Align Lysine/ornithine decarboxylase; LDC; EC 4.1.1.17; EC 4.1.1.18 (uncharacterized)
to candidate 6936221 Sama_0410 ornithine decarboxylase (RefSeq)
Query= curated2:O50657 (393 letters) >FitnessBrowser__SB2B:6936221 Length = 391 Score = 176 bits (445), Expect = 1e-48 Identities = 117/364 (32%), Positives = 185/364 (50%), Gaps = 12/364 (3%) Query: 11 VKTLAKRIPTPFLVASLDKVEENYQFMRRHLPRAGVFYAMKANPTPEILSLLAGLGSHFD 70 ++ AK TPF+V + + + Y M + P A V+YA+KANP EIL+LL GS+FD Sbjct: 21 IQEFAKDKATPFVVIDTNIIAKQYDDMVTNFPFANVYYAVKANPAKEILTLLKDKGSNFD 80 Query: 71 VASAGEMEILHELGVDGSQMIYANPVKDARGLKAAADYNVRRFTFDDPSEIDKMAKAVPG 130 +AS E++++ +GV ++ + N +K + ++A + VR F D +++ +A+ PG Sbjct: 81 IASIYELDMVMAVGVTADRVSFGNTIKKRKDVRAFYERGVRLFASDSEADLRMIAEEAPG 140 Query: 131 ADVLVRIAVRNNK-ALVDLNTKFGAPVEEALDLLKAAQDAGLHAMGICFHVGSQSLSTAA 189 + V VRI ++ A L+ KFG E A +LL A++ GL GI FHVGSQ A Sbjct: 141 SKVYVRILTEGSQTADWPLSRKFGCQNEMAYELLALAKELGLDPYGISFHVGSQQRDIGA 200 Query: 190 YEEALLVARRLFDE-AEEMGMHLTDLDIGGGFPVPDAKGLNVDLAAMMEAINKQIDRLFP 248 ++ A+ + LFD E+ G+ L +++GGGFP N L + I + F Sbjct: 201 WDAAIGKVKVLFDRLREDHGIVLKMINMGGGFPANYIDKTN-QLGVYAQQIKHFLKEDFG 259 Query: 249 D--TAVWTEPGRYMCGTAVNLVTSVIGTKTRGE---QPWYILDEGIYGCFSGIMYDHWTY 303 D + EPGR + A L++ V+ + + W D G + M + Y Sbjct: 260 DELPEIILEPGRSLISNAGVLISEVVLISRKSHTALERWVYTDVGKFSGLIETMDEAIKY 319 Query: 304 PLHCFGKGNKKPSTFGGPSCDGIDVLYRDF---MAPELKIGDKVLVTEMGSYTSV-SATR 359 P+ KG GP+CD D++Y + + +L IGD++ G+YT+ SA Sbjct: 320 PIFTEKKGELDKCVIAGPTCDSADIMYEHYAYGLPADLAIGDRLYWLTAGAYTTTYSAVC 379 Query: 360 FNGF 363 FNGF Sbjct: 380 FNGF 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: 392 Number of extensions: 20 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