Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate WP_093392448.1 BM091_RS00090 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A0RWW0 (348 letters) >NCBI__GCF_900114975.1:WP_093392448.1 Length = 346 Score = 278 bits (712), Expect = 1e-79 Identities = 156/350 (44%), Positives = 214/350 (61%), Gaps = 8/350 (2%) Query: 1 MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFTDLTFSELD 60 +KVGV+G SGY G E +RLL HP+V+I AV+SR + P+ R F DL + D Sbjct: 2 LKVGVLGGSGYTGFELIRLLATHPEVKIVAVSSRAQEESAVSEHYPAFRKFVDLRYVLPD 61 Query: 61 YDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHPHP 120 D+VF+A+PHG + V L ++ ++VIDLSAD+R+ D A Y +WY H P Sbjct: 62 DPVFEKGVDVVFSALPHGASMKAVSGLVEKGVRVIDLSADFRIRDAAVYEQWYE-PHTSP 120 Query: 121 DYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKIGS 180 D L +V+G+PEL+R EI SA+LV+ PGC + ILALAP ++ L++ + I++DSK G Sbjct: 121 DLLKDAVYGLPELYRREIASARLVANPGCYPTSIILALAPLLKNRLIEEDSIIIDSKSGV 180 Query: 181 SGAGAGAG-TAHAMRAGV-IRPYK-PAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDVVR 237 +GAG G T H + YK HRH EIEQELS I+GK+IRV+ +PH V + R Sbjct: 181 TGAGRGLSLTTHFCEVNEGFKAYKVGGVHRHIPEIEQELSLISGKEIRVTFTPHLVPMSR 240 Query: 238 GILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCDIG 297 GIL T +V ++ + YR Y +E FVRL+ G + P + GSNFCDIG Sbjct: 241 GILSTLYVVPREGVKAGEIDEAYRTMYADEPFVRLV----GSGEMPSTLQVRGSNFCDIG 296 Query: 298 FDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347 + LD + RL+ +SA DNL +GA+G A+ NMNIM G+ E +GL Y P P Sbjct: 297 WKLDGRSGRLIVVSAIDNLTRGASGQAVCNMNIMFGIPETTGLFYVPWQP 346 Lambda K H 0.320 0.137 0.412 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: 329 Number of extensions: 17 Number of successful extensions: 4 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: 348 Length of database: 346 Length adjustment: 29 Effective length of query: 319 Effective length of database: 317 Effective search space: 101123 Effective search space used: 101123 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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