Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate HSERO_RS05715 HSERO_RS05715 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__HerbieS:HSERO_RS05715 Length = 403 Score = 207 bits (526), Expect = 5e-58 Identities = 129/372 (34%), Positives = 194/372 (52%), Gaps = 13/372 (3%) Query: 7 MRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYRA 66 +RR+LH PE F+E +T ++ +++S V+ TGV + G R I RA Sbjct: 21 LRRDLHAHPELRFEEHRTADVVVRELQSLGYT-VTRGLGGTGVVASLAGADPQRGIVLRA 79 Query: 67 DIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVV-FLFQPAE 125 D+D LPI EA S G MHACGHD H + LG R + + P++ V F+FQP E Sbjct: 80 DLDALPIVEANDFAHASCTHGVMHACGHDGHTVMLLGAARLLKQGPMLPGSVHFVFQPGE 139 Query: 126 EGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQSG 185 EG GA MI LFE++ ++G+H P P G RPG + A+ + ITI G+ Sbjct: 140 EGGAGARKMIDDGLFEQFPTEAVFGMHNWPGLPAGQFGLRPGPIMAAGSRLKITITGKGA 199 Query: 186 HAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALLDG 245 HAA PHL +D + ++++Q QTI +R +P++ +VI++ AG +NVI RA L G Sbjct: 200 HAAQPHLGLDPIPLACSMVLQCQTIAARHKDPVDPAVISVCMFHAGDTDNVIPDRAELRG 259 Query: 246 TMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVKMN 305 T+R L+ T +KL++ +R + + ++G K++++F Y +N D ++ Sbjct: 260 TIRTLSSTLQQKLQEDIRRMCHALAEAYGAKVEVEFFQYYPATINTPAETDFCERVIRQT 319 Query: 306 AN----YIECDAAMTGEDFGFMLKEIPGMMFWLG---VNNATSGLHQP--TLNPD--EEA 354 A MT EDFGFML+E PG +G + A+ LH P N D E Sbjct: 320 FGDDRIRTGIPANMTSEDFGFMLEERPGAYVLIGNAPQDRASHSLHHPHYDFNDDIIEAG 379 Query: 355 IPFVINLLDHYF 366 + + + L YF Sbjct: 380 VRYWVALAQGYF 391 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: 465 Number of extensions: 31 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: 403 Length adjustment: 30 Effective length of query: 340 Effective length of database: 373 Effective search space: 126820 Effective search space used: 126820 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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