Align serine racemase (EC 5.1.1.18) (characterized)
to candidate GFF2483 PS417_12665 hypothetical protein
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__WCS417:GFF2483 Length = 340 Score = 192 bits (489), Expect = 7e-54 Identities = 110/318 (34%), Positives = 170/318 (53%), Gaps = 14/318 (4%) Query: 5 LVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNA 64 L P YD A +TP+ + ++ +V K E+ Q +FK RGA N Sbjct: 23 LAAPVYD-----------LAVRTPLQAAPALSALLGNQVLLKREDLQPTFSFKIRGAYNK 71 Query: 65 LSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVI 124 L QL QR GV+T S+GNHAQ +AL+A+ LGI A+I+MP PE KV + G Q + Sbjct: 72 LVQLTPEQRARGVVTASAGNHAQGVALAARELGIKARIVMPASTPELKVLGVRSRGAQAV 131 Query: 125 MYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELF-EEVGPLDALFVCLG 183 ++ A +++E G T + P+D P V+AGQGT A E+ ++ GPLDA+FV +G Sbjct: 132 LHGASFPFALAYALQLAESSGCTFVSPFDDPDVIAGQGTVAMEILRQQQGPLDAIFVPVG 191 Query: 184 GGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLG 243 GGGL++G A ++ P+ + GVEPE + + R G V + + ADG +G Sbjct: 192 GGGLIAGVAAYVKYLRPDVRIIGVEPEGSSCLLAALRAGERVVLPSVDGFADGTAVAQVG 251 Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNK 301 + F I ++ VD+++TVS++ L +K + + EP+G L+ A R L+ + Sbjct: 252 AHGFEICRDWVDEVITVSNDALCSAIKLIYDDTRSITEPSGALAVAGIRQYVATHNLRGQ 311 Query: 302 RIGIIISGGNVDIERYAH 319 + I SG N++ + H Sbjct: 312 TLVAINSGANINFDSLRH 329 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: 253 Number of extensions: 8 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: 340 Length adjustment: 28 Effective length of query: 295 Effective length of database: 312 Effective search space: 92040 Effective search space used: 92040 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