Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate GFF1548 Psest_1585 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__psRCH2:GFF1548 Length = 423 Score = 196 bits (499), Expect = 7e-55 Identities = 117/340 (34%), Positives = 182/340 (53%), Gaps = 13/340 (3%) Query: 8 RRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYRAD 67 R +H+ PE GF EF T + D + ++ + V TGV ++ G +G RAD Sbjct: 39 RHAIHQNPELGFAEFATSRLVADCLETWGYE-VHTGIATTGVVGILRWGDGQPRLGLRAD 97 Query: 68 IDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALG------LLRRIVELPVMDDVVFLF 121 +D LP++E TGLP+ S P MHACGHD H SI LG L++R L + +F Sbjct: 98 MDALPVQELTGLPWASRTPDQMHACGHDGHTSILLGAAQSFALMQREGLLGASGTLTLIF 157 Query: 122 QPAEE--GPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHIT 179 QPAEE G GGA M+ L E++ ++ +H P P G R G AS+ V I Sbjct: 158 QPAEELGGSGGARRMLDEGLLERFPCDAVFAMHNYPGIPTGHFRFREGPFMASSDRVVIR 217 Query: 180 IYGQSGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAG 239 G+ GH A PH+ ID ++ AA ++ LQ+IV R+++P++ +VI++G++ AG NVI Sbjct: 218 FNGKGGHGALPHMAIDPMLPAAATVLALQSIVGRNVDPVDAAVISVGRIAAGNTYNVIPE 277 Query: 240 RALLDGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQR----VV 295 A ++ ++RAL + LE R+R ++ G A+FGV ++ + Y ++N R V Sbjct: 278 TAEMELSVRALRPDVRDLLEMRIRALVEGQAAAFGVTCEVLYERGYPVLINSARETCLAV 337 Query: 296 DKFSSFVKMNANYIECDAAMTGEDFGFMLKEIPGMMFWLG 335 + + V ++ EDF F+L+++PG +G Sbjct: 338 EAARALVGDERVEVDGAPISGSEDFAFILQQVPGCYLLIG 377 Lambda K H 0.323 0.140 0.417 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: 412 Number of extensions: 24 Number of successful extensions: 4 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: 370 Length of database: 423 Length adjustment: 31 Effective length of query: 339 Effective length of database: 392 Effective search space: 132888 Effective search space used: 132888 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 (21.9 bits) S2: 50 (23.9 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