Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate GFF998 PGA1_c10150 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__Phaeo:GFF998 Length = 388 Score = 237 bits (605), Expect = 4e-67 Identities = 141/355 (39%), Positives = 199/355 (56%), Gaps = 7/355 (1%) Query: 8 RRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGL--TGNRTIGYR 65 RR LH+IPE ++ KT AF+ +++RS+ ++ TGV ++G T R IG R Sbjct: 18 RRHLHQIPELLYEVHKTAAFVEEKLRSFGITDITTGIGRTGVVAVIEGKANTSGRVIGLR 77 Query: 66 ADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDD-VVFLFQPA 124 AD+D LPI EATGL + S+ PG MHACGHD H SI LG + + E D VV +FQPA Sbjct: 78 ADMDALPITEATGLDYASQTPGLMHACGHDGHTSILLGTAKYLAETRNFDGKVVLIFQPA 137 Query: 125 EEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQS 184 EEG G + M + +++ E+YGLH AP PVG A RPG L AS+ E I + G Sbjct: 138 EEGGAGGKAMCDDGMMDRWGIQEVYGLHNAPGIPVGEFAIRPGPLLASSDEFEIIVTGVG 197 Query: 185 GHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDA-GIRENVIAGRALL 243 GHAA PH IDT + + +++ L +IVSR+I+P+ V+T+G + NVIA A L Sbjct: 198 GHAANPHEAIDTTLVASQIVVSLHSIVSRNIDPLKHVVLTVGTFETDSTASNVIAHTARL 257 Query: 244 DGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVK 303 GT+R L + E RVR I + +++G + ++ + Y VN + + Sbjct: 258 QGTVRTLETECRGQAEIRVRRIAEDVASAYGARAEVVWTPGYPVTVNTETETGYAVEAAR 317 Query: 304 MNANYI--ECDAAMTGEDFGFMLKEIPGMMFWLGVNNATSGLHQPTLNPDEEAIP 356 A + + D M EDF +ML+E PG +LG N T+ H P + D+EAIP Sbjct: 318 AVAAKVTDDTDPIMPSEDFAYMLEERPGAYIFLG-NGDTAMCHHPAYDFDDEAIP 371 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: 410 Number of extensions: 16 Number of successful extensions: 6 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: 388 Length adjustment: 30 Effective length of query: 340 Effective length of database: 358 Effective search space: 121720 Effective search space used: 121720 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