Align serine racemase (EC 5.1.1.18) (characterized)
to candidate GFF3271 HP15_3213 threonine dehydratase biosynthetic
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Marino:GFF3271 Length = 511 Score = 213 bits (542), Expect = 8e-60 Identities = 111/301 (36%), Positives = 178/301 (59%), Gaps = 3/301 (0%) Query: 19 RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78 R+ A +TP+ + +++K F + K E+ Q + +FK RGA N ++QL+E Q+ GV+ Sbjct: 13 RVYDVAIETPLTEARSLSKRFGNNILLKREDLQPVFSFKIRGAYNRIAQLSEEQKAKGVI 72 Query: 79 TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAK 138 S+GNHAQ +AL+AK LGI A I+MP PE KV + + +G +V++ D+ A+ Sbjct: 73 CASAGNHAQGVALAAKNLGIKAVIVMPQTTPEIKVRSVRDHGAKVVLKGDAFDEAAAHAQ 132 Query: 139 EISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVG-PLDALFVCLGGGGLLSGSALAARH 197 E+ + G T IPPYD P V+AGQGT A E+ + P+ A+F+C+GGGGL++G A ++ Sbjct: 133 ELIAKHGYTYIPPYDDPDVIAGQGTVAMEIMWQFSKPIHAIFICVGGGGLIAGMAAYIKY 192 Query: 198 FAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDI 257 P +V GVEPE N Q + + G V +D ADG + +G Y + I K+ VD++ Sbjct: 193 LRPEIKVIGVEPEDSNCLQAAMKAGKRVVLDEVGIFADGVAVKQIGKYPWEICKDHVDEV 252 Query: 258 LTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAM--KEKLKNKRIGIIISGGNVDIE 315 +TVS +E+ +K + + EP G L A + +EK++ + + +SG N++ + Sbjct: 253 ITVSTDEICAAIKDVFEDTRSIAEPAGALGVAGIKKYIEREKVEGENLIATLSGANMNFD 312 Query: 316 R 316 R Sbjct: 313 R 313 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: 356 Number of extensions: 14 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: 511 Length adjustment: 31 Effective length of query: 292 Effective length of database: 480 Effective search space: 140160 Effective search space used: 140160 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