Align serine racemase (EC 5.1.1.18) (characterized)
to candidate GFF3797 Psest_3866 threonine ammonia-lyase, biosynthetic, long form
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__psRCH2:GFF3797 Length = 504 Score = 194 bits (494), Expect = 3e-54 Identities = 109/306 (35%), Positives = 173/306 (56%), Gaps = 3/306 (0%) Query: 17 SERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAG 76 + R+ A +TP+ + +++ ++ K E+ Q + +FK RGA N L+QL+ + G Sbjct: 11 TSRVYDVAIETPLQPARQLSERIGNQILLKREDLQPVFSFKVRGAYNKLAQLSAEELARG 70 Query: 77 VLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKM 136 V+T S+GNHAQ +AL+AK LGI A I+MP PE KV + GG+V+++ + Sbjct: 71 VVTASAGNHAQGVALAAKQLGIKATIVMPRTTPELKVQGVRARGGKVVLHGDAFPEALAY 130 Query: 137 AKEISEREGLTIIPPYDHPHVLAGQGTAAKELF-EEVGPLDALFVCLGGGGLLSGSALAA 195 + ++ E +G I PYD P V+AGQGT A E+ + GP+DA+FV +GGGGL++G A Sbjct: 131 SLKLVEEKGYVYIHPYDDPDVIAGQGTVAMEILRQHQGPIDAIFVPVGGGGLVAGIAAYV 190 Query: 196 RHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVD 255 ++ P +V GVEP+ N Q + G V ++ ADG +G +TF I + VD Sbjct: 191 KYLYPQTKVIGVEPDDSNCLQAAMAAGERVVLEQVGLFADGVAVAQIGQHTFEICRHYVD 250 Query: 256 DILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGNVD 313 +++TVS +E+ +K + + EP G LS A + +E + + + I SG NV+ Sbjct: 251 EVITVSTDEICAAIKDIYDDTRSITEPAGALSVAGIKKYVEREGVSGQVLVGIDSGANVN 310 Query: 314 IERYAH 319 +R H Sbjct: 311 FDRLRH 316 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: 364 Number of extensions: 13 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: 323 Length of database: 504 Length adjustment: 31 Effective length of query: 292 Effective length of database: 473 Effective search space: 138116 Effective search space used: 138116 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: 50 (23.9 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