Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate Synpcc7942_2201 Synpcc7942_2201 alanine racemase
Query= BRENDA::Q04HB7 (371 letters) >FitnessBrowser__SynE:Synpcc7942_2201 Length = 406 Score = 164 bits (415), Expect = 4e-45 Identities = 120/375 (32%), Positives = 194/375 (51%), Gaps = 25/375 (6%) Query: 11 IEFSKSSLAYNVQYTKQ-VSGAKTLWLAVKSNAYGHGLLQVSKIARECGVDGLAVSVLDE 69 +E + ++A N + +Q ++ + L VK++AYGHG + ++ G L V+ + E Sbjct: 29 VEVDQGAIAANTRQIRQFLAPSCELMAVVKADAYGHGAVAIASTVLGAGATALGVATIPE 88 Query: 70 GIAIRQAGIDDFILILGPI-DVKYAPIASKYHFLTTVSSLDWLKSADKILGK--EKLSVN 126 G+ +R+AGI IL+LG I + + ++S+ ++L + + L V+ Sbjct: 89 GVRLREAGITAPILLLGSIHSPDEVQAIAHWQIQPSLSTPKQALICAEVLDRLGQSLPVH 148 Query: 127 LAVDTGMNRIGVRSKKDLKDEIEFLQ--EHSDHFSYDGIFTHFASSDNPDDHYFQRQKNR 184 L +DTGM+R+G + +EFLQ +++HFA++D+PD Q+Q Sbjct: 149 LKLDTGMSRLGA----PWQTAVEFLQLVHGLPSLQLASLYSHFATADSPDRAPLQQQHAA 204 Query: 185 WYELI-----DGLIMPRYVHVMNSGAAMYHSKELPGCNSIARVGTVVYGVEPSEGVLGPI 239 + + I +GL +P+ +H+ NS A + S RVG +YG+ P+ LG Sbjct: 205 FEQAIAQIQAEGLPVPK-LHIANSAATLLDSSLH---YDQVRVGLALYGLYPAPH-LGDR 259 Query: 240 DKLKPVFELKSALTFVKKIPAGEGISYGSKFVTSRDTWIGTLPIGYGDGW-LAEYQDFQL 298 L P +K+ +T V +PAG+G+SYG ++VT R+T I + IGY DG A ++ Sbjct: 260 LSLYPALSVKARVTHVTTLPAGQGVSYGHRYVTQRETPIAVVGIGYADGVPRALSNQMEV 319 Query: 299 LIDGQKCRQVGQIAMDQMMV---ALPHEYPIGTEVTLIGKSGKYENTLYDLHKHSGVPPW 355 L GQ+ Q+G I MDQMM+ A+P P G VTL+G+SG + T D + W Sbjct: 320 LYRGQRLPQIGAITMDQMMIDISAMPQLAP-GDVVTLLGRSGSEQITADDWADRANTISW 378 Query: 356 KITVAFSDRLKRMVV 370 +I F DRL R V Sbjct: 379 EILCGFKDRLPRFAV 393 Lambda K H 0.319 0.137 0.410 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: 374 Number of extensions: 23 Number of successful extensions: 6 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: 371 Length of database: 406 Length adjustment: 30 Effective length of query: 341 Effective length of database: 376 Effective search space: 128216 Effective search space used: 128216 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 (21.7 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