Align serine racemase (EC 5.1.1.18) (characterized)
to candidate BPHYT_RS03145 BPHYT_RS03145 threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__BFirm:BPHYT_RS03145 Length = 507 Score = 171 bits (434), Expect = 3e-47 Identities = 98/304 (32%), Positives = 169/304 (55%), Gaps = 6/304 (1%) Query: 19 RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78 R+ A +T + + ++ V+ K E+ Q + +FK RGA N ++ ++ + GV+ Sbjct: 14 RVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHISAEALERGVI 73 Query: 79 TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGG---QVIMYDRYKDDREK 135 T S+GNHAQ +ALSA +G+ A I++P+ P+ KV A + +GG +V+ + D + Sbjct: 74 TASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQFGESYSDAYE 133 Query: 136 MAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEE-VGPLDALFVCLGGGGLLSGSALA 194 A ++ + LT + P+D P+V+AGQGT A E+ + GP+ A+FV +GGGGL +G A Sbjct: 134 HAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGGLAAGVAAY 193 Query: 195 ARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKV 254 + P +V GV+ + S + G V ++ +DG + +G TF + E + Sbjct: 194 VKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEETFRLCSEYL 253 Query: 255 DDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGNV 312 DD+L V+ + L +K + V+EP G L+ A A+ A +E ++N+ + I SG N+ Sbjct: 254 DDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTLIAITSGANM 313 Query: 313 DIER 316 + +R Sbjct: 314 NFDR 317 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: 331 Number of extensions: 11 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: 507 Length adjustment: 31 Effective length of query: 292 Effective length of database: 476 Effective search space: 138992 Effective search space used: 138992 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