Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_072788965.1 BUA36_RS25770 threo-3-hydroxy-L-aspartate ammonia-lyase
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_900143065.1:WP_072788965.1 Length = 321 Score = 452 bits (1163), Expect = e-132 Identities = 222/318 (69%), Positives = 266/318 (83%) Query: 5 LVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNA 64 L LPTY+D+ +ASERI A++TPVLTSST N E AEVFFKCENFQ+MGAFKFRG N+ Sbjct: 4 LKLPTYEDIVAASERIAGVAHRTPVLTSSTANAELGAEVFFKCENFQRMGAFKFRGGYNS 63 Query: 65 LSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVI 124 L++ QRKAGV+ FSSGNHAQA+ALSAK+LGIPA I+MP DAP AKVAAT+GYG QV+ Sbjct: 64 LAKFTPEQRKAGVVAFSSGNHAQAVALSAKLLGIPATIVMPHDAPAAKVAATRGYGAQVV 123 Query: 125 MYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGG 184 +YDRYK+DRE++ ++++ R GLT+IPPYDH V+AGQGTAAKELFEEVG LD +F LGG Sbjct: 124 IYDRYKEDREQIGRDLAARHGLTLIPPYDHADVIAGQGTAAKELFEEVGRLDYVFAPLGG 183 Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGN 244 GGLLSG+AL+ R +P VYGVEP AGNDGQQSFR GSIVHI+TPKTIADGAQTQHLGN Sbjct: 184 GGLLSGTALSTRALSPTATVYGVEPAAGNDGQQSFRSGSIVHIETPKTIADGAQTQHLGN 243 Query: 245 YTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIG 304 TF II+ V+DILT +DE+L ++F+A RMK+VVEPTGCL AAAR++KE+L+ KR+G Sbjct: 244 LTFPIIQRDVNDILTATDEQLRAEMRFFAERMKMVVEPTGCLGLAAARSIKEQLQGKRVG 303 Query: 305 IIISGGNVDIERYAHFLS 322 IIISGGNVDI RYA L+ Sbjct: 304 IIISGGNVDIARYAELLA 321 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: 352 Number of extensions: 8 Number of successful extensions: 1 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: 321 Length adjustment: 28 Effective length of query: 295 Effective length of database: 293 Effective search space: 86435 Effective search space used: 86435 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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