Align serine racemase (EC 5.1.1.18) (characterized)
to candidate SMa1872 SMa1872 threonine dehydratase
Query= BRENDA::Q2PGG3 (331 letters) >FitnessBrowser__Smeli:SMa1872 Length = 323 Score = 228 bits (581), Expect = 2e-64 Identities = 124/313 (39%), Positives = 187/313 (59%), Gaps = 5/313 (1%) Query: 12 ILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLD 71 I I+EA +R+KP++ TP+L +E + +G L+ K E LQ GAFK RGA N LSL Sbjct: 7 IQDIREARERLKPHVRHTPLLRAEKIEKAAGCQLYLKPETLQITGAFKIRGALNKALSLS 66 Query: 72 AEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEAT 131 E+ A G++ SSGNHA LS AAK+ G+ +V+P PK K++N G +VI + Sbjct: 67 REEIANGIIATSSGNHAQGLSYAAKMLGVKVILVLPVTTPKIKIENTKALGAEVILFDGD 126 Query: 132 MSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEIDAIVVPISGGGLIS 191 ++R + ++ + +IH + D +++GQGTI E+LE + ++D ++VP+ GGGLIS Sbjct: 127 NAARWKKVYEIAEGNKYAVIHGFEDPVVMAGQGTIGCEILEDLDDVDTVIVPLGGGGLIS 186 Query: 192 GVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASL-GDLTWPV 250 G+A A K KPS+R+I AEP S+V + +LP+ NTIADGLR S+ G +P+ Sbjct: 187 GIATAIKETKPSVRVIGAEPALTPKYFHSRVNKERTSLPLKNTIADGLRISVPGQNPYPI 246 Query: 251 VRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKNIG 310 + VD++V +E+ II M+ + K+ EP+ +IG+ A+L+ + C Sbjct: 247 IEKYVDEIVLVEDEHIIAGMRALAKDAKLIAEPAASIGVGALLAGIIDVKLDEKVC---- 302 Query: 311 IVLSGGNVDLGSL 323 VLSGGN DL L Sbjct: 303 AVLSGGNWDLRDL 315 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: 291 Number of extensions: 12 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: 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 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