Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Echvi_1427 Echvi_1427 amidohydrolase
Query= curated2:B7HMV1 (376 letters) >FitnessBrowser__Cola:Echvi_1427 Length = 397 Score = 202 bits (514), Expect = 1e-56 Identities = 120/367 (32%), Positives = 196/367 (53%), Gaps = 11/367 (2%) Query: 3 VSKFVQIRRDLHKIPEIGFKEWKTQRYILDYIGTLSNEHVEVKVWRTGVIVKVKGKNP-E 61 +++ + IRR +H PE+ F+E +T ++ ++ + +++ K TG++ ++GKNP + Sbjct: 14 LNQTIAIRRHIHAHPELSFEEHQTCAFVEKHLQEIGITNIQRKA-NTGLVALIEGKNPSK 72 Query: 62 KVIGYRADIDGLPITEETGYEFASVHEGMMHACGHDLHTT--IGLGLLTAAVTERIDDDL 119 KVI RAD+D LPI E+ + S EG+MHACGHD+HT+ +G + AV ++ + + Sbjct: 73 KVIALRADMDALPIVEQNDVPYKSNKEGVMHACGHDVHTSSLLGAASILHAVKDQFEGTV 132 Query: 120 VFLFQPAEEG-PGGALPMLESEELKEWKPNIILGLHIAPEYPVGTIATKEGLLFANTSEL 178 +FQP EE PGGA M++ + L+ +P+ I+G H+ P G + ++G+ A+ EL Sbjct: 133 KLIFQPGEEKIPGGASLMIKDKALENPRPSGIVGQHVMPLIDAGKVGFRKGMYMASADEL 192 Query: 179 YVDLKGKGGHAAYPHTANDMIVAASHLVTQLQSVISRNVNPLDSAVITIGKITGGTVQNI 238 Y+ + GKGGH A P T D ++ ASH++ LQ VISRN +P +V++ G+I N+ Sbjct: 193 YLKVIGKGGHGAMPETLVDPVLIASHIIVALQQVISRNASPKVPSVLSFGRIEALGATNV 252 Query: 239 IAEKSRLEGTIRTLSVESMSRVKSRIEAIVAGIEASFQCEAIIDYGAMYHQVYNHEALT- 297 I + ++GT RTL + ++ I GI + Y + N LT Sbjct: 253 IPNEVNIQGTFRTLDETWRAEAHQKMVKIAEGIAEGMGGSVDFEVRKGYPFLQNAPELTD 312 Query: 298 REFMQFVSEQTDMKVITCTEAMTGEDFGYMLQEIPGFMFWLGVNSE-----YGLHHAKLK 352 R + + + V M EDF Y QE+ G + LG+ +E G+H Sbjct: 313 RAYKAAQAYLGEENVEDLDIWMAAEDFSYYTQEMDGCFYRLGIRNEEKGITSGVHTPTFD 372 Query: 353 PDEEAIE 359 DE A+E Sbjct: 373 IDESALE 379 Lambda K H 0.319 0.136 0.400 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: 372 Number of extensions: 22 Number of successful extensions: 6 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: 376 Length of database: 397 Length adjustment: 30 Effective length of query: 346 Effective length of database: 367 Effective search space: 126982 Effective search space used: 126982 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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