Align serine racemase (EC 5.1.1.18) (characterized)
to candidate Echvi_3354 Echvi_3354 threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Cola:Echvi_3354 Length = 416 Score = 176 bits (446), Expect = 9e-49 Identities = 103/316 (32%), Positives = 169/316 (53%), Gaps = 7/316 (2%) Query: 9 TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68 ++ + ASE +++ + TP+ + +++E+ V+ K E+ Q + ++K RGA + +S L Sbjct: 5 SFQGIIEASEALQEVLHPTPLQFNEQLSEEYGCRVYLKREDLQAVRSYKIRGAYHKISSL 64 Query: 69 NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQ----VI 124 +E ++ GV+ S+GNHAQ +A + K LGI I +P K+ K +G + V+ Sbjct: 65 SEEEKSRGVVCASAGNHAQGVAFACKKLGIKGTIFIPSTTSAQKINRMKLFGKEMVEIVL 124 Query: 125 MYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVG-PLDALFVCLG 183 D Y DD + A E E G + P+D P V+ GQGT AKE+ ++ P+D LF+ +G Sbjct: 125 SGDTY-DDAYQTAAEYCEERGAVFVHPFDDPKVIEGQGTIAKEILDDAEFPVDYLFLPIG 183 Query: 184 GGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLG 243 GGG+ +G + +P ++ G EP+ S + +D DGA + +G Sbjct: 184 GGGMAAGVSTYFEQSSPETKLIGTEPKGAPSMLTSIQNLKNTVLDEIDGFVDGAAVKKVG 243 Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAM-KEKLKNKR 302 N TF I ++ +D++L V + + + IVVEP G ++ AA KEKLK K Sbjct: 244 NITFEICRKSLDEMLLVPEGRICTTILNLYNNEGIVVEPAGAMTLAALSLYDKEKLKGKN 303 Query: 303 IGIIISGGNVDIERYA 318 + ++SGGN DI R A Sbjct: 304 VVCVVSGGNNDIMRTA 319 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: 318 Number of extensions: 13 Number of successful extensions: 4 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: 416 Length adjustment: 30 Effective length of query: 293 Effective length of database: 386 Effective search space: 113098 Effective search space used: 113098 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