Align serine racemase (EC 5.1.1.18) (characterized)
to candidate 3607475 Dshi_0888 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= BRENDA::Q2PGG3 (331 letters) >FitnessBrowser__Dino:3607475 Length = 324 Score = 291 bits (746), Expect = 1e-83 Identities = 151/306 (49%), Positives = 203/306 (66%), Gaps = 5/306 (1%) Query: 18 AHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQAAK 77 AH+RIKP+IHRTPVLTS N + G LFFKCE QK GAFK RGACNAV L A + Sbjct: 19 AHERIKPHIHRTPVLTSSYFNDLVGAELFFKCENFQKAGAFKVRGACNAVFGLSDALAER 78 Query: 78 GVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSSREE 137 GV THSSGNHA +LS AA +GIP +V+P+ AP+ K V YGG + E + +SRE Sbjct: 79 GVATHSSGNHALSLSYAAGRRGIPCNVVMPRTAPEAKKAAVRGYGGIITECEPSTTSREA 138 Query: 138 IASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEIDAIVVPISGGGLISGVALAA 197 + ++V + TG+ +HPYND R+++GQGT + E +EQ +D ++ PI GGG+ISG L Sbjct: 139 VFAEVQERTGAEFVHPYNDPRVVAGQGTCSREFMEQTDGLDMMIAPIGGGGMISGCCLTL 198 Query: 198 KSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASLGDLTWPVVRDLVDD 257 +I P ++IIAAEP+ ADDA +S AG II TIADGL+ L DLTW V + V D Sbjct: 199 SNIAPEVQIIAAEPEQADDAYRSFKAGHIIADDAPVTIADGLKVPLKDLTWHFVSNHVSD 258 Query: 258 VVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKNIGIVLSGGN 317 ++T E EII+AMK+ ++ +K+ +EPS A+ LA +L N + K +G++++GGN Sbjct: 259 ILTASEQEIIDAMKLTWQRMKIVMEPSCAVPLATILKNKDKFAG-----KRVGVIVTGGN 313 Query: 318 VDLGSL 323 VDL L Sbjct: 314 VDLDKL 319 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: 286 Number of extensions: 11 Number of successful extensions: 2 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: 324 Length adjustment: 28 Effective length of query: 303 Effective length of database: 296 Effective search space: 89688 Effective search space used: 89688 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 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