Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate HSERO_RS04135 HSERO_RS04135 amidohydrolase
Query= curated2:Q836H7 (378 letters) >FitnessBrowser__HerbieS:HSERO_RS04135 Length = 402 Score = 208 bits (529), Expect = 2e-58 Identities = 139/381 (36%), Positives = 199/381 (52%), Gaps = 25/381 (6%) Query: 5 EQEELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQV--RTWQTGILVFIEGKN 62 ++ +L++IRR LH PE+ EEK T +F+ D ++ L V G++ + Sbjct: 13 KEMDLVSIRRHLHAHPELRFEEKRTASFVA---DMLRSYGLTVAENIGGYGVVATLRKGK 69 Query: 63 PQKTIGWRADIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELSQQ-QPDNN 121 + I RAD+D LP+ E+ + S G MHACGHD H T+ LG + LS++ + D Sbjct: 70 STRAIALRADMDALPMSEQNDFSHISTCAGKMHACGHDGHTTMLLGAARRLSREVEFDGT 129 Query: 122 FLFLFQPAEENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEV 181 F+FQPAEE AG LM ED F + D + +H P LP G+ R G L A++ Sbjct: 130 VHFVFQPAEEGGAGARLMIEDGLFERFPADAIFGVHNWPGLPAGSFGLRPGPLMASSNTF 189 Query: 182 NITLKGKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFHAGTACNV 241 + TL G+G H A PH++ D VLAA L Q+IV+RN++P AV++ H GTA NV Sbjct: 190 SATLFGRGAHGAQPHRSIDPVLAAAQLTLAWQSIVTRNINPNHRAVISVTQLHTGTADNV 249 Query: 242 IAEEATLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVNEPACT 301 I E+ATLSGT+R+ AET + + R+ I+E I Q F V H ++ Y VVN P T Sbjct: 250 IPEQATLSGTVRSFDAETLDLIEHRMAAIAEAIGQMFDLRVQFHFERL-YPAVVNHPEAT 308 Query: 302 TNFIEYMSKQATVQFQQ----APVAMTGEDFGYLLSKVPGTMFWLG------------VA 345 ++ M A V +Q A EDF + L PG +LG A Sbjct: 309 QQAMQAM--MAAVGAEQVDGDTEPAFASEDFAFYLQHKPGCYAFLGNGVIADGKQAGSQA 366 Query: 346 SPYSLHSAKFEPNEEALLFGV 366 + LHS ++ N++ + GV Sbjct: 367 TSRELHSPFYDFNDDIIDAGV 387 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: 368 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: 402 Length adjustment: 30 Effective length of query: 348 Effective length of database: 372 Effective search space: 129456 Effective search space used: 129456 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 Jul 25 2024. The underlying query database was built on Jul 25 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