Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate GFF3572 Psest_3639 N-acetyl-gamma-glutamyl-phosphate reductase, common form
Query= curated2:A0RWW0 (348 letters) >FitnessBrowser__psRCH2:GFF3572 Length = 344 Score = 239 bits (609), Expect = 1e-67 Identities = 140/350 (40%), Positives = 190/350 (54%), Gaps = 10/350 (2%) Query: 1 MKVGVVGASGYVGGETLRLLVNHPDVEIAAVTSRQHVGEYLHRVQPSLRGFTD-LTFSEL 59 +KVG+VG +GY G E LRLL HP E+A +TSR G + + P+LRG D L FS Sbjct: 2 IKVGIVGGTGYTGVELLRLLAQHPQAEVAVITSRSEDGVKVTDMYPNLRGHYDNLAFSVP 61 Query: 60 DYDRLSDSCDLVFTAVPHGTATDIVRALYDRDIKVIDLSADYRLHDPADYTKWYGWEHPH 119 D L +CD+VF A PHG A + L +VIDLSAD+RL D ++ WYG H Sbjct: 62 DAATLG-ACDVVFFATPHGVAHALAGELLAAGTRVIDLSADFRLQDADEWATWYGQAHGA 120 Query: 120 PDYLSKSVFGIPELHREEIRSAKLVSCPGCMAVTSILALAPPVREGLVDTEHIVVDSKIG 179 P+ L ++V+G+PE++RE+IR A+L++ PGC + L P + GL D ++ D K G Sbjct: 121 PELLPEAVYGLPEVNREQIRKARLIAVPGCYPTATQLGFLPLLENGLADASRLIADCKSG 180 Query: 180 SSGAGAGA--GTAHAMRAGVIRPYKPAKHRHTGEIEQELSGIAGKKIRVSMSPHAVDVVR 237 SGAG A G+ + Y HRH EI Q L A I ++ PH ++R Sbjct: 181 VSGAGRAAKIGSLFTEAGESMMAYAVKGHRHLPEISQGLRRAARGDIGLTFVPHLTPMIR 240 Query: 238 GILCTNHVFLTREASEKDLWKMYRQAYGEERFVRLIRDKKGLYKFPDPKFLVGSNFCDIG 297 GI T ++ T E DL ++Y Q Y E FV D P+ + + G+N C I Sbjct: 241 GIHAT--LYATVEDKSVDLQRLYEQRYANEPFV----DVMPAGSHPETRSVRGANVCRIA 294 Query: 298 FDLDEDNNRLVAISASDNLMKGAAGSAIQNMNIMAGLDEMSGLRYTPLTP 347 + N +V +S DNL+KGA+G AIQNMNI+ LDE GL L P Sbjct: 295 VHRPQGGNLVVVLSVIDNLVKGASGQAIQNMNILFDLDERLGLGNVALLP 344 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: 285 Number of extensions: 14 Number of successful extensions: 5 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: 344 Length adjustment: 29 Effective length of query: 319 Effective length of database: 315 Effective search space: 100485 Effective search space used: 100485 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