Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate GFF3844 HP15_3785 ornithine decarboxylase
Query= curated2:O50657 (393 letters) >FitnessBrowser__Marino:GFF3844 Length = 391 Score = 181 bits (460), Expect = 2e-50 Identities = 120/367 (32%), Positives = 184/367 (50%), Gaps = 14/367 (3%) Query: 9 KEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSH 68 K +K A TPF+V ++ Y + P A V+YA+KANP P+IL++L G+ Sbjct: 19 KRIKDFADGKETPFVVIDTATIDRQYDELVEGFPYAKVYYAVKANPAPQILTMLRDKGAS 78 Query: 69 FDVASAGEMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAV 128 FD+AS E++ + LGV G ++ Y N +K A+ ++ + VR F D +++ +AKA Sbjct: 79 FDIASVYELDKVMALGVTGERISYGNTIKKAKDIRTFYEKGVRMFATDSEADLRNIAKAA 138 Query: 129 PGADVLVRIAVRNN-KALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLST 187 PG+ V VRI A L+ KFG + A+DLL A+D GL G+ FHVGSQ Sbjct: 139 PGSKVYVRILTEGTLTADWPLSRKFGCQTDMAMDLLILARDLGLVPYGVSFHVGSQQREI 198 Query: 188 AAYEEALLVARRLFDE-AEEMGMHLTDLDIGGGFP---VPDAKGLNVDLAAMMEAINKQI 243 A++ AL + +F+ EE G+ L +++GGGFP + L V + +++ Sbjct: 199 GAWDAALNKVKVIFERLKEEDGIELKMINMGGGFPANYITRTNELKVYAEEIARFLHEDF 258 Query: 244 DRLFPDTAVWTEPGRYMCGTAVNLVTSV--IGTKTR-GEQPWYILDEGIYGCFSGIMYDH 300 P+ + EPGR + A LV+ V I K+R W D G + + + Sbjct: 259 GAELPEIII--EPGRSLISNAGVLVSEVVLISRKSRTALHRWVFTDVGKFSGLIETLDEA 316 Query: 301 WTYPLHCFGKGNKKPSTFGGPSCDGIDVLYRDFMAP---ELKIGDKVLVTEMGSYTSV-S 356 +P+ G + GP+CD D++Y P L IGD++ G+YT+ S Sbjct: 317 IKFPIWTEKVGEGEDCVIAGPTCDSADIMYEHHKYPLPLNLAIGDRMYWLSTGAYTTTYS 376 Query: 357 ATRFNGF 363 A FNGF Sbjct: 377 AIEFNGF 383 Lambda K H 0.320 0.137 0.407 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: 16 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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 Sep 17 2021. The underlying query database was built on Sep 17 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