Align acetylornithine deacetylase (EC 3.5.1.16) (characterized)
to candidate BWI76_RS14620 BWI76_RS14620 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase
Query= ecocyc::ACETYLORNDEACET-MONOMER (383 letters) >FitnessBrowser__Koxy:BWI76_RS14620 Length = 370 Score = 127 bits (318), Expect = 7e-34 Identities = 105/360 (29%), Positives = 155/360 (43%), Gaps = 29/360 (8%) Query: 31 SNADLITLLADWFKDLGFNVEVQPVPGTRNKFNMLASIGQGAGGLLLA--GHTDTVPFDD 88 S AD + ADW GF V + +R+ N++A + G LA GH DTVP + Sbjct: 22 SEADCMRYFADWLNANGFAVSLSSFGESRS--NLIAWLPGATPGKPLAFTGHLDTVPLGN 79 Query: 89 GRWTRDPFTLTEHDGKLYGLGTADMK-GFFAFILDALRDVDVTKLKKPLYILATADEETS 147 RW DPF DG+LYG G++DMK AF + ++ + + +L T EET Sbjct: 80 ARWRYDPFGSQMEDGRLYGRGSSDMKAAIAAFAVACVQQRETILAGRGAVLLITGGEETG 139 Query: 148 MAGARYFAETTAL-RPDCAIIGEPTSLQPVRAHKGHISNAIRIQGQSGHSSDPARGVNAI 206 GAR + L I+GEPT+ PV HKG + +G++ H + P G+NAI Sbjct: 140 CDGARALIASAPLPEVGALIVGEPTANYPVIGHKGALWLRCETRGKTAHGAMPELGINAI 199 Query: 207 ELMHDAIGHILQLRDNLKERYHYEAFTVPYPTLNLGHIHGGDASNRICACCELHMDIRPL 266 L DA+ I + PT+N+G I GG N + +DIR Sbjct: 200 YLAADALAKIQHFSPGAPHP------LMKQPTVNVGRIEGGLNINSVPDRTRFDVDIRSA 253 Query: 267 PGMTLNELNGLLNDALAPVSERWPGRLTVDELHPPIPGYECPPNHQLVEVVEKLL----- 321 P + + L L +TV L +P +H ++ V + Sbjct: 254 PDLQHATIRQRLTTLLGE-------SVTVSTL-VDLPAVLSEQDHAWIKQVYQRCQPLHD 305 Query: 322 -GAKTEVVNYCTEAPFIQTLC---PTLVLGPGSINQAHQPDEYLETRFIKPTRELITQVI 377 + VV Y T+A + P ++LGPG + AHQ DEY ++ +L +I Sbjct: 306 RPLEPRVVPYFTDASLLLPALGNPPCIILGPGEPSMAHQTDEYCLLSRLEEAEQLYGNLI 365 Lambda K H 0.320 0.139 0.430 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: 375 Number of extensions: 15 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: 383 Length of database: 370 Length adjustment: 30 Effective length of query: 353 Effective length of database: 340 Effective search space: 120020 Effective search space used: 120020 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 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