFGKTNVPEFGLVPVTEPV 134 Query: 134 AFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIVGLKPTYG 193 FG RNPWD ER PGGSS G+AAAVAAG P+A TD GGSIR PA+ G+VGLK + G Sbjct: 135 LFGPCRNPWDTERTPGGSSGGAAAAVAAGVVPMAHATDGGGSIRIPASCCGLVGLKTSRG 194 Query: 194 YVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDA---TNAGRTPPALKFGGE 250 V F + R V D A + G R DA PP L+ Sbjct: 195 L---NPVEPFTPDYVVDHVVSRTVRDSAAALDATCG--RADAGFLAGLDAPPPRLRIA-- 247 Query: 251 PSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEY--ALSAYYV 308 V +L + P VK ++EA L LG VE+ P+ +Y SA+ + Sbjct: 248 --------VVRSAMLAGAVSPVVKTALDEAARLLASLGHHVEDAE-PALDYDAFASAFLI 298 Query: 309 IAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTYVLS--AG 366 A L + G RAA K + GT+ L+ G Sbjct: 299 EWATGARFILDKLPPALIG-RAA--------------------TKDDVEFGTWTLTTIGG 337 Query: 367 HYDAYYRRAQQVRTLVVRDFERAFERYDALVTPT------------TPF---TAWKIGEK 411 H + AQ F RYD L++P PF TA KI + Sbjct: 338 HLMSQRAEAQATLATESAKLIDFFTRYDVLLSPVLATPPLRISEAGAPFPEKTAAKIADA 397 Query: 412 VDDPVSM-----------YLGDICTIPVNLAGLPAVSVP-CGFVDGLPVGMQLIGKPFAD 459 V P M + + P N++G PA+SVP C DGLP+GMQ + D Sbjct: 398 VGSPERMRSIVRAVARKSFAFAAFSAPFNMSGQPAISVPLCETPDGLPIGMQFAARIGDD 457 Query: 460 TQILQIAWAYQKVTKHHEARP 480 +L++A ++ E RP Sbjct: 458 GLLLRLARELEQAAPWGERRP 478 Lambda K H 0.318 0.135 0.391 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: 696 Number of extensions: 51 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: 490 Length adjustment: 34 Effective length of query: 454 Effective length of database: 456 Effective search space: 207024 Effective search space used: 207024 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 (21.7 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