Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate 3607880 Dshi_1288 amidohydrolase (RefSeq)
Query= curated2:Q836H7 (378 letters) >FitnessBrowser__Dino:3607880 Length = 388 Score = 220 bits (560), Expect = 6e-62 Identities = 132/362 (36%), Positives = 195/362 (53%), Gaps = 6/362 (1%) Query: 8 ELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQVRTWQTGILVFIEGKNPQ--K 65 E+ A R+ H PE+ + T + ++ + +TG++ I+G+ + Sbjct: 13 EITAWRQDFHAHPELLFDTHRTAGIVAEKLHAFGCDEVVEGLGRTGVVGVIKGRQTGSGR 72 Query: 66 TIGWRADIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELSQQQP-DNNFLF 124 IG RAD+D LPI EE + SK PG MHACGHD H + LG K L++ + D + Sbjct: 73 VIGLRADMDALPIPEETGVPYASKVPGKMHACGHDGHTAMLLGAAKYLAETRNFDGTCVV 132 Query: 125 LFQPAEENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEVNIT 184 +FQPAEE GG M ED + +E Y +H P +P G+ + R G FAAT + +I Sbjct: 133 IFQPAEEGGGGGREMVEDGLMERFGIEEIYGMHNWPGVPTGSFAIRPGPFFAATDQFDIV 192 Query: 185 LKGKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFH-AGTACNVIA 243 +KGKGGHAA P + D +AA+ ++ QTI SRN DP+ VV+ +F + TA NVI Sbjct: 193 IKGKGGHAAKPQETVDPTVAASQVVLALQTIASRNADPIRQIVVSVTSFQTSSTAFNVIP 252 Query: 244 EEATLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVNEPACTTN 303 ++ L GT+RTL + +RR+ EI+ GIAQ+ E V KGY PV+ T Sbjct: 253 QQVALKGTVRTLDEDVRAMAERRLTEIATGIAQAMGAEAEVQY-HKGY-PVMVNSGPETE 310 Query: 304 FIEYMSKQATVQFQQAPVAMTGEDFGYLLSKVPGTMFWLGVASPYSLHSAKFEPNEEALL 363 F ++++ + +AP+ M GEDF YLL+ PG +G ++H + N+EA+ Sbjct: 311 FAADVARKVSGDCAEAPLVMGGEDFAYLLNARPGAYILVGNGDTAAVHHPAYNFNDEAIP 370 Query: 364 FG 365 G Sbjct: 371 AG 372 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: 364 Number of extensions: 16 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: 378 Length of database: 388 Length adjustment: 30 Effective length of query: 348 Effective length of database: 358 Effective search space: 124584 Effective search space used: 124584 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