Align Putative [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase; EC 1.2.1.103; EC 1.2.1.106 (uncharacterized)
to candidate 199470 SO0275 N-acetyl-gamma-glutamyl-phosphate reductase (NCBI ptt file)
Query= curated2:A1RR73 (352 letters) >FitnessBrowser__MR1:199470 Length = 326 Score = 155 bits (392), Expect = 1e-42 Identities = 111/341 (32%), Positives = 172/341 (50%), Gaps = 26/341 (7%) Query: 1 MKKVCIVGASGFTGGELLRILLQHRGVEI---VCATSRRFKGEYV---YRVHPNLRGFTQ 54 MK + I+GASG+TG +L ++ + I + + KG + Y V+ ++ Sbjct: 1 MKNIAIIGASGYTGAQLTALVHAESELSIQGLYVSENSLDKGRALADLYPVYSHIELTLS 60 Query: 55 LKFVEPSIDVALKADVVFLALPHGESVKWVPKLYESGVAVFDLSADFRLKDPNAYVEWYK 114 E ++ +AD V LA H S+ Y G+AVFDLS +R D Y +WY Sbjct: 61 PLTEEAKANIVAEADAVVLATEHSVSLHLAAWFYSQGLAVFDLSGAYRFSDVAQYPKWYG 120 Query: 115 WPQPHPYPDLLQKAVYGQPELHRDELVGAKLVAVPGCMATASILMLAPLAKFGLLSDTPP 174 + H YP++L KAVYG E + ++ K++AVPGC TAS+ L PL LL+ P Sbjct: 121 FE--HEYPEVLAKAVYGLAEWNAKDVAATKMIAVPGCYPTASLTALKPLK--NLLTSAYP 176 Query: 175 VVDAKIGSSGAGAEGSVVDLH-SFRTYVVRPYEPVHHRHIAEIEQELTRLAGRKVRIAFT 233 V++A G +GAG + LH SF + PY + HRH EI +L + + FT Sbjct: 177 VINAVSGVTGAGRK---AQLHTSFCEVSLTPYGVLGHRHQPEIATQLGQ------EVIFT 227 Query: 234 PHAVDIVRGIFTTGHVYVEKLPSETDMWRYYRALYGDSKFIRIVKDRLGISRYPNVKYVL 293 PH + RGI T V ++ + D+ Y ++Y + + + + +++P V V+ Sbjct: 228 PHLGNFKRGILATITVQLKPGTTTADVAAAY-SVYDQAPLVTVKQ-----NQFPKVDDVV 281 Query: 294 GTNIVDLGFELDPRLNRVVTFAAIDNLVRGAAGQAVQAFNI 334 T LG++ D +V +AIDNL++GAA QA+Q I Sbjct: 282 LTPNCHLGWKFDESSGYLVVASAIDNLMKGAASQALQCIKI 322 Lambda K H 0.323 0.141 0.429 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: 272 Number of extensions: 12 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: 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 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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