Align serine racemase (EC 5.1.1.18) (characterized)
to candidate GFF448 PGA1_c04590 putative threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Phaeo:GFF448 Length = 324 Score = 207 bits (528), Expect = 2e-58 Identities = 121/320 (37%), Positives = 178/320 (55%), Gaps = 5/320 (1%) Query: 7 LPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALS 66 + ++ +A+A++R+ A +TP+L+S +++ V K E Q G+FKFRG ALS Sbjct: 1 MTSFAAIAAAADRLSGHARETPLLSSPFLDEIAGRRVLIKAECLQHTGSFKFRGGWAALS 60 Query: 67 QLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMY 126 L + QR GVL +SSGNHAQ +A +A PA I+MP DAP K+A T+ G +V+++ Sbjct: 61 ALTDEQRHRGVLAYSSGNHAQGVAAAAAAHTTPAVILMPQDAPAIKIANTRALGAEVVLF 120 Query: 127 DRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDA----LFVCL 182 DR KD+R+ + E++E GLT+I PYD V+AGQGT E+ + LD + VC Sbjct: 121 DRAKDNRDAIGAELAEARGLTLIKPYDDVEVVAGQGTVGLEIARQAADLDVTEADVLVCC 180 Query: 183 GGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHID-TPKTIADGAQTQH 241 GGGGL +G ALA AP +V EPE +D +S G I + + ++ D T Sbjct: 181 GGGGLTAGVALALEQTAPKMKVSPCEPERFDDVTRSLVAGKICRNEASAGSLCDAILTPA 240 Query: 242 LGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNK 301 G TF I+ + VS+E+ + + R+KIV+EP G +S AAA ++L Sbjct: 241 PGEITFPILARLCGSGIVVSEEDAMRAMVLAFLRLKIVLEPGGAVSLAAALFHGDQLSGP 300 Query: 302 RIGIIISGGNVDIERYAHFL 321 I +GGNVD + L Sbjct: 301 AAIAIATGGNVDAALFTEAL 320 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: 232 Number of extensions: 6 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: 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