Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate BPHYT_RS27410 BPHYT_RS27410 amidohydrolase
Query= curated2:Q836H7 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS27410 Length = 396 Score = 196 bits (499), Expect = 7e-55 Identities = 128/365 (35%), Positives = 184/365 (50%), Gaps = 13/365 (3%) Query: 12 IRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQVRTWQTGILVFIEGKNPQKTIGWRA 71 +RR LH PE+ EE T + E++++ + TG++ + G NP I RA Sbjct: 21 LRRDLHAHPELRFEEHRTADVVARELEELGYTVSR-GLGGTGVVASLPGANPDWGIVLRA 79 Query: 72 DIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELS-QQQPDNNFLFLFQPAE 130 D+D LPI E S G MHACGHD H + LG + L Q + F+FQP E Sbjct: 80 DMDALPIHEANDFTHASCTHGIMHACGHDGHTVMLLGAARILKGMPQLPGSVHFVFQPGE 139 Query: 131 ENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEVNITLKGKGG 190 E AG M ++ F + + + +H P LP G RVG + AA IT+ GKG Sbjct: 140 EGGAGARKMIDEGLFEHYPTEAVFGMHNWPGLPGGHFGLRVGPIMAAGSRFKITVTGKGA 199 Query: 191 HAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFHAGTACNVIAEEATLSG 250 HAA PH D + A +++ QTI +R+ DPV AV++ HAG NVI + A L G Sbjct: 200 HAAQPHLGLDPIPLACSMVLHCQTIAARHKDPVDPAVISVCMIHAGDTDNVIPDSAELRG 259 Query: 251 TIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVNEPACTTNFIEYMSK 310 TIRTL++E ++ QR I+ + EG+A + +V V Q Y P T E + + Sbjct: 260 TIRTLSSELQQKLQRDIQLMCEGLAAAHGAQVEVTFFQ--YYPATINTRAETQLCEAVIR 317 Query: 311 QA---TVQFQQAPVAMTGEDFGYLLSKVPGTMFWL-----GVASPYSLHSAKFEPNEEAL 362 + P MT EDFG++L + PGT + G A+P LH+ K++ N+E + Sbjct: 318 ETFGDERTHADVPANMTSEDFGFMLEERPGTYVLIGNAHAGTAAP-GLHNPKYDFNDEII 376 Query: 363 LFGVE 367 GV+ Sbjct: 377 PAGVQ 381 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: 447 Number of extensions: 21 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: 396 Length adjustment: 30 Effective length of query: 348 Effective length of database: 366 Effective search space: 127368 Effective search space used: 127368 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