Align serine racemase (EC 5.1.1.18) (characterized)
to candidate CCNA_03203 CCNA_03203 threo-3-hydroxyaspartate ammonia-lyase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Caulo:CCNA_03203 Length = 325 Score = 249 bits (636), Expect = 6e-71 Identities = 122/315 (38%), Positives = 196/315 (62%), Gaps = 5/315 (1%) Query: 12 DVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEA 71 D+ +A+ R+K A +TP++ S +N +F K E Q+ GAFKFRGA N LSQL++ Sbjct: 7 DIQAAAVRLKGSAVETPLIESPALNDRLGGRIFLKPETLQRAGAFKFRGAYNRLSQLSDE 66 Query: 72 QRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKD 131 ++ GV+ FSSGNHAQ +AL+A++LG+PA I+MP D+P KV T+G+G + YDR+ + Sbjct: 67 EKARGVVAFSSGNHAQGVALAARLLGVPALIVMPSDSPSVKVEGTRGFGADIRFYDRFTE 126 Query: 132 DREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEV----GPLDALFVCLGGGGL 187 DR +A +I+ G ++P YD PH++AGQGT E+ + LD L C+GGGGL Sbjct: 127 DRVAIADQIAAERGCVVVPSYDDPHIIAGQGTVGLEIVAQAAAQGATLDRLICCVGGGGL 186 Query: 188 LSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHID-TPKTIADGAQTQHLGNYT 246 ++G++ A + +P E++GVEP ++ ++S G ID ++I D T G+ T Sbjct: 187 IAGTSTAVKALSPATEIWGVEPAGFDETRRSLESGRRETIDKDARSICDALLTPIPGDLT 246 Query: 247 FSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGII 306 + I ++ + ++ V+D E+ + +++ + +K+VVEP GC++ AA K + K + I+ Sbjct: 247 WPINQKNLSGVVAVTDAEVAEAMRYAFSTLKLVVEPGGCVALTAALTGKVDVAGKTVAIV 306 Query: 307 ISGGNVDIERYAHFL 321 +SGGNVD +A L Sbjct: 307 LSGGNVDPGLFAQVL 321 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: 228 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: 325 Length adjustment: 28 Effective length of query: 295 Effective length of database: 297 Effective search space: 87615 Effective search space used: 87615 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: 48 (23.1 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