Align serine racemase (EC 5.1.1.18) (characterized)
to candidate H281DRAFT_05256 H281DRAFT_05256 threonine ammonia-lyase, biosynthetic, long form
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Burk376:H281DRAFT_05256 Length = 341 Score = 164 bits (416), Expect = 2e-45 Identities = 99/304 (32%), Positives = 160/304 (52%), Gaps = 12/304 (3%) Query: 6 VLPTYDDVASASERIKK--------FANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFK 57 V T D VA + +KK A +T + + ++ V+ K E+ Q + +FK Sbjct: 31 VAETADSVALRHDYLKKTLTARVYDVARETELERAPQLSARLRNPVYLKREDNQPVFSFK 90 Query: 58 FRGALNALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATK 117 RGA N ++ + GV+T S+GNHAQ +ALSA +G+ A I++P+ P+ KV A + Sbjct: 91 VRGAYNKMAHIPAEALTRGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVR 150 Query: 118 GYGG---QVIMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEE-VG 173 +GG +V+ + D A ++ E GLT + P+D P+V+AGQGT A E+ + G Sbjct: 151 AHGGPTVEVVQFGESYSDAYGHAVQLQEERGLTFVHPFDDPYVIAGQGTVAMEILSQHQG 210 Query: 174 PLDALFVCLGGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTI 233 P+ A+FV +GGGGL +G A + P +V GV+ + S + G V ++ Sbjct: 211 PIHAIFVPIGGGGLAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLF 270 Query: 234 ADGAQTQHLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARA 293 +DG + +G TF + E +DD+L V+ + L +K + V+EP G L+ A A+ Sbjct: 271 SDGTAVKLVGEETFRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQ 330 Query: 294 MKEK 297 E+ Sbjct: 331 YAER 334 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: 231 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: 341 Length adjustment: 28 Effective length of query: 295 Effective length of database: 313 Effective search space: 92335 Effective search space used: 92335 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 Apr 09 2024. 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