Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate 5210245 Shew_2688 amidohydrolase (RefSeq)
Query= SwissProt::O34916 (374 letters) >FitnessBrowser__PV4:5210245 Length = 445 Score = 188 bits (478), Expect = 2e-52 Identities = 147/402 (36%), Positives = 200/402 (49%), Gaps = 48/402 (11%) Query: 6 LIAIRRDLHRIPELGFQEFKTQQYLLNVLEQYPQDRIEIEKWRTG---LFVKVNGTAPEK 62 L ++ +LH+ PEL + E QQ + ++ IE+ + G + + NG P Sbjct: 42 LSSLYLELHQAPELSYHE---QQSGERMAAEFEALGIEVTRDFGGHGVVGIYRNGKGPTV 98 Query: 63 MLAYRADIDALSIEEQTGLPFASE---------HHGNMHACGHDLHMTIALGIIDHFVHH 113 ML RAD DAL I E+TG +AS+ G MHACGHD+HMT +G + Sbjct: 99 ML--RADTDALPIVEETGKAYASKVTTLDAQGNQVGVMHACGHDVHMTNLVGTAQQLIQQ 156 Query: 114 PVKHD--LLFLFQPAEEGPGGAEPMLESDVLKKWQ-PDFITALHIAPELPVGTIATKSGL 170 K L+ + QPAEE GGA+ ML+ + ++ PD I LH++ +P G +A G Sbjct: 157 KDKWQGTLMLVAQPAEEVGGGAKAMLKQGLFSQFPTPDHILGLHVSASVPAGKVAIAPGY 216 Query: 171 LFANTSELVIDLEGKGGHAAYPHLAEDMVVAASTLVTQLQTIISRNTDPLDSAVITVGTI 230 AN + I ++G+GGH AYPH D VV A+ +V LQTI+SR PL VITVG+I Sbjct: 217 ALANVDSVDISVKGRGGHGAYPHTTVDPVVLAARIVLALQTIVSREVSPLSPNVITVGSI 276 Query: 231 TGGSAQNIIAETAHLEGTIRTLSEESMKQVKERIEDVVKGIEIGFRCKGKVTYPSVY-HQ 289 GGS NII L+ T+R+ + +Q IE + KGI I + +P VY HQ Sbjct: 277 HGGSKHNIIGNEVKLQLTLRSYDPKVREQQIAAIERLTKGIAISAGL-SEAEWPDVYVHQ 335 Query: 290 ------VYNTSGLTEEFMSFVAEHQLA--TVIEAKEAMTGEDFG-YML--KKYPGFMFWL 338 YN T + + +A+ QL V+EA M GEDFG Y L K P +FWL Sbjct: 336 EESIPSTYNDPEQTAKVRASIAK-QLGDDNVLEASPVMAGEDFGLYGLTPAKRPITLFWL 394 Query: 339 GA-------------DSEHGLHHAKLNPD-ENAIETAVHVMT 366 GA S LH +K PD IE V M+ Sbjct: 395 GAVPAVDYAASQASGASLPSLHSSKFAPDYPVTIEAGVQAMS 436 Lambda K H 0.319 0.135 0.397 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: 415 Number of extensions: 21 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: 374 Length of database: 445 Length adjustment: 31 Effective length of query: 343 Effective length of database: 414 Effective search space: 142002 Effective search space used: 142002 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 (21.7 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