Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate GFF369 PGA1_c03800 putative lysine/ornithine decarboxylase
Query= curated2:O50657 (393 letters) >FitnessBrowser__Phaeo:GFF369 Length = 393 Score = 168 bits (426), Expect = 2e-46 Identities = 118/355 (33%), Positives = 171/355 (48%), Gaps = 16/355 (4%) Query: 21 PFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSHFDVASAGEMEIL 80 P LV V Y + + L RA + YA+KANP P+IL L +G++FD AS E+E+ Sbjct: 35 PTLVIDSQAVARQYAALAQGLGRARIHYAVKANPEPQILRRLTRMGANFDAASRAEIEMC 94 Query: 81 HELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLVRIAVR 140 G SQ+ + N +K + A + + F D +E+DK+A PGA V +R+ V Sbjct: 95 LAAGAKPSQITFGNTIKRPADIAFAHEIGITHFAVDALAELDKLADHAPGARVCIRLLVE 154 Query: 141 NNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALLVARRL 200 A L+ KFG AL L+ A+D L G+ FHVGSQ+ + + L ++ Sbjct: 155 ATGADWPLSRKFGCTAAMALTLMDRARDLDLCVSGLSFHVGSQTREPQMWADTLDQVAQV 214 Query: 201 FDEAEEMGMHLTDLDIGGGFPV---PDAKGLNVDLAAMMEAINKQIDRLFPDTA-VWTEP 256 + A+ G LT L+IGGGFP + N +M +N + FPD + + EP Sbjct: 215 WRAAKTAGHELTLLNIGGGFPASYGTEVMAPNRYAQEVMALVNAR----FPDASEIMAEP 270 Query: 257 GRYMCGTAVNLVTSVIGTKTRGEQP---WYILDEGIYGCFSGIMYDHWTYPLHC-FGKGN 312 GR + A + V+ + W LD G + + M + Y + G G Sbjct: 271 GRGLVAEAGAIAAEVLLVSRKDADDLHRWVYLDIGKFSGLAETMDEAIRYRITTEHGDGQ 330 Query: 313 KKPSTFGGPSCDGIDVLYRD---FMAPELKIGDKVLVTEMGSYTSVSAT-RFNGF 363 P GPSCD DVLY M ELK GD+V++ G+YT+ A+ FNGF Sbjct: 331 TGPCILAGPSCDSADVLYEKQLYQMPLELKSGDRVVIHACGAYTTTYASVGFNGF 385 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: 357 Number of extensions: 21 Number of successful extensions: 3 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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