Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate GFF3286 Psest_3350 Diaminopimelate decarboxylase
Query= curated2:O50657 (393 letters) >FitnessBrowser__psRCH2:GFF3286 Length = 387 Score = 178 bits (451), Expect = 3e-49 Identities = 120/370 (32%), Positives = 189/370 (51%), Gaps = 12/370 (3%) Query: 5 RLSEKEVKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAG 64 R + +++K A + TPF+V + + + Y +R A V+YA+KANP EI+ LL Sbjct: 11 RATFQKMKAFADQHETPFVVIDTETISKAYDDLRAGFEFASVYYAVKANPAVEIIDLLRD 70 Query: 65 LGSHFDVASAGEMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKM 124 GS FD+AS E++ + GV ++ Y N +K ++ ++ + VR F D +++ + Sbjct: 71 KGSSFDIASIYELDKVMSRGVGPERISYGNTIKKSKDIRYFYEKGVRMFATDSEADLRNI 130 Query: 125 AKAVPGADVLVRIAVR-NNKALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQ 183 AKA PGA V VRI + A L+ KFG + A+DLL A+ L GI FHVGSQ Sbjct: 131 AKAAPGAKVYVRILTEGSTTADWPLSRKFGCQTDMAMDLLILARQLKLEPYGISFHVGSQ 190 Query: 184 SLSTAAYEEALLVARRLFDE-AEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQ 242 + ++ A+ + +F+ EE G+ L +++GGGFP N L E I + Sbjct: 191 QRDISVWDAAIAKVKVIFERLKEEDGIELKMINMGGGFPANYITRTN-SLETYAEEIIRF 249 Query: 243 IDRLFPD--TAVWTEPGRYMCGTAVNLVTSV--IGTKTR-GEQPWYILDEGIYGCFSGIM 297 + F D + EPGR + A LV+ V + K+R + W +D G + M Sbjct: 250 LKEDFGDDLPEIILEPGRSLIANAGILVSEVVLVARKSRTAVERWVYVDVGKFSGLIETM 309 Query: 298 YDHWTYPLHCFGKGNKKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSY-T 353 + +P++ KG + GP+CD D++Y ++ + L IGD++ G+Y T Sbjct: 310 DESIKFPIYAEKKGEVEEVVIAGPTCDSADIMYENYKYGLPLNLAIGDRLYWLSTGAYTT 369 Query: 354 SVSATRFNGF 363 S SA FNGF Sbjct: 370 SYSAVEFNGF 379 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: 366 Number of extensions: 18 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: 387 Length adjustment: 31 Effective length of query: 362 Effective length of database: 356 Effective search space: 128872 Effective search space used: 128872 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