Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate HSERO_RS15925 HSERO_RS15925 amidohydrolase
Query= curated2:B1MZM9 (387 letters) >FitnessBrowser__HerbieS:HSERO_RS15925 Length = 399 Score = 201 bits (512), Expect = 2e-56 Identities = 131/366 (35%), Positives = 193/366 (52%), Gaps = 12/366 (3%) Query: 7 ETLQTFRRELHQIPETALEEFKTHDYLLTKLKSWQQDYMTIKTVEALPTAILVYFQGTNP 66 + + RR LHQ PE + EE T + +L+ W Y + + ++ + + Sbjct: 20 DEITAIRRHLHQHPELSFEEVDTAALVAQRLEQW--GYAVTRHIGG--NGLVATLRVGSS 75 Query: 67 VRTIGYRTDIDALPIQEATGLDFASQHPGKMHACGHDVHMTMALGLAQYFSQHQPKDNLI 126 R+IG R D+DALPIQE TGLD+AS PG MHACGHD H M LG A++ ++ + D + Sbjct: 76 ARSIGLRADMDALPIQEETGLDWASVKPGAMHACGHDGHTAMLLGAARHLARTRRFDGTL 135 Query: 127 -IFFQPAEEA--ESGGKVAYDMGLFEGKWRPDEFYGIHDQPNLPAGTLSTLAGTLFAGTA 183 + FQPAEEA +SG + GLFE ++ + +GIH+ P + AGT +G A Sbjct: 136 NLIFQPAEEAGFDSGAQKMLADGLFE-RFPCEAVFGIHNHPGVEAGTFMFRSGPFMAACD 194 Query: 184 ELKVDVIGTGGHAAYPHLAKDPIVIAAELIIQLQTVVSRSVDPIAGGVVSVGVINGGFAN 243 +K+ + G G HAA PHL+ DP+V+AA L++ LQTVVSR++DP+ VV+VG ++ G A+ Sbjct: 195 TVKIRITGRGSHAARPHLSVDPVVVAASLVMALQTVVSRNIDPMDSAVVTVGSLHAGKAS 254 Query: 244 NVIPDQVHFEGTVRSMTRTGLETMLTRIRKIAEGLAIANEVTINVSLESGSYLPVEND-- 301 NVIP+ E +VRS E + RIR + A + + G + V +D Sbjct: 255 NVIPEFATMELSVRSFKPEVRELLEQRIRALVSTHAQSYGAQAEIDYLRGYPVLVNSDAE 314 Query: 302 PILATQVINFMQKQSDINFELAQPAMTGEDFGYLLQHIPGVMLWLGVNDSHP-LHSAQLT 360 A V + + P EDF Y L+ PG L +G P LH+A Sbjct: 315 TDFARSVAEELVGPEKVIAPFG-PIAGSEDFAYFLRQRPGCFLRVGNGQGKPMLHNAGYD 373 Query: 361 IDESAI 366 +++ I Sbjct: 374 FNDANI 379 Lambda K H 0.319 0.135 0.398 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: 413 Number of extensions: 21 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: 387 Length of database: 399 Length adjustment: 31 Effective length of query: 356 Effective length of database: 368 Effective search space: 131008 Effective search space used: 131008 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: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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