Align serine racemase (EC 5.1.1.18) (characterized)
to candidate Ac3H11_37 Threonine dehydratase, catabolic (EC 4.3.1.19)
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_37 Length = 324 Score = 465 bits (1197), Expect = e-136 Identities = 224/317 (70%), Positives = 271/317 (85%) Query: 7 LPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALS 66 LPTYDDV +A+ RI A++TPVLTS TVN+EF A+VFFKCEN Q+MGAFKFRGA NAL+ Sbjct: 8 LPTYDDVVAAAGRIAGVAHRTPVLTSRTVNEEFGAQVFFKCENLQRMGAFKFRGAYNALA 67 Query: 67 QLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMY 126 Q + AQRKAGV+ FSSGNHAQ IAL+A+ LGIPA I+MP DAP AKVAAT+GYG QV+ + Sbjct: 68 QFSPAQRKAGVVAFSSGNHAQGIALAARELGIPATILMPQDAPAAKVAATQGYGAQVVFF 127 Query: 127 DRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGG 186 DRY DRE++ ++++ER GLT+IPPYDH VLAGQGTAAKELFEEVGPLDA FVCLGGGG Sbjct: 128 DRYTQDREQLTRDLAERHGLTLIPPYDHADVLAGQGTAAKELFEEVGPLDAFFVCLGGGG 187 Query: 187 LLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYT 246 LLSGSALA R +P ++YGVEP AGNDGQQSFR GSIVHIDTP TIADGAQTQHLG+ T Sbjct: 188 LLSGSALATRALSPQTKLYGVEPAAGNDGQQSFRSGSIVHIDTPTTIADGAQTQHLGHIT 247 Query: 247 FSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGII 306 F+II+ VDDILTV+DE+L+D ++F+A RMK+VVEPTGCL FAAARAM+ +LK +R+G++ Sbjct: 248 FAIIRRDVDDILTVTDEQLVDAMRFFAERMKLVVEPTGCLGFAAARAMQSELKGQRVGVL 307 Query: 307 ISGGNVDIERYAHFLSQ 323 ISGGNVD+ R+ +++ Sbjct: 308 ISGGNVDLARFCALVAR 324 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: 349 Number of extensions: 9 Number of successful extensions: 1 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: 324 Length adjustment: 28 Effective length of query: 295 Effective length of database: 296 Effective search space: 87320 Effective search space used: 87320 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