Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate 8500255 DvMF_1012 amidohydrolase (RefSeq)
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__Miya:8500255 Length = 400 Score = 237 bits (604), Expect = 5e-67 Identities = 134/364 (36%), Positives = 199/364 (54%), Gaps = 11/364 (3%) Query: 3 YAIEMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTI 62 + +++RR LH+IPE GF E +T A + +++ + V TGV + T+ Sbjct: 14 HIVDLRRRLHRIPETGFNEVRTAALVAEELAALGLP-VRTGIAGTGVTALLDSGRPGPTV 72 Query: 63 GYRADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDD------ 116 RAD+D LPI EATGLP+ SEHPG MHACGHD+H ++ LG R + L + Sbjct: 73 MLRADMDALPITEATGLPYASEHPGCMHACGHDMHMAMLLGAARVLAGLAEQNPDALRGR 132 Query: 117 VVFLFQPAEEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREV 176 ++FLFQPAEEGPGGA PMI++ + + G HV PE P G + +PG L A+ Sbjct: 133 ILFLFQPAEEGPGGAAPMIEAGVLDDPGVDVCIGAHVWPEIPAGFVGVKPGPLMAAMDRF 192 Query: 177 HITIYGQSGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENV 236 +T+ G+ GHAA PHL +D + ++ LQ +VSR +P+ ++TIG++ AG NV Sbjct: 193 ELTVLGKGGHAANPHLCVDALETATQVVGALQRVVSRMTSPLEPVILTIGELHAGTAYNV 252 Query: 237 IAGRALLDGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVD 296 I G A + GT+RA + EQR+ + G+ A+ G L F + V+ND R Sbjct: 253 IPGEARMAGTVRAFAPEVRNRWEQRINQVAGGVCAAMGATHRLDFQWCHPAVINDPRAAA 312 Query: 297 KF--SSFVKMNANYI-ECDAAMTGEDFGFMLKEIPGMMFWLGVNN-ATSGLHQPTLNPDE 352 + ++ + A+ + E M GEDF L+ +PG F++G + +H P PDE Sbjct: 313 EVRRAALDAVGADRVMEPVPTMGGEDFSMFLQRVPGCFFFVGCGGPGVAPVHNPCFAPDE 372 Query: 353 EAIP 356 +P Sbjct: 373 SCLP 376 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: 406 Number of extensions: 19 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: 400 Length adjustment: 30 Effective length of query: 340 Effective length of database: 370 Effective search space: 125800 Effective search space used: 125800 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