Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate SMa1377 SMa1377 amidase
Query= curated2:B8J405 (486 letters) >FitnessBrowser__Smeli:SMa1377 Length = 471 Score = 231 bits (590), Expect = 3e-65 Identities = 157/483 (32%), Positives = 235/483 (48%), Gaps = 45/483 (9%) Query: 1 MTDICSLSLTAVAQALQKKELSAVDVTTACLDRITATEPHLAALLYVNAENALARATTLD 60 MT + +LS+ +A ++ +E+SAVDVTT L RI A + L E AL A LD Sbjct: 1 MTALENLSIRKLAAMVRAREISAVDVTTHFLGRIVAYDDALCGFNVPAPEAALDAAHDLD 60 Query: 61 S--EGPDAARPLWGVPVTLKDAFSTRGMPTTAGSRMLEGYTPFYDAFAVQKLHEAGAVIL 118 + A L G+P+++KD G+P+ S G T DA V ++ AG ++L Sbjct: 61 TYLNAGGEAGALAGIPLSIKDTADVAGLPSAGASASRSGRTATADATVVARMKAAGGIVL 120 Query: 119 GKTNLDEFAMGSSTENSAFKVTRNPWNLNKVPGGSSGGSAASVTAGQCFASLGTDTGGSI 178 GK N E A G + + F RNPWNL++ PGGSS GS +V AG C SL TDT GSI Sbjct: 121 GKANCHELAFGGPSFDLPFPPARNPWNLDRFPGGSSSGSGVTVAAGLCLGSLATDTAGSI 180 Query: 179 RQPASFCGCVGLKPTYGRVSRYGVIAYGSSLDQVGPLTRSVEDCARVLTAIAGYDSRDNT 238 R PA+ CG GLKP + + G+ +++D VGP+ R+ +D + +AG Sbjct: 181 RLPATMCGVFGLKPGHDTLPLDGIAVLAATMDHVGPVARTADDTRILFDVMAGRS----- 235 Query: 239 CDPRPAEDYAATLSSRPLKGARLGIPREFY--GQGLSDEVRAACEAAIQAARNQDAELVE 296 P + + LKG R+G+P + G+ + +VRAA + AI+ AR++ A++V Sbjct: 236 ----PGSPFVGS-----LKGLRIGVPENEWDVGRLIHPDVRAAIDGAIEVARSEGADIVP 286 Query: 297 VSLPHTDAAIATYYIIAMAEASSNLARFDGVRFGHRSADIKNLDDLYVHSRTEGFGPEVK 356 + LP + A ++ M E ++ A V + + FG + Sbjct: 287 LRLPSLEDFHAPGTVLMMCEVAAEHA-------------------ASVRAAWDKFGAIFR 327 Query: 357 RRIMLGAYVLSSGYYDAYYRKAAQVRRLIRDELLAALGQCDALLAPVSPVTARDLGGNTA 416 R ++G G +R A ++R ++R LL A+ D LL P + L + Sbjct: 328 ARALVG-----EGIAVHDFRLAERLRPVLRKRLLDAMSNVDCLLVPGALAPPGPLA--SV 380 Query: 417 DPLQIYLMDAYTLSLNLAGLPGLSLPVGLGAKSGMPVGMQIIGKPFEETQVLALGHSLEQ 476 DP + N G P L+ P G G GMPVG+QI+G P E ++L + S E+ Sbjct: 381 DPFYFMKDPIPNIVANYTGFPALAFPAGFGG-DGMPVGVQIMGVPRSEHRLLDIAESFER 439 Query: 477 ALP 479 A P Sbjct: 440 ADP 442 Lambda K H 0.317 0.133 0.388 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: 504 Number of extensions: 22 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: 486 Length of database: 471 Length adjustment: 34 Effective length of query: 452 Effective length of database: 437 Effective search space: 197524 Effective search space used: 197524 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: 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