Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate HSERO_RS04670 HSERO_RS04670 amidase
Query= curated2:Q9HR43 (423 letters) >FitnessBrowser__HerbieS:HSERO_RS04670 Length = 504 Score = 246 bits (628), Expect = 1e-69 Identities = 156/437 (35%), Positives = 232/437 (53%), Gaps = 28/437 (6%) Query: 3 LNAFITETTIQGAADGPLDGTTVAVKDNISTKGVPTTCGSKMLADYEPPYNATVVEDLLA 62 LNA+ ++T++GAA+G L G TV +KDN++ GVP GS L + P Y+AT+V LL Sbjct: 71 LNAWACKSTVKGAAEGKLAGRTVVLKDNVALAGVPMMNGSSTLEGFVPSYDATIVTRLLD 130 Query: 63 AGGTIVGKTNMDEFGMGTTTETSYFGPTKNPVDETRVPGGSSGGSAAAVANGDADLALGS 122 AG TI+GK + F + + TS P NP GGSS GSAA VA G+AD+A+G Sbjct: 131 AGATILGKATCEHFCLSGGSHTSDPAPVHNPRRHGYGSGGSSSGSAALVAAGEADMAIGG 190 Query: 123 DTGGSVRAPAAYCGVVGLKPTYGLVSRYGLVAYANSLEQIGPIAPTVEGAAELLDVIAGP 182 D GGS+R P+A+CG G+K T+GLV G++ +++ +GPI V A +L+VIAG Sbjct: 191 DQGGSIRIPSAFCGTYGMKATHGLVPYTGVMPIEATVDHVGPITANVRDNALMLEVIAGA 250 Query: 183 DEHDGTTRDAGADADYASAATGDVDGLTIGVPQELTDG-----ADDRVVERFEAALADLR 237 D D + A Y +A V GL IG+ LT+G D RV ++ + A+A L Sbjct: 251 DGLD-PRQYAPEVQPYTAALDRGVRGLKIGI---LTEGFALGNMDKRVADKVQEAIAQLE 306 Query: 238 AEGATTVDVALPSCEYAVAAYYVIAMSEASSNLARFDGVRYGTGGGFD-------GNWNE 290 GA+ V++ A A + I + + +G+ + G +D +W E Sbjct: 307 KLGASVATVSVEEHALAGALWQPIGCEGLTMQMMHGNGMGFNWKGLYDLGLLQHHAHWRE 366 Query: 291 TFADARADGFGDEVTRRILLGTYALSAGYHDKYYKQAQEARAWVKQDFDETFADVDVVAS 350 AD + + +G Y L+ Y ++Y +AQ + +D+ AD D++ Sbjct: 367 -----HADDLSATLKLCMFVGQYGLTR-YQGRFYAKAQNIARRARAGYDKALADFDLLVM 420 Query: 351 PTMPVLPPKLGESLDDPVQMYLADA-----NTTPANLANLPAISVPAGDADGLPVGVQLV 405 PT+P++ L + P+ Y+A A NT P ++ PA+S+P G DGLPVG+ LV Sbjct: 421 PTVPIIAQPL-PAAGCPLAEYVARAFEMIGNTAPLDITGHPAMSIPCGTVDGLPVGLMLV 479 Query: 406 GPKFGEETIINAAAAVE 422 G + E T+ AAAA E Sbjct: 480 GKHYAEATLYQAAAAFE 496 Lambda K H 0.312 0.132 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: 554 Number of extensions: 29 Number of successful extensions: 3 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: 423 Length of database: 504 Length adjustment: 33 Effective length of query: 390 Effective length of database: 471 Effective search space: 183690 Effective search space used: 183690 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 51 (24.3 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