Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_025764552.1 X939_RS0117325 pyridoxal-phosphate dependent enzyme
Query= BRENDA::Q2PGG3 (331 letters) >NCBI__GCF_000566685.1:WP_025764552.1 Length = 323 Score = 288 bits (738), Expect = 1e-82 Identities = 147/310 (47%), Positives = 209/310 (67%), Gaps = 6/310 (1%) Query: 15 IKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQ 74 ++EAH RI P+IHRTP++TS+ LN ++G LFFK E LQK GAFK RGA NA+LSLD+ Sbjct: 17 LREAHQRITPFIHRTPLMTSQMLNELTGAHLFFKPENLQKIGAFKIRGALNAMLSLDSAV 76 Query: 75 AAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSS 134 A G+ THSSGNHA A++ AA ++GI AYIV+P APK KV V YG + + E T Sbjct: 77 LANGLATHSSGNHAQAIACAAALRGIKAYIVMPHNAPKVKVSAVRGYGASITFCENTPED 136 Query: 135 REEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQE-IDAIVVPISGGGLISGV 193 RE + ++++ ETG+ IHP+N ++ GQ T+A E++E E D ++ P+ GGGL+SG Sbjct: 137 REAVVARIVAETGATFIHPFNHYGVMEGQATVAKEMIEDSTEPFDYLLAPVGGGGLLSGT 196 Query: 194 ALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASLGDLTWPVVRD 253 AL+A + +I AEP+GA DA S +G I P +TIADGL LGD T+PV+ Sbjct: 197 ALSAHYFSKNTLVIGAEPEGAADAVLSLQSGSIQKAPYVDTIADGLLTYLGDKTFPVIHK 256 Query: 254 LVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKNIGIVL 313 V ++V + + EI+EAM++ +E +K+ VEPSGA+ LAA++ + + K +G+++ Sbjct: 257 FVSEIVLVSDQEIVEAMRLIWERMKLVVEPSGAVTLAAII-----RHKKLFEGKRVGVIV 311 Query: 314 SGGNVDLGSL 323 SGGNVDLG+L Sbjct: 312 SGGNVDLGNL 321 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: 281 Number of extensions: 10 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: 323 Length adjustment: 28 Effective length of query: 303 Effective length of database: 295 Effective search space: 89385 Effective search space used: 89385 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: 48 (23.1 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