Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate N515DRAFT_3530 N515DRAFT_3530 carboxypeptidase Ss1. Metallo peptidase. MEROPS family M20D
Query= curated2:Q836H7 (378 letters) >FitnessBrowser__Dyella79:N515DRAFT_3530 Length = 446 Score = 192 bits (487), Expect = 2e-53 Identities = 127/386 (32%), Positives = 193/386 (50%), Gaps = 30/386 (7%) Query: 8 ELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQVRTW--QTGILVFIEGKNPQK 65 ++ A RR++HQ PE+ E T A + ++ K+ L+VRT TG++ ++G P Sbjct: 36 QVTAWRREIHQHPELSNRETRTAALVAAQLKKLG---LEVRTGIAHTGVVGILKGGQPGP 92 Query: 66 TIGWRADIDGLPIQEEVVSAFQSKRPG--------FMHACGHDFH--MTIGLGVLKELSQ 115 + RAD+D LP+ EEV F SK G MHACGHD H M +GL + + Sbjct: 93 KLAIRADMDALPVTEEVDLPFASKAQGEYRGKSTGVMHACGHDTHTAMLLGLATVLAGMR 152 Query: 116 QQPDNNFLFLFQPAEEN-----EAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTR 170 Q+ +FLFQPAEE + G LM ++ F ++ PD +A+HV L GT++ R Sbjct: 153 QELSGEVMFLFQPAEEGAPAGEQGGAPLMLQEGVFRDFAPDAMFAMHVISTLNAGTVAVR 212 Query: 171 VGTLFAATCEVNITLKGKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVD-PVVGAVVT 229 G + + + G+ H A P D ++ A ++ QAQTIVSR +D + AV++ Sbjct: 213 PGPALSGADGFKLVVHGRQTHGAMPWHGVDPIVTAAQIVTQAQTIVSRRLDIGTLPAVLS 272 Query: 230 FGTFHAGTACNVIAEEATLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQK 289 FG G N++ ++ L GT+RT +Q +R+I+E +A + V + Sbjct: 273 FGIVEGGARHNIVPDKVELQGTLRTFDPAMRQQAIDGLRDIAEHVAAANGATVEAQIPMD 332 Query: 290 GYLPV-VNEPACTTNFIEYMSKQ-ATVQFQQAPVAMTGEDFGYLLSKVPGTMFWLGV--- 344 G +PV VNE T ++K Q +AP AM EDF Y VP F++G Sbjct: 333 GSVPVTVNEATLTARVRASLAKAIGGEQVLEAPPAMPSEDFAYFARAVPSVYFFVGATPA 392 Query: 345 ----ASPYSLHSAKFEPNEEALLFGV 366 A + HS +F +E+AL G+ Sbjct: 393 GQDPAKAPANHSPRFFVDEDALRVGM 418 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: 408 Number of extensions: 26 Number of successful extensions: 7 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: 446 Length adjustment: 31 Effective length of query: 347 Effective length of database: 415 Effective search space: 144005 Effective search space used: 144005 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