Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate PfGW456L13_3755 Amidase (EC 3.5.1.4)
Query= curated2:B8J405 (486 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3755 Length = 374 Score = 152 bits (385), Expect = 1e-41 Identities = 128/410 (31%), Positives = 179/410 (43%), Gaps = 61/410 (14%) Query: 72 GVPVTLKDAFSTRGMPTTAGSRML-EGYTPFYDAFAVQKLHEAGAVILGKTNLDEFAMGS 130 G V +KD+ G PT +GSR + +A V + +AG I+GKTNL E A G Sbjct: 14 GKRVAIKDSIDIAGHPTRSGSRAFADAPAATQNAEVVDAILDAGWQIVGKTNLHELAFGV 73 Query: 131 STENSAFKVTRNPWNLNKVPGGSSGGSAASVTAGQCFASLGTDTGGSIRQPASFCGCVGL 190 + N NP ++VPGGSS GSA++V AG ++GTDTGGS+R PA+ CG GL Sbjct: 74 TGINDWTGTPINPQAPDRVPGGSSSGSASAVAAGLADIAIGTDTGGSVRVPAACCGIAGL 133 Query: 191 KPTYGRVSRYGVIAYGSSLDQVGPLTRSVEDCARVLTAIAGYDSRDNTCDPRPAEDYAAT 250 KPTYGRVSR G SSLD VGP +S++D + I T Sbjct: 134 KPTYGRVSRVGAHPLESSLDCVGPFAKSMDDLIAAMQVICP----------------GFT 177 Query: 251 LSSRPLKGARLGIPREFYGQGLSDEVRAACEAAIQAARNQDAELV-----EVSLPHTDAA 305 P GAR+G + AC++ +QA+ A+ + L +AA Sbjct: 178 AQGLPGDGARVGF------------LEVACDSHLQASLGAAADRAGWRRSNLHLSEFEAA 225 Query: 306 IATYYIIAMAEASSNLARFDGVRFGHRSADIKNLDDLYVHSRTEGFGPEVKRRIMLGAYV 365 A + E + FGH + K L G +V+ R++ + Sbjct: 226 FAAGLTVINFE--------NWAAFGHLTG--KGL-----------IGADVETRLLAASRT 264 Query: 366 LSSGYYDAYYRKAAQVRRLIRDELLAALGQCDALLAPVSPVTARDLGGNTADPLQIYLMD 425 D A VR ++ AAL LL P P L A + M Sbjct: 265 TREELAD-----ACAVRTRFTQQVDAALEDFAVLLLPTLPTLPPTLSEARAGSKAVAGMT 319 Query: 426 AYTLSLNLAGLPGLSLPVGLGAKSGMPVGMQIIGKPFEETQVLALGHSLE 475 NL+G P L++PV L G+ VG+QI+G+ ++ V A G L+ Sbjct: 320 PLVRPFNLSGHPALTVPVELDC-GGLKVGLQIVGRKGQDELVCAFGAQLQ 368 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: 397 Number of extensions: 21 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: 374 Length adjustment: 32 Effective length of query: 454 Effective length of database: 342 Effective search space: 155268 Effective search space used: 155268 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