Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate WP_012631353.1 MNOD_RS40255 peptidase M20
Query= BRENDA::Q92Y75 (374 letters) >NCBI__GCF_000022085.1:WP_012631353.1 Length = 373 Score = 130 bits (327), Expect = 6e-35 Identities = 103/315 (32%), Positives = 151/315 (47%), Gaps = 26/315 (8%) Query: 65 IISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAAVLAAVPKLA--AMPLR 122 + +GH+D VP W+ DP R + RLYGRG +DMK +AA +AAV +A A L Sbjct: 68 VFTGHLDTVPLGSAPWSFDP-RGEIRDGRLYGRGASDMKAGVAAFVAAVLDVAHSAAVLT 126 Query: 123 RPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMRAIRAHKGKAAARLTVR 182 R + L L+ EE GC G + R + + G ++ EPT R AHKG R Sbjct: 127 RGVTLVLTAGEETGCLGAADLARR--GVLGEASGLVVAEPTSNRLALAHKGALHLRARTH 184 Query: 183 GRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL-VGGPFEHVFEPPYSSLQIGTVKGGQA 241 G + H S P+ G NA+ T+AV G P + P +L + ++ GG+A Sbjct: 185 GATAHGSMPELGDNAVLKA----TRAVEALRNFEFGVPTHPLLGSP--TLAVTSLHGGEA 238 Query: 242 VNIIPDSCEVEFEARAISGVDPAELLAPVRKTAEALTTLGFEVEWQ-ELSAYPALSLEPD 300 VN+IPDSC + + R + G D A LA ++ LG +V + L+ PA+ EP Sbjct: 239 VNVIPDSCTLTLDLRTLPGQDHARTLAMLQ------DQLGPDVVFDPPLADLPAVGTEPS 292 Query: 301 ---APLAALLEELTGREALPAVS--YGTEAGLFQRA--GIDAIICGPGDIGRAHKPDEYI 353 A AA +E A+ Y T+ + Q A G +I GPG+ G+AH+ +E+ Sbjct: 293 DGFAMAAARSVRKVTQEVGEAIGMPYFTDGSVLQGAFGGCPTVILGPGEPGQAHQTNEWC 352 Query: 354 LIDELMACRAMVEAL 368 + + AL Sbjct: 353 ATSAITIAHRIYGAL 367 Lambda K H 0.319 0.137 0.410 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: 365 Number of extensions: 18 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: 374 Length of database: 373 Length adjustment: 30 Effective length of query: 344 Effective length of database: 343 Effective search space: 117992 Effective search space used: 117992 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 10 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