Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate Ga0059261_3753 Ga0059261_3753 Diaminopimelate decarboxylase
Query= curated2:O50657 (393 letters) >FitnessBrowser__Korea:Ga0059261_3753 Length = 402 Score = 151 bits (381), Expect = 4e-41 Identities = 107/327 (32%), Positives = 171/327 (52%), Gaps = 20/327 (6%) Query: 48 YAMKANPTPEILSLLAGLG-SHFDVASAGEMEILHELGVDGSQMIYANPVKDARGLKAAA 106 YA+KANP+PE+L +L G +H+DVAS GE+ + + + + + +PVK ++ A Sbjct: 45 YAVKANPSPELLQILWDAGITHYDVASIGEVRMARR-ALPKAVLCFMHPVKAEEAIEEAY 103 Query: 107 D-YNVRRFTFDDPSEIDKMAKAVPGADVL---VRIAVRNNKALVDLNTKFGAPVEEALDL 162 + VR F+ D E++K+ +A GA L VRI V ++ + + L KFGA E+ +L Sbjct: 104 FVHGVRTFSLDTMDELEKIVRATRGAQDLNLCVRIRVSSDHSKLSLAAKFGAEPEDVAEL 163 Query: 163 LKAAQDAGLHAMGICFHVGSQSLSTAAYEEALLVARRLFDEAEEMGMHLTDLDIGGGFPV 222 L A + A A+GICFHVGSQ+++ AAY EA+ R+ + + +D+GGGFP Sbjct: 164 LVATRQAA-DALGICFHVGSQAMTPAAYAEAM---ERVRVAIVASSVTVDIVDVGGGFPS 219 Query: 223 PDAKGLNVDLAAMMEAINKQIDRL--FPDTAVWTEPGRYMCGTAVNLVTSVIGTKTRGEQ 280 L A I+ + L +W EPGR +C +L+ V K RG++ Sbjct: 220 TYPGMEPPPLDAYFGVIHNAFENLPISYSAELWCEPGRALCAEYSSLIVRV--EKRRGDE 277 Query: 281 PWYILDEGIYGCFSGIMYDHWTYPLHCFGKG---NKKPSTFGGPSCDGIDVLYRDFMAP- 336 + +++G YG + W +P+ +G + +F GP+CD +D + F P Sbjct: 278 LY--INDGAYGALFDAAHVGWRFPVTLLREGVAAETEAFSFYGPTCDDMDHMAGPFELPA 335 Query: 337 ELKIGDKVLVTEMGSYTSVSATRFNGF 363 ++ GD + V +G+Y T FNGF Sbjct: 336 DVAAGDYIEVGMLGAYGCAMRTAFNGF 362 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: 370 Number of extensions: 25 Number of successful extensions: 8 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: 402 Length adjustment: 31 Effective length of query: 362 Effective length of database: 371 Effective search space: 134302 Effective search space used: 134302 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