Align Putative [LysW]-L-2-aminoadipate 6-phosphate reductase; EC 1.2.1.103 (uncharacterized)
to candidate CA265_RS18540 CA265_RS18540 N-acetyl-gamma-glutamyl-phosphate reductase
Query= curated2:B9KZP8 (352 letters) >FitnessBrowser__Pedo557:CA265_RS18540 Length = 326 Score = 179 bits (453), Expect = 1e-49 Identities = 126/355 (35%), Positives = 185/355 (52%), Gaps = 45/355 (12%) Query: 1 MVVSVAILGGSGYTGGELLRLLLSHPEVEVKQVTSRSRAGKFVHTVHPNLRKRTALKFVP 60 M + I+GG+GYTGGE+LR+L++HP VE+ V S S AG + VH +L T LKFV Sbjct: 1 MKIKAGIIGGAGYTGGEMLRILVNHPNVEIAFVNSTSNAGNLISDVHTDLIGDTDLKFV- 59 Query: 61 PEALEPVDLLFACLPHGETA------PIVDRLLELAPIVIDLSADFRLRDPAAYEQWYHW 114 + + +D+LF C+ HG+ PI D + +IDLS DFRL A++ Sbjct: 60 SDIPQDIDVLFLCVGHGDAKKFLTANPIKDNIK-----IIDLSQDFRLHANASFS----- 109 Query: 115 THPRPDLLAQAVYGLPELHREEIRNARYIACPGCNSTTVILGLAPLFRAGLIDLDLPVTV 174 VYGLPEL+R++I+ A+ IA PGC +T + LGL PL GLI + V + Sbjct: 110 -------TKDFVYGLPELNRDKIKAAKNIANPGCFATCIQLGLLPLAAKGLIQNE--VHI 160 Query: 175 ECKVGSSGAGGEAGPASHHPERSGVIRPFKPGGHRHTAEVLQELTVCGRTPSLGLSVTSV 234 GS+GAG SH R+ + +K H+H E+ + L PS+ ++ + Sbjct: 161 NATTGSTGAGQSLSTTSHFSWRNNNLSIYKAFEHQHLNEISESLLQL--QPSISEALNFI 218 Query: 235 EA----VRGILATAHLFPKQPLTDRDLWQVYRAAYGQEPFIRLVKEASGIHRYPEPKILA 290 RGILA +L + L+ + +Y A Y PF + ++ + K + Sbjct: 219 PQRGAFTRGILAAMYL--ESDLSLEEAQNIYEAYYSAHPFTHVSRKNIDL------KQVV 270 Query: 291 GSNYCDIGWELDELPGGRQRLVVMSAIDNLMKGAAGQAVQAMNIRLGFPETLGLE 345 +N + E GG +L ++S IDNL+KGA+GQAVQ MN+ G ET GL+ Sbjct: 271 NTNKALVHLEKH---GG--KLFIISIIDNLLKGASGQAVQNMNLMFGLDETAGLK 320 Lambda K H 0.321 0.140 0.431 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: 270 Number of extensions: 12 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: 352 Length of database: 326 Length adjustment: 28 Effective length of query: 324 Effective length of database: 298 Effective search space: 96552 Effective search space used: 96552 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