Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate SMc02256 SMc02256 hippurate hydrolase
Query= curated2:Q836H7 (378 letters) >FitnessBrowser__Smeli:SMc02256 Length = 393 Score = 236 bits (602), Expect = 8e-67 Identities = 138/369 (37%), Positives = 205/369 (55%), Gaps = 18/369 (4%) Query: 8 ELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQVRTWQTGILVFIEGKNPQKTI 67 EL+AIRR LH PE+GLEE T AF+ ++++ + +TG++ + ++I Sbjct: 17 ELVAIRRDLHAHPELGLEETRTSAFIARHLEELGYE-VATGIAKTGVVGTLRNGTGSRSI 75 Query: 68 GWRADIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELSQQQP-DNNFLFLF 126 G RADID LPIQEE A+ S +PG MHACGHD H + LG + L++++ D +F Sbjct: 76 GIRADIDALPIQEETGVAYASTKPGLMHACGHDGHTAMLLGAARALAERRNFDGTIHLIF 135 Query: 127 QPAEENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEVNITLK 186 QPAEEN G +M ++ F + D +ALH P+LP G + R G + AA E IT+ Sbjct: 136 QPAEENAGGAKIMVDEGLFDRFPCDAVFALHNEPNLPFGQFALREGPIMAAVDEARITVH 195 Query: 187 GKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFHAGTACNVIAEEA 246 G+GGH A P D ++ +++ QTIV+RN+ P+ +VVT G FHAG+A N+I E A Sbjct: 196 GRGGHGAEPQATADPIVCGASIVMALQTIVARNIHPMDPSVVTVGAFHAGSASNIIPERA 255 Query: 247 TLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVNEPACTTNFIE 306 + IR+ ++ +RRIR I+E A SF TV ++ Y +N A T+F+ Sbjct: 256 EIVVGIRSFDPAVRDELERRIRMIAEAQASSFGMRATVDY-ERSYDATINHKA-ETDFL- 312 Query: 307 YMSKQATVQFQQAPVA-------MTGEDFGYLLSKVPGTMFWLG---VASPYSLHSAKFE 356 ++A ++F A M EDF Y+L + PG+ F+LG SLH ++ Sbjct: 313 ---REAAIRFAGADKVVDLARPFMGSEDFAYMLKERPGSYFFLGSRVTGEEKSLHHPGYD 369 Query: 357 PNEEALLFG 365 N++ L G Sbjct: 370 FNDDLLPIG 378 Lambda K H 0.319 0.135 0.398 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: 370 Number of extensions: 17 Number of successful extensions: 5 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: 393 Length adjustment: 30 Effective length of query: 348 Effective length of database: 363 Effective search space: 126324 Effective search space used: 126324 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 (21.8 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