Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate CCNA_02540 CCNA_02540 N-acyl-L-amino acid amidohydrolase
Query= curated2:B7GIC0 (378 letters) >FitnessBrowser__Caulo:CCNA_02540 Length = 432 Score = 174 bits (442), Expect = 3e-48 Identities = 120/347 (34%), Positives = 176/347 (50%), Gaps = 19/347 (5%) Query: 6 RRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTWRTGILVRVHGTAPTKTIGYRAD 65 RRD+H+ PELG QE +T I L L E ++ +TG++ + G P K + RAD Sbjct: 44 RRDIHENPELGNQEVRTAALIAKELKALGIE-VREGVGKTGVVGVLKGGKPGKVVALRAD 102 Query: 66 MDGLPIDEQTDVPFRS----THEGR----MHACGHDMHMAIALGVLTHV--VHHPIRDDM 115 MD LP++E+T +PF S T EGR MHACGHD H+A+ LG T + + I+ + Sbjct: 103 MDALPVEEKTGLPFASKVKATWEGRTVPVMHACGHDTHVAMLLGAATVLAGMKQDIQGTV 162 Query: 116 LFIFQPAEEGP-----GGALPMLESDEMKQWMPDMILALHIAPAYPVGTIATKEGLLFAN 170 +FIFQPAEEGP GGA M+ + D + +HI P P EG +A+ Sbjct: 163 VFIFQPAEEGPPAGEEGGAKLMIRDGALDNPKVDAVFGVHIGPGDPHELNYRPEGF-YAS 221 Query: 171 TSELFIDLIGKGGHAAFPHETKDMVVAASSLIMQLQTIVSRNVNP-LDSAVITIGKLTSG 229 + + I + G+ H A P DM A+ +I I +R V+ + +V+TI + G Sbjct: 222 SDRITITVKGRQTHGARPWAGIDMASVAADIIQATNQIAARQVDVGVSPSVLTIATINMG 281 Query: 230 TVQNVIAERARLEGTIRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDYGSMYYQVYND 289 QN+I E ++EGT+RT S E E + R++ V I Y +A + + Y YND Sbjct: 282 FRQNIIPEDLKMEGTMRTFSKERREDLIARMQKSVTAIGDRYGAKAEVAFTQPYPVTYND 341 Query: 290 ETLTNEFMQFVEKETDVHLVRCQEAMTG-EDFGYMLARIPGFMFWLG 335 L+ +EK + + +TG EDF ++PG LG Sbjct: 342 PALSKWVKGTLEKASPGKVDDNAALVTGAEDFSMYAEKVPGVFIQLG 388 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: 425 Number of extensions: 23 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: 432 Length adjustment: 31 Effective length of query: 347 Effective length of database: 401 Effective search space: 139147 Effective search space used: 139147 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