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_041100505.1 SUTH_RS15540 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A0RWW0 (348 letters) >NCBI__GCF_000828635.1:WP_041100505.1 Length = 345 Score = 249 bits (636), Expect = 7e-71 Identities = 141/352 (40%), Positives = 205/352 (58%), Gaps = 13/352 (3%) Query: 1 MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFTDLTFSELD 60 +K G+VG +GY G E LRLL H VE+ A+TSR G + + SLRG +L FS+ Sbjct: 2 IKAGIVGGTGYTGVELLRLLAQHSGVELTAITSRGEAGTAVAEMFSSLRGSVNLKFSD-P 60 Query: 61 YDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHPHP 120 D + CD+VF A P+G A +L + ++VIDL+AD+R+ D A + +WYG H P Sbjct: 61 KDAPLNECDVVFFATPNGIAMQQAASLLESGVRVIDLAADFRIKDIALWEQWYGMSHASP 120 Query: 121 DYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKIGS 180 ++++V+G+PE++RE+IR+A+LV+ PGC + L P V+ G +D H++ D+K G Sbjct: 121 ALVAEAVYGLPEVNREQIRTARLVANPGCYPTATQLGFLPLVQSGCIDLGHLIADAKSGV 180 Query: 181 SGAG--AGAGTAHAMRAGVIRPYKPAKHRHTGEIEQELSGIAGK---KIRVSMSPHAVDV 235 SGAG A GT + + + Y HRH EI Q L+ AGK +I ++ PH + Sbjct: 181 SGAGRKAEIGTLFSEASDNFKAYGVPGHRHLPEIRQGLARAAGKETNQIGLTFVPHLTPM 240 Query: 236 VRGILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCD 295 +RGI T + +TR E+D M+ Q Y E FV ++ K P+ + + +N C Sbjct: 241 IRGIHATLYARITR---EEDFQAMFEQRYAAEPFVDVLPPK----SHPETRSVRAANTCR 293 Query: 296 IGFDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347 I + + LV +S DNL+KGAAG A+QNMNIM GLDE SGL P+ P Sbjct: 294 IAIHRPQGGDTLVVLSVIDNLVKGAAGQAVQNMNIMFGLDECSGLSQVPVLP 345 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: 259 Number of extensions: 14 Number of successful extensions: 6 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: 345 Length adjustment: 29 Effective length of query: 319 Effective length of database: 316 Effective search space: 100804 Effective search space used: 100804 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 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