Align serine racemase (EC 5.1.1.18) (characterized)
to candidate Ga0059261_3754 Ga0059261_3754 Threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Korea:Ga0059261_3754 Length = 322 Score = 191 bits (485), Expect = 2e-53 Identities = 119/322 (36%), Positives = 173/322 (53%), Gaps = 16/322 (4%) Query: 8 PTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQ 67 PT V A+ ++ TP+L + V FK E Q +GAFK RGA + L+ Sbjct: 7 PTRAGVRDAAAKVAAILPPTPLLVAEIRG----IPVMFKAECLQPIGAFKIRGAWHRLTA 62 Query: 68 LNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYD 127 ++ QR+ GV+ FSSGNHAQ +A +AK LGIPA I+MP DAP AK +T G +V+ YD Sbjct: 63 IDPEQREKGVVAFSSGNHAQGVAWAAKRLGIPAVIVMPADAPAAKRDSTLALGAEVVAYD 122 Query: 128 RYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPL-----DALFVCL 182 R K+DR K+A ++ G T++PP+D P ++ GQG+ A E+ + + + V Sbjct: 123 RMKEDRVKIAAHLAHARGATLVPPFDDPWIIEGQGSMAIEVLTQAAEMRLPDPGRIVVPC 182 Query: 183 GGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHI--DTPKTIADGAQTQ 240 GGGGL SG LA P + VEPE +D +S G I I P T D QT Sbjct: 183 GGGGLASGVTLA----LPEAQTTIVEPEGWDDMCRSLANGWIESIGESPPPTACDALQTF 238 Query: 241 HLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKN 300 TF ++ + + VS+ E+ ++ A ++++VVEP G ++ AA A K Sbjct: 239 QPAQLTFDVLSRRGATGVAVSEAEVRAAQRWAARKLRLVVEPGGAVALAALLAGKVDPTP 298 Query: 301 KRIGIIISGGNVDIERYAHFLS 322 + +I+SGGN D + YA L+ Sbjct: 299 DTL-VILSGGNADPDAYARVLA 319 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: 243 Number of extensions: 11 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: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 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