Align serine racemase (EC 5.1.1.18) (characterized)
to candidate Pf6N2E2_802 Threonine dehydratase biosynthetic (EC 4.3.1.19)
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_802 Length = 335 Score = 173 bits (439), Expect = 5e-48 Identities = 99/303 (32%), Positives = 161/303 (53%), Gaps = 3/303 (0%) Query: 20 IKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVLT 79 + + A +TP+ + +++ + K E+ Q +FK RGA N L QL QR GV+T Sbjct: 23 VYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGAYNKLVQLTPEQRARGVIT 82 Query: 80 FSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAKE 139 S+GNHAQ +AL+A+ LGI A I+MP+ P+ KV + G + I++ A E Sbjct: 83 ASAGNHAQGVALAARELGISASIVMPVTTPQLKVLGVRNRGAEAILHGESFPFALAHALE 142 Query: 140 ISEREGLTIIPPYDHPHVLAGQGTAAKELF-EEVGPLDALFVCLGGGGLLSGSALAARHF 198 ++E+ G + P+D P V+AGQGT A E+ + G LDA+FV +GGGGL++G A ++ Sbjct: 143 LAEQSGWEFVSPFDDPDVIAGQGTVAMEILRQHPGQLDAIFVPVGGGGLIAGIAAYVKYL 202 Query: 199 APNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDIL 258 P + GVE + Q + G V + T ADG +G + I + VD+++ Sbjct: 203 RPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGVAVAQIGAHGLDICRFCVDEVM 262 Query: 259 TVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGNVDIER 316 TVS+++L +K + + EP+G L+ A + + + + I SG N++ + Sbjct: 263 TVSNDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAGTGARGQTLVAIDSGANINFDS 322 Query: 317 YAH 319 H Sbjct: 323 LRH 325 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: 237 Number of extensions: 8 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: 323 Length of database: 335 Length adjustment: 28 Effective length of query: 295 Effective length of database: 307 Effective search space: 90565 Effective search space used: 90565 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: 49 (23.5 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