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_028490259.1 Q394_RS0116805 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A0RWW0 (348 letters) >NCBI__GCF_000621325.1:WP_028490259.1 Length = 346 Score = 273 bits (697), Expect = 6e-78 Identities = 153/349 (43%), Positives = 208/349 (59%), Gaps = 9/349 (2%) Query: 2 KVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFTDLTFSELDY 61 K+G+VGA+GY G E LRLLV+HPDVEI VTSR+H G + + P+LRG+ DL F+ Sbjct: 4 KIGIVGATGYTGVELLRLLVSHPDVEITCVTSREHAGSRVDAMFPNLRGYLDLAFTAPSD 63 Query: 62 DRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHPHPD 121 + LS +CDLVF A P+G A + L D KVIDL+AD+R+ D A + KWYG +H P+ Sbjct: 64 EALS-ACDLVFFATPNGVAMKSTQTLLDAGTKVIDLAADFRIKDIAIWEKWYGMQHASPN 122 Query: 122 YLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKIGSS 181 + ++V+G+PEL+RE IR A+LV+ PGC L L P V GL+D E I+ D+K G S Sbjct: 123 LVEEAVYGLPELNREHIRQARLVANPGCYPTAVTLGLLPLVENGLIDLEGIIADTKSGVS 182 Query: 182 GAGAGAGTAHAMRAGV---IRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDVVRG 238 GAG A HA+ A + Y A HRH EI Q LS +A I PH + ++RG Sbjct: 183 GAGRKA-EVHALLAEAGDNFKAYAVAGHRHQPEIAQTLSTVAQISIDPVFVPHLLPMIRG 241 Query: 239 ILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCDIGF 298 I T + L+ EA++ DL ++Y Y E FV D P+ + + G+N C + Sbjct: 242 IHATLYAMLSVEAAQADLQQLYTTRYANEPFV----DVMPAGSHPETRSVRGANVCRMAI 297 Query: 299 DLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347 + R+V +S DNL+KGAAG A+QNMN+M GL E L+ L P Sbjct: 298 HRPGNARRVVVLSVIDNLVKGAAGQAVQNMNLMLGLSEHIALQQPGLLP 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: 273 Number of extensions: 12 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