Align Lysine racemase; Lys racemase; Ornithine racemase; EC 5.1.1.5; EC 5.1.1.12 (characterized)
to candidate GFF1737 PGA1_c17610 putative alanine racemase
Query= SwissProt::Q9X1T3 (354 letters) >FitnessBrowser__Phaeo:GFF1737 Length = 373 Score = 172 bits (436), Expect = 1e-47 Identities = 122/353 (34%), Positives = 185/353 (52%), Gaps = 7/353 (1%) Query: 1 MVYPRLLINLKEIEENARKVVEMASRRGIEIVGVTKVTLGDPRFAETLRKAGIGILGESR 60 M PR+ I+L +I +N R +VE GI + GVTK G P A + G L ++R Sbjct: 1 MTAPRIKIDLHKIRDNTRCLVERLKPLGITVTGVTKGVCGHPGVARAMLDGGAIGLADAR 60 Query: 61 IRNVLRMKKAGIEGPFMLLRLPMMSELVEDVKHFDYIMVSDPDVAKKVDELSREMKRNVK 120 + NV RM+KAG+ P +++R PM+S+ + V+ + ++ V K+ + + + Sbjct: 61 LANVRRMRKAGLTCPILMIRTPMLSQAGQIVETCEASCNTETSVIAKLAAAALRRGISHE 120 Query: 121 IIYMIDVGDLREGVWFE---KAVEEIAQCRGANIVGIGTNFGCYGGIIPTREKFEILLDI 177 II M+++GD REG+ E A + + G + GIG NFGC PT + +L + Sbjct: 121 IILMVEMGDGREGIMPEDLTNAALHVTRTPGVLLKGIGANFGCLADAAPTSQAMAVLSSL 180 Query: 178 KEKLEKNHGFNIEIVSGGNTPALYALENGEIPEGINQLRIGEAIVLGRDITNNRVIDWLS 237 ++ E G +E VSGG++ L +G + IN LRIGEAI+LG D + I L Sbjct: 181 ADETEGACGPFVETVSGGSSANLSWALDGGPADRINNLRIGEAILLGTDPVSGHPISGLY 240 Query: 238 QNTFLIEAEVIEVKEKPSVPLGKRGLDVFGRKVDFV-DRGIRKRAICALGEQDIDSRGLI 296 + F + AEVIE K K S P+ + D + V R+I ALG QD D+ GL Sbjct: 241 TDAFTLLAEVIETKIK-SKPVPLKLSDPALSALSLVPGNHWTTRSILALGLQDTDAAGL- 298 Query: 297 PVDKGVEVLHASSDHIVLDVTDFGDVKVGDVFRFRMTYSCLLKAMTSPFVEKV 349 V A+SDHIV++ T+ +++G +M+YS L +AM +P V KV Sbjct: 299 TFPAAVIFAGATSDHIVVETTNC-PLRIGSEMSMKMSYSALARAMEAPDVSKV 350 Lambda K H 0.321 0.142 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: 289 Number of extensions: 14 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: 354 Length of database: 373 Length adjustment: 29 Effective length of query: 325 Effective length of database: 344 Effective search space: 111800 Effective search space used: 111800 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: 49 (23.5 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