Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BWI76_RS10270 BWI76_RS10270 acetylornithine deacetylase
Query= BRENDA::Q92Y75 (374 letters) >FitnessBrowser__Koxy:BWI76_RS10270 Length = 391 Score = 142 bits (358), Expect = 2e-38 Identities = 104/330 (31%), Positives = 152/330 (46%), Gaps = 32/330 (9%) Query: 49 RSNIFATIGPKEARGYIISGHMDVVPAAETGWTSDPFRLRVEADRLYGRGTTDMKGFLAA 108 R+N+ A + + + + H+D VPA +GWTSDPF L RLYGRG D KG L A Sbjct: 57 RTNVIAVLHNGPGQCFAFNTHIDTVPAG-SGWTSDPFTLAERGGRLYGRGACDAKGPLVA 115 Query: 109 VLAAVPKLAAMPLR--RPLHLALSYDEEAGCRGVPHMIARLPELCRQPLGAIIGEPTGMR 166 ++ A+ LAA R L + DEE G + P A+IGEPT Sbjct: 116 MVEALRLLAATRQRWSGTLMGVFTADEEVASEGAKFYVRDNPPAID---FAVIGEPTSNA 172 Query: 167 AIRAHKGKAAARLTVRGRSGHSSRPDQGLNAIHGVAGVL--------TQAVAEADRLVGG 218 AHKG R+ V+G + HS P+ G+NAI+ A +L Q LVG Sbjct: 173 TFSAHKGSLRPRVRVKGVTAHSGTPELGVNAIYQSARLLGLIEEAHHQQVRCRCHDLVGN 232 Query: 219 PFEHVFEPPYSSLQIGTVKGGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTAE-AL 277 +SL + + GG A N++PDSCE+ + R + G D A + A +++ + A Sbjct: 233 ----------ASLTVTRIHGGHADNVVPDSCELLLDRRMVPGEDEAVVKAELQQLLDHAH 282 Query: 278 TTLGFEVE---WQELSAYPALSLEPDAPLAALLEELTGREALPAVSYGTEAGL----FQR 330 G E E WQ + + +A + L +G + G F+ Sbjct: 283 AHAGVEAEIIAWQPTTGGATQTDSSEAIVEQSLAACRRHGQSEPGPFGFQGGCDLVHFRS 342 Query: 331 AGIDAIICGPGDIGRAHKPDEYILIDELMA 360 G ++ GPG + AHKPDE++ +DE +A Sbjct: 343 LGAKGVVIGPGSLAVAHKPDEFVPVDEFIA 372 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: 400 Number of extensions: 18 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: 391 Length adjustment: 30 Effective length of query: 344 Effective length of database: 361 Effective search space: 124184 Effective search space used: 124184 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