Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate SMc02983 SMc02983 ornithine, DAP, or arginine decarboxylase
Query= curated2:O50657 (393 letters) >FitnessBrowser__Smeli:SMc02983 Length = 379 Score = 211 bits (538), Expect = 2e-59 Identities = 132/362 (36%), Positives = 191/362 (52%), Gaps = 19/362 (5%) Query: 16 KRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSHFDVASAG 75 +R P LV LD V +N++ R LP + ++YA+KANP PEIL LLAGLGS+FD AS Sbjct: 15 RRPEGPCLVVDLDVVRDNFKAFRHALPDSAIYYAVKANPAPEILRLLAGLGSNFDCASVA 74 Query: 76 EMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLV 135 E+E+ + G +++ Y N +K R + A + F D E++K+A+A PGA V Sbjct: 75 EIEMALDAGATPNRISYGNTIKKERDVARAHALGISLFAVDSHEEVEKIARAAPGARVFC 134 Query: 136 RIAVRNNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALL 195 R+ A L+ KFG + A+D+L A GL + G+ FHVGSQ A++ AL Sbjct: 135 RVLTDGEGAEWPLSRKFGCVPQMAVDVLVYAHQLGLVSYGVSFHVGSQMTKLDAWDAALA 194 Query: 196 VARRLFDEAEEMGMHLTDLDIGGGFP------VPDAKGLNVDLAAMMEAINKQIDRLFPD 249 A+R+F + + G+ L +++GGGFP VP A+ A+ A+ K P+ Sbjct: 195 DAKRVFVQLAKQGIELKMVNMGGGFPTKYLRDVPSAEAYG---QAIFGALKKHFGNNIPE 251 Query: 250 TAVWTEPGRYMCGTAVNLVTSVIGTKTRGEQP---WYILDEGIYGCFSGIMYDHWTYPLH 306 T + EPGR M G A + V+ + + W LD G +G + M + YP+ Sbjct: 252 TII--EPGRGMVGNAGVIKAEVVLVSKKSDNDSHRWVFLDIGKFGGLAETMDEAIRYPIR 309 Query: 307 CFGKGN-KKPSTFGGPSCDGIDVLYRDFMAP---ELKIGDKVLVTEMGSYTSV-SATRFN 361 + +P GP+CD DVLY M P L IGD+VL+ G+YT+ SA FN Sbjct: 310 TARDADAMEPCVLAGPTCDSADVLYEKNMYPLPISLTIGDEVLIEGTGAYTTTYSAVAFN 369 Query: 362 GF 363 GF Sbjct: 370 GF 371 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: 377 Number of extensions: 24 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: 379 Length adjustment: 30 Effective length of query: 363 Effective length of database: 349 Effective search space: 126687 Effective search space used: 126687 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