Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Ac3H11_1969 N-acetyl-L,L-diaminopimelate deacetylase (EC 3.5.1.47)
Query= curated2:B7GIC0 (378 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1969 Length = 447 Score = 188 bits (477), Expect = 3e-52 Identities = 127/376 (33%), Positives = 187/376 (49%), Gaps = 28/376 (7%) Query: 3 VNIRRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTWRTGILVRVHGTAPTKTIGY 62 VN RRD+H PEL QE +T + + ++L L E +Q TG++ + G P K + Sbjct: 50 VNWRRDIHAYPELSGQEVRTAKLVAEHLKKLGME-VQTGVGGTGVVGTLKGGLPGKVVAL 108 Query: 63 RADMDGLPIDEQTDVPFRS----THEGR----MHACGHDMHMAIALGVLTHV--VHHPIR 112 RADMD LP+ E T +PF S T+ G+ MHACGHD H A+ +G + + + Sbjct: 109 RADMDALPVLENTGLPFASKAKATYLGKEVPVMHACGHDAHTAMLMGAAEVLAGMKAQLP 168 Query: 113 DDMLFIFQPAEEGPG------------GALPMLESDEMKQWMPDMILALHIAPAYPVGTI 160 + FIFQPAEEG GA M+E+ +K I LHI P G + Sbjct: 169 GTVKFIFQPAEEGAPVEADANGKVPSFGAKAMIEAGALKD--VQAIYGLHITSNLPGGVV 226 Query: 161 ATKEGLLFANTSELFIDLIGKGGHAAFPHETKDMVVAASSLIMQLQTIVSRNVN-PLDSA 219 + G L A + + I + G+GGH + P T D +VAAS ++M LQT+VSR +N + A Sbjct: 227 GYRSGPLMAGSDNITIHVEGRGGHGSSPWATIDPIVAASQVVMGLQTVVSRQLNISQEPA 286 Query: 220 VITIGKLTSGTVQNVIAERARLEGTIRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDY 279 V+TIG++ GT N+I ++ + GT+RT + ++ RI I A +A + + Sbjct: 287 VVTIGQIQGGTRYNIIPDKVEMMGTLRTFDEDMRQEALKRITTTAESIAAASGAKASVRF 346 Query: 280 GSMYYQV-YNDETLTNEFMQFVEKETDVHLVRCQEAMTGEDFGYMLARIPGFMFWLGVQS 338 G + Y V N LT + + + + EDF +PGF ++LG Sbjct: 347 GPVAYPVTTNPAQLTQASLPALNLAMGGKTMVIPKVAGSEDFSEFQKVVPGFFYFLGA-P 405 Query: 339 PFGLHHAKLNPNEEAI 354 P G AK PN A+ Sbjct: 406 PKGKEFAKAPPNHSAL 421 Lambda K H 0.322 0.137 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: 372 Number of extensions: 17 Number of successful extensions: 7 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: 378 Length of database: 447 Length adjustment: 31 Effective length of query: 347 Effective length of database: 416 Effective search space: 144352 Effective search space used: 144352 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