Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_009763905.1 MICLODRAFT_RS21385 threo-3-hydroxy-L-aspartate ammonia-lyase
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000262405.1:WP_009763905.1 Length = 335 Score = 396 bits (1018), Expect = e-115 Identities = 195/316 (61%), Positives = 245/316 (77%) Query: 7 LPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALS 66 LPTY+DV +A+ RI A++TPVLTS T ++ +FFK ENFQ+ GAFKFRGA NA++ Sbjct: 19 LPTYEDVVAAARRIDGVAHRTPVLTSRTADERTGGRLFFKAENFQRGGAFKFRGAYNAIA 78 Query: 67 QLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMY 126 +L+ +K GV+ FSSGNHAQAIA + ++ +P IIMP DAP KVAATKGYGG+V++Y Sbjct: 79 RLSPDAKKRGVVAFSSGNHAQAIAYAGQLQEVPTVIIMPQDAPAMKVAATKGYGGEVVLY 138 Query: 127 DRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGG 186 DRYK+DRE + +++S+ GLT+IPPYDH V+AGQGTA KEL EEVGPLD L VC+GGGG Sbjct: 139 DRYKEDREAIGRKLSQERGLTLIPPYDHEDVIAGQGTATKELIEEVGPLDMLLVCVGGGG 198 Query: 187 LLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYT 246 LL+GSALA++ +P+C +YGVEPEAGND QQSFR GSIV I P TIADGAQT ++GN T Sbjct: 199 LLAGSALASKALSPDCRIYGVEPEAGNDAQQSFRTGSIVKIPVPTTIADGAQTTYVGNKT 258 Query: 247 FSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGII 306 F I++ DDILTVSD +L+D ++F+ RMKIVVEPTGCL+ AAA K+KR+GII Sbjct: 259 FPIMRAFADDILTVSDTQLVDTMRFFVERMKIVVEPTGCLAAAAALHGIVPCKDKRVGII 318 Query: 307 ISGGNVDIERYAHFLS 322 ISGGNVD A FL+ Sbjct: 319 ISGGNVDPRALAGFLA 334 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: 330 Number of extensions: 5 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: 335 Length adjustment: 28 Effective length of query: 295 Effective length of database: 307 Effective search space: 90565 Effective search space used: 90565 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 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