Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 3607637 Dshi_1046 Amidase (RefSeq)
Query= curated2:O83983 (506 letters) >FitnessBrowser__Dino:3607637 Length = 376 Score = 148 bits (373), Expect = 4e-40 Identities = 141/428 (32%), Positives = 186/428 (43%), Gaps = 84/428 (19%) Query: 82 GSVSGKPLLGLPFAVKDNISVKGKHCTCGSKLLADYRAPYDATVVARLRAAGAIPLGRTN 141 GS +G PL GL VK NI+V G+ T G + A DA V+ARLRAAGA L Sbjct: 27 GSGTG-PLAGLRIGVKSNIAVAGQAWTAGIAGRGEVLAEADAEVIARLRAAGADLLPGLT 85 Query: 142 MDEFAMGSSTEYSVYGPTRNPRDRSRTSGGSSGGSAAAVAGGQAPFALGTETGGSVRLPA 201 MDE A+G++TE S T+NP + GGSSGG+AAAVA G P ALG++T GSVR+PA Sbjct: 86 MDEAALGAATETSGLRATQNPFAPGHSVGGSSGGAAAAVACGAVPVALGSDTLGSVRIPA 145 Query: 202 AYCGLYGLKPTYGLLSRYGVVAFGSSLDQIGFFATCIDDIALALSVTSGKDLYDSTSTCP 261 AYCG+ G KP G+L GVV +LD +G A + D+ +V + Sbjct: 146 AYCGVLGFKPGAGVLPLGGVVPLDPALDTLGLLARRVADLRAVYAVLA------------ 193 Query: 262 PPATGRHAVSHHLAPFSAHEC------SILRAAVPRELVDAPGVHPDVSAQFQRFLTWLR 315 P A A LAP + C ++ RAA L+DA G PD R Sbjct: 194 PEAVAETAQVVQLAPQADVACAPEVQTALARAA---RLLDASG--PD------------R 236 Query: 316 AQNVQVEEVTLPALQAAVPVYYLVATAEAASNLARFDGIRYGQRGDTDALLENYYRAVRT 375 + + E + + A + +++A + YG R D L RA Sbjct: 237 LEGWEAEALRMAAFTRVCAAAATTLADQPIASVAVRSAMAYGARLTPDGLA----RAEAL 292 Query: 376 SGFGPEVQRRIIVGNYVLSRHFSGDYYRTSVRVRSRIEQECTQLLCSYHFIVCPTAATGA 435 R + +R+R+ L PT T A Sbjct: 293 CD-------------------------RVAAALRARLPPGTVAL--------TPTTPTPA 319 Query: 436 FPLGERIHDPLAMYCSDLFTTFVNLARLPALSVPVGTSGTGLPIGIQIIGSQWQECAVLR 495 F G P A S FT NLA LPA+SVP+G P +Q++ QE +L Sbjct: 320 FARGT---PPPADQAS--FTVLANLAGLPAISVPMG------PASVQLMAGPGQEGTLLA 368 Query: 496 LAKRWEEA 503 LA R A Sbjct: 369 LADRLSAA 376 Lambda K H 0.320 0.134 0.403 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: 473 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 506 Length of database: 376 Length adjustment: 32 Effective length of query: 474 Effective length of database: 344 Effective search space: 163056 Effective search space used: 163056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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