Align serine racemase (EC 5.1.1.18) (characterized)
to candidate RR42_RS05695 RR42_RS05695 pyridoxal-5'-phosphate-dependent protein subunit beta
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Cup4G11:RR42_RS05695 Length = 339 Score = 189 bits (479), Expect = 1e-52 Identities = 106/319 (33%), Positives = 175/319 (54%), Gaps = 5/319 (1%) Query: 8 PTYDDVASASERIKKFANKTPVL---TSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNA 64 P+ ++ S + R++ +TPV T + + + +V+ K E FQ G FK RGALN+ Sbjct: 14 PSLPEIQSTARRLQGKVLETPVWRWQTGAALQLDAGTQVWLKLELFQITGTFKVRGALNS 73 Query: 65 LSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVI 124 + ++ + R GV+ S+GNHA A+A +AK+ G+ AK+ MP A A+VAA + G +V+ Sbjct: 74 IEHMDASARARGVVAASAGNHAMAVAYAAKVAGVGAKLAMPATASPARVAACREAGAEVL 133 Query: 125 MYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGG 184 + + +++ EG T++ PYD P + G T EL +V LDA+ V +GG Sbjct: 134 LLPDVHAAFAHALQLVAD-EGRTMVHPYDGPLIAQGTATVGLELMRQVAGLDAVVVPVGG 192 Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGN 244 GGL G A A + P C VYGVEPE + +SF G ++ T+AD + + Sbjct: 193 GGLCGGIAAAVKQINPACRVYGVEPEGADAMNRSFEAGRPQTLERVATVADSLGAPYALD 252 Query: 245 YTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARA-MKEKLKNKRI 303 Y++ + ++ VD ++ VSDE + ++ MK+ EP +S AA +++ L K++ Sbjct: 253 YSYGVCRQFVDGMVRVSDEAIRAAMRILYRDMKLATEPATAVSTAALLGPLRQTLAGKKV 312 Query: 304 GIIISGGNVDIERYAHFLS 322 +I+ G N+D R+A L+ Sbjct: 313 ALIVCGSNLDAARFAELLA 331 Lambda K H 0.318 0.135 0.384 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: 226 Number of extensions: 7 Number of successful extensions: 3 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: 323 Length of database: 339 Length adjustment: 28 Effective length of query: 295 Effective length of database: 311 Effective search space: 91745 Effective search space used: 91745 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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