Align serine racemase (EC 5.1.1.18) (characterized)
to candidate CA265_RS15860 CA265_RS15860 threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Pedo557:CA265_RS15860 Length = 416 Score = 175 bits (444), Expect = 2e-48 Identities = 105/316 (33%), Positives = 164/316 (51%), Gaps = 3/316 (0%) Query: 4 NLVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALN 63 N P D SAS+R+K +TP+ ++ ++ + A ++ K E+ Q + ++K RGA N Sbjct: 2 NTTTPNTLDFQSASQRLKGVVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYN 61 Query: 64 ALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGG-- 121 +S L + GV+ S+GNHAQ +A S K LGI I MP P+ KV T +GG Sbjct: 62 KISSLPQDALINGVVCASAGNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDN 121 Query: 122 -QVIMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFV 180 +V++ DD K A S + T IPP+D V+ GQ T E++E++ LD + + Sbjct: 122 VEVVLVGDTFDDCLKEALAYSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIVM 181 Query: 181 CLGGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQ 240 +GGGGL SG + + P ++ GVEP + G ++ DGA + Sbjct: 182 PVGGGGLASGVSAYMKTVKPEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVK 241 Query: 241 HLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKN 300 +G+ T+ KE +D + + + ++ + IVVEP G LS AA +K+++ Sbjct: 242 RIGHITYEYCKELLDQMHLIPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKDQITG 301 Query: 301 KRIGIIISGGNVDIER 316 K + I+SGGN DIER Sbjct: 302 KTVVCIVSGGNNDIER 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: 300 Number of extensions: 18 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: 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