Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate WP_011383798.1 AMB_RS07020 type III PLP-dependent enzyme
Query= curated2:O50657 (393 letters) >NCBI__GCF_000009985.1:WP_011383798.1 Length = 376 Score = 206 bits (524), Expect = 9e-58 Identities = 130/355 (36%), Positives = 187/355 (52%), Gaps = 13/355 (3%) Query: 20 TPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSHFDVASAGEMEI 79 TP +V LD V +NY +RR LP A V+YA+KANP PEI+ +L GS FDVAS GE+++ Sbjct: 16 TPCVVVDLDVVRDNYHGLRRWLPLAEVYYAVKANPAPEIVRMLTEEGSRFDVASRGEIDL 75 Query: 80 LHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLVRIAV 139 G ++ + N +K + A VR + FD +E++K+A+A PG+ V RI + Sbjct: 76 CLANGAPAERISFGNTIKKQSDIAYAYAKGVRLYAFDSEAELEKLAEAAPGSRVFCRILM 135 Query: 140 RNNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALLVARR 199 + A L+ KFG ++ A DLL A++ GL G+ FHVGSQ ++ A+ A Sbjct: 136 TCDGAEWPLSRKFGCEIDMAKDLLVKAREMGLDPYGVSFHVGSQQTDLRQWDIAVGKAAM 195 Query: 200 LFDEAEEMGMHLTDLDIGGGFPV---PDAKGLNVDLAAMMEAINKQIDRLFPDTAVWTEP 256 LF + G+ L +++GGGFP + GL A+M+A+ K P + EP Sbjct: 196 LFSALDAAGIELRMVNLGGGFPARYRKEVDGLERYAEAVMDAMTKHFGNNIPSMII--EP 253 Query: 257 GRYMCGTAVNLVTSVIGTKTRG---EQPWYILDEGIYGCFSGIMYDHWTYPLHCFGKG-N 312 GR + G A L T V+ +G + W LD G +G + M + Y + G + Sbjct: 254 GRSLVGDAGILETEVVLISRKGYDDDVRWVYLDVGKFGGLAETMDEAIKYRIVTTRDGDD 313 Query: 313 KKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSY-TSVSATRFNGF 363 P GP+CD D+LY M LK+GDKV + G+Y TS SA FNGF Sbjct: 314 TAPVVLAGPTCDSADILYEKAGYEMPLSLKVGDKVRILSTGAYTTSYSAVNFNGF 368 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: 376 Number of extensions: 22 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: 376 Length adjustment: 30 Effective length of query: 363 Effective length of database: 346 Effective search space: 125598 Effective search space used: 125598 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