Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF3560 PS417_18230 amidase
Query= curated2:Q8THJ1 (476 letters) >FitnessBrowser__WCS417:GFF3560 Length = 504 Score = 263 bits (673), Expect = 8e-75 Identities = 162/439 (36%), Positives = 242/439 (55%), Gaps = 37/439 (8%) Query: 52 KIDVEG-HEGPLAGVPIAIKDNISVVGLPNSCGSKILEGYVPPFNAHVIEKLLDAGAVIL 110 + +V G +G LAG +A+KDNIS+ G+P G+K LEG+VP F+A V+ +LLDAGA IL Sbjct: 77 RTEVSGARDGKLAGKTVALKDNISLAGVPMMNGAKPLEGHVPSFDATVVTRLLDAGATIL 136 Query: 111 GKTNLDEFAMGSSTETSYYGPTANPWDLERVPGGSSGGSAAVVAAGEAPFALGSDTGGSV 170 GK + + + + TS P NP+ GGSS GSAA+VAAGE A+G D GGS+ Sbjct: 137 GKATCEHYCLSGGSHTSDPAPVHNPYRHGFASGGSSSGSAALVAAGEVDLAVGGDQGGSI 196 Query: 171 RCPAAFCGVVGLKPTYGAVSRYGVVAYANSLEQVGPLANNVEDIAILMDVIAGYD----R 226 R P+AFCG G+KPT+G V G++A +++ GP+ NV D A++++V+AG D R Sbjct: 197 RIPSAFCGTYGMKPTHGLVPYTGIMAIEATIDHAGPITANVRDNALMLEVMAGADGLDPR 256 Query: 227 RDSTSIDSKTEYQKALVDDVKGLKIGVPKEFFG-EGIHPGVEKAVWNAIHKFESLGATRQ 285 + + +D+ ++Y L V GLKIGV +E F P V +V NAI +F LGA + Sbjct: 257 QAAPQVDTYSDY---LARGVSGLKIGVLREGFELANQDPRVASSVRNAIARFSQLGAQVE 313 Query: 286 EVSMPNINYALASYYIIAMSEASSNLARFDGTRYGFRANGENWHAMVS----------KT 335 EVS+P A A ++ I + + +G G NW + + Sbjct: 314 EVSVPEHAIAGALWHPIGCEGLTMQMMHGNGA-------GFNWKGLYDVGLLDKQAGWRD 366 Query: 336 RAEGFGTEVKRRILLGTYALSAGYHDKYYLKALKVRTLVKQDFDKALSTVDLLMAPTM-- 393 +A+ +K + +G Y + Y+ ++Y KA +R L + +D AL+ DLL+ PT+ Sbjct: 367 QADDLSASLKLCMFVGQYGVER-YNGRFYAKAQNLRRLARSAYDAALARYDLLVMPTVPI 425 Query: 394 -----PNPAFRIGEKIEDPLTLYLSDVNTCPINLAGVPSVSVPCGFTDGLPVGLQIMGKP 448 P P I E + L + N ++ G P++S+PCG DGLPVGL ++GK Sbjct: 426 IAQPHPEPDCSITEYVARALEMI---GNASAQDITGHPAMSIPCGLVDGLPVGLMLVGKH 482 Query: 449 FDEPTVLRAAYTFEKNTDY 467 + E T+ +AA FE D+ Sbjct: 483 YAEGTIYQAAAAFEAAVDW 501 Lambda K H 0.315 0.134 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: 583 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: 476 Length of database: 504 Length adjustment: 34 Effective length of query: 442 Effective length of database: 470 Effective search space: 207740 Effective search space used: 207740 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 (21.5 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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