Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate AZOBR_RS00105 AZOBR_RS00105 ornithine decarboxylase
Query= curated2:O50657 (393 letters) >FitnessBrowser__azobra:AZOBR_RS00105 Length = 378 Score = 201 bits (511), Expect = 3e-56 Identities = 128/361 (35%), Positives = 186/361 (51%), Gaps = 15/361 (4%) Query: 16 KRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSHFDVASAG 75 +R TP LV LD VE NY + LP A +FYA+KANP PEIL LL LGS FD AS Sbjct: 12 QRPQTPCLVVDLDVVEANYHDLEEALPDAKIFYAVKANPAPEILGLLTRLGSAFDTASVP 71 Query: 76 EMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPGADVLV 135 E++++ G ++ Y N +K ++ A + VR F FD +E++K+A+A PGA V Sbjct: 72 EIQMVLAAGCAPERISYGNTIKKEADIRRAFELGVRLFAFDSEAELEKIARAAPGARVFC 131 Query: 136 RIAVRNNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAAYEEALL 195 RI A L+ KFG + A +LL A+ + G+ FHVGSQ ++ A+ Sbjct: 132 RILTSGEGAEWPLSRKFGCDLAMARELLLKAKGMNVVPYGVSFHVGSQQKDLMQWDHAIF 191 Query: 196 VARRLFDEAEEMGMHLTDLDIGGGFPV---PDAKGLNVDLAAMMEAINKQIDRLFPDTAV 252 +LF E E +G+ L +++GGGFP D A+ E++ P+ V Sbjct: 192 QVAQLFRELEVLGVDLGMINLGGGFPTRYRTDVPETTAYGQAIFESLRTHFGNRLPEAIV 251 Query: 253 WTEPGRYMCGTAVNLVTSVIGTKTRGE---QPWYILDEGIYGCFSGIMYDHWTYPLHCF- 308 EPGR M G A + + V+ + + W LD G + + M + YP+ Sbjct: 252 --EPGRSMVGNAGIIESEVVLVSRKSANDVKRWVYLDIGKFSGLAETMDEAIQYPIQVMG 309 Query: 309 --GKGNKKPSTFGGPSCDGIDVLYR--DFMAP-ELKIGDKVLVTEMGSYTSV-SATRFNG 362 G+G+ + GP+CD DVLY ++ P +LK GD+V + G+YT+ SA FNG Sbjct: 310 DDGEGDSEAVVLAGPTCDSADVLYERAEYKLPMDLKAGDRVRIHATGAYTTTYSAVCFNG 369 Query: 363 F 363 F Sbjct: 370 F 370 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: 408 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: 378 Length adjustment: 30 Effective length of query: 363 Effective length of database: 348 Effective search space: 126324 Effective search space used: 126324 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