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_013553969.1 NITSA_RS05180 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A0RWW0 (348 letters) >NCBI__GCF_000186245.1:WP_013553969.1 Length = 335 Score = 194 bits (492), Expect = 4e-54 Identities = 130/352 (36%), Positives = 192/352 (54%), Gaps = 23/352 (6%) Query: 1 MKVGVVGASGYVGGETLRLLVNHPDVEI--AAVTSRQHVGEYLHRVQPSLRGFTDLTFSE 58 + VG+VGA GY G E +++L+NHP + A TS + E LH PSL E Sbjct: 2 INVGIVGAGGYTGLELVKMLLNHPRFRLNYLATTSGDIMVEELH---PSLLDLITFPVEE 58 Query: 59 LDYDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHP 118 D + ++D C+LVF A+PH + + + L R +K++DLSADYRL + Y Y H Sbjct: 59 ADPELIADKCELVFLALPHKASMGLAKELIVRGVKIVDLSADYRL-ERETYEAAY-CPHE 116 Query: 119 HPDYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTE-HIVVDSK 177 P++L ++V+G+ E +R+EIR A+LV+ PGC ++L L P + +DT I +D+K Sbjct: 117 DPEHLGEAVYGLIEYYRDEIRVARLVAGPGCYPTATLLGLLPFI--PYIDTSAPIFIDAK 174 Query: 178 IGSSGAGAG-AGTAHAMRAG-VIRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDV 235 G SGAG + T+H + I Y P KHRH EI ++++ I G +I V+ PH + Sbjct: 175 SGVSGAGKKLSETSHFVTINDNIFAYNPLKHRHAPEIAEKIAKIHGAEISVNFVPHLIPA 234 Query: 236 VRGILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCD 295 RG L + + L E D ++ +AY ERF+RL +K D K + G++FCD Sbjct: 235 TRGELVSVYATLKEEI---DPQEVLEKAYDTERFIRL------RHKPVDIKSVAGTHFCD 285 Query: 296 IGFDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347 I + L SA DNL++GAA A+ N+M GLDE + L P Sbjct: 286 I--YAQRNGKALFISSAIDNLLRGAASQALAAANLMMGLDEGTALPVIAYVP 335 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: 291 Number of extensions: 15 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: 335 Length adjustment: 29 Effective length of query: 319 Effective length of database: 306 Effective search space: 97614 Effective search space used: 97614 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