Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate 5210966 Shew_3392 ornithine decarboxylase (RefSeq)
Query= curated2:O50657 (393 letters) >FitnessBrowser__PV4:5210966 Length = 391 Score = 181 bits (458), Expect = 4e-50 Identities = 114/366 (31%), Positives = 188/366 (51%), Gaps = 12/366 (3%) Query: 9 KEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSH 68 + +K A+ PTPF+V + + Y M + P A ++YA+KANP E+L+LL G++ Sbjct: 19 ERIKAFAQDKPTPFVVIDTKIIAKQYDDMVHNFPYASIYYAVKANPAKEVLTLLRDRGAN 78 Query: 69 FDVASAGEMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAV 128 FD+AS E++++ ++GV ++ Y N +K + ++A + VR + D +++ +A+ Sbjct: 79 FDIASIYELDMVSDIGVTPDRVSYGNTIKKRKDVRAFYERGVRMYASDSEADLRMIAEEA 138 Query: 129 PGADVLVRIAVR-NNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLST 187 PG+ V VRI + A L+ KFG E A +LL A+ GL GI FHVGSQ Sbjct: 139 PGSRVYVRILTEGTHTADWPLSRKFGCQNEMAFELLVLAKTLGLEPYGISFHVGSQQRDI 198 Query: 188 AAYEEALLVARRLFDE-AEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQIDRL 246 A++ A+ + +F+ EE G+ L +++GGGFP N +L E I + Sbjct: 199 GAWDSAIAKVKSIFERLREEHGIELKMINLGGGFPANYLDKTN-ELGTYAEQITHFLKED 257 Query: 247 FPD--TAVWTEPGRYMCGTAVNLVTSVIGTKTRGE---QPWYILDEGIYGCFSGIMYDHW 301 F D + EPGR + A LV+ V+ + + + W D G + M + Sbjct: 258 FGDQLPQIILEPGRSLLSNAGVLVSEVVLISKKSQTALERWVFTDVGKFSGLIETMDEAI 317 Query: 302 TYPLHCFGKGNKKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSYTSV-SA 357 +P++ +G GP+CD D++Y + + +L IGD++ G+YT+ SA Sbjct: 318 KFPIYTERQGELDRCVIAGPTCDSADIMYEHYSYGLPLDLAIGDRMYWLTAGAYTTTYSA 377 Query: 358 TRFNGF 363 FNGF Sbjct: 378 VCFNGF 383 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: 381 Number of extensions: 19 Number of successful extensions: 4 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: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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