Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.- (uncharacterized)
to candidate GFF354 HP15_352 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:A8AAF8 (356 letters) >FitnessBrowser__Marino:GFF354 Length = 388 Score = 263 bits (671), Expect = 7e-75 Identities = 151/353 (42%), Positives = 214/353 (60%), Gaps = 17/353 (4%) Query: 1 MTYEVAIVGASGYTGGELLRVLAVHPDVNVKVVTSREYANKPVYYAHPHLRGIYPASLKF 60 M +V IVG +GYTG ELLR+LAVHP+V+V +TSR A PV +P+LRG Y + Sbjct: 43 MVIKVGIVGGTGYTGVELLRILAVHPEVSVSCITSRSEAGMPVAEMYPNLRGHYDLAFS- 101 Query: 61 KRLDDPDQLSDVVGDVDLVFLALPHKVSLHYVPKALEVGYKVVDLSADYRLKRVEDYKTW 120 +PD +V+G DLVF A PH V++ VP+ + G +VVDLSAD+RLK ++ + W Sbjct: 102 ----EPDV--NVLGACDLVFFATPHGVAMRMVPELMSAGVRVVDLSADFRLKDLDVWANW 155 Query: 121 YGYEHPYPDLLEKAVYGLPELYGDKIRGAQLVANPGCNATSSILAVLPPAAERIIDLDRI 180 YG H P+ EKAVYGLPE+ D+IR AQLVANPGC T+ L LP + ++D R+ Sbjct: 156 YGMAHESPEWAEKAVYGLPEVVRDEIRNAQLVANPGCYPTAVQLGFLPLLEQGLVDPKRL 215 Query: 181 VVDVKVGSSEAGAKPYRGGHHPEREGTARPYDAEGHRHVAELEQVIRDYTGRDVKVGFTP 240 + D K G+S AG + G H E + + Y A GHRH+ E+ Q + G DV V F P Sbjct: 216 IADAKSGASGAGRQGKIGMLHGEIGESFKAYGASGHRHLPEIRQGLCGAAGGDVGVTFVP 275 Query: 241 HAVSMIRGSLASAYSWLTKDLAPLD-VQRIYAKYYAGKKFVKIVRGAPMPY---PDVKNV 296 H + MIRG A+ Y+ L K+ A D +Q ++ + + + FV + MP+ P+ ++V Sbjct: 276 HLIPMIRGIEATLYAEL-KNPADFDRLQALFEQRFDDEPFVDV-----MPFGSHPETRSV 329 Query: 297 YGSNYAEVGFALDKRVGRLAMFAAIDNLMKGAAGTAVQNMNLMLGMDEDEGLK 349 G+N + ++ + + + IDNL+KGAAG AVQNMN+M G+ E GL+ Sbjct: 330 RGANQCRMALHRQEQSNIVIVSSVIDNLVKGAAGQAVQNMNIMFGLKETMGLE 382 Lambda K H 0.319 0.138 0.410 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: 452 Number of extensions: 23 Number of successful extensions: 3 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: 356 Length of database: 388 Length adjustment: 30 Effective length of query: 326 Effective length of database: 358 Effective search space: 116708 Effective search space used: 116708 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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