Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_011513321.1 PCRYO_RS05055 pyridoxal-phosphate dependent enzyme
Query= BRENDA::Q2PGG3 (331 letters) >NCBI__GCF_000013905.1:WP_011513321.1 Length = 326 Score = 300 bits (769), Expect = 2e-86 Identities = 159/311 (51%), Positives = 204/311 (65%), Gaps = 9/311 (2%) Query: 17 EAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQAA 76 EAH+RIKPYIHRTPVLTS LN ++G +FFKCE QK GAFK RGA NAV L E A Sbjct: 18 EAHERIKPYIHRTPVLTSRFLNELAGCEMFFKCENFQKAGAFKVRGASNAVFGLSDEDAK 77 Query: 77 KGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSSRE 136 GV THSSGNHA +LS AA +GIP +V+P AP+ K V YGG + E + +SRE Sbjct: 78 NGVCTHSSGNHALSLSYAAGQRGIPCNVVMPHSAPEAKKAAVRGYGGIITECEPSTTSRE 137 Query: 137 EIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEI----DAIVVPISGGGLISG 192 E+ +KV ETG +HPYND R+I+GQ T + E LEQ++EI D +V PI GGG+ISG Sbjct: 138 EVFAKVQAETGGDFVHPYNDPRVIAGQATCSREFLEQMEEIGEKPDMVVAPIGGGGMISG 197 Query: 193 VALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASLGDLTWPVVR 252 L ++ P ++I AAEP ADDAA+S AG II NT+ADGL+ L DLTW V Sbjct: 198 TCLTLSNLAPDVKIYAAEPLNADDAARSFKAGHIIADDAPNTVADGLKVPLKDLTWHFVS 257 Query: 253 DLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKNIGIV 312 + V D++T E EI+EAMK+ + +K+ +EPS A+ LA +L N K +G++ Sbjct: 258 NYVTDILTATEEEIVEAMKLTWTHMKIIIEPSCAVPLAVILKNK-----DVFAGKKVGVI 312 Query: 313 LSGGNVDLGSL 323 ++GGNVDL L Sbjct: 313 ITGGNVDLDKL 323 Lambda K H 0.316 0.133 0.380 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: 320 Number of extensions: 16 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: 331 Length of database: 326 Length adjustment: 28 Effective length of query: 303 Effective length of database: 298 Effective search space: 90294 Effective search space used: 90294 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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