Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_012967651.1 KVAR_RS08400 amidohydrolase
Query= curated2:Q88V24 (384 letters) >NCBI__GCF_000025465.1:WP_012967651.1 Length = 394 Score = 210 bits (534), Expect = 6e-59 Identities = 122/343 (35%), Positives = 181/343 (52%), Gaps = 11/343 (3%) Query: 14 HLHQIPEIGLQEHETQAYLLSIIGKMPQEWLTIKTIPTLDTAILVKVSGLKHDYRIGYRT 73 HLH+ PE+ E T A + +++ K + + +P L T ++ ++ G+ + R+ Sbjct: 21 HLHRHPELSNDEFNTTASIRAVLEKYQ---IRVIDLP-LKTGLVAEIGGINPGELVVLRS 76 Query: 74 DIDALPVTENTGLPFASTHPGVMHACGHDIHMSVALG--ILSYFAENRPATDMVFMFQPA 131 DIDALP+ E + + + S +PGVMHACGHD H S ALG IL E+ + + +FQ A Sbjct: 77 DIDALPIEEKSAVDYTSQNPGVMHACGHDFHTSAALGAAILLKAQEDSLSGTVRILFQAA 136 Query: 132 EENASGGQRLYESGALDGDWMPDEIFAFHDNPNLPTGAIGCRMGTLFAGTCEIHAHLSGK 191 EE G L +GALD + IF H++P+LP G IG + G L AG +SG Sbjct: 137 EETGHGAPTLISTGALDNAAV---IFGIHNDPSLPVGVIGSKDGALTAGVDRFAIAISGT 193 Query: 192 SGHAAYPHQANDMVVAGAALVSQLQTIVARNVDPIQSGVVTLGHFTAGTIGNVIAGEAQI 251 HAA PH+ ND ++ ++S LQT++ARNV + VV++ +G+ NVI A + Sbjct: 194 GSHAARPHEGNDPIIIAGQVISALQTLIARNVPSAHNAVVSITQVHSGSTWNVIPDSAWL 253 Query: 252 DGTIRALTQEMNMHIQRRVRTITEGIALAYDCNIDLKLNQGGYYPVENNDAITADFIKYM 311 +GT+R Q+ I+RR+R + GIA A+D +I L G P N A DF Sbjct: 254 EGTVRTFNQDTRELIERRLRQVLTGIAAAFDTDISLDWQPGP--PSVVNTAKWVDFALAH 311 Query: 312 QEDDDVNFIETEPAMTGEDFGYLIHQIPGTMFWLGVDSPYSLH 354 E E + GEDF + ++PG +G PY+LH Sbjct: 312 GEGSGFEARRVEASPIGEDFAFYQQKLPGAFIMIGSGGPYALH 354 Lambda K H 0.320 0.136 0.411 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: 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: 384 Length of database: 394 Length adjustment: 30 Effective length of query: 354 Effective length of database: 364 Effective search space: 128856 Effective search space used: 128856 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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