Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_044051092.1 RCA23_RS15620 threonine ammonia-lyase IlvA
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000738435.1:WP_044051092.1 Length = 411 Score = 152 bits (384), Expect = 1e-41 Identities = 94/311 (30%), Positives = 160/311 (51%), Gaps = 8/311 (2%) Query: 11 DDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNE 70 + A A+ER+++ TP+ + ++ + A+++ K E+ + ++K RGA NA+ + + Sbjct: 6 NQAAEATERMRQLFPATPLQRNDHLSNVYDADIWLKREDLSPVRSYKLRGAFNAMGK--Q 63 Query: 71 AQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGG---QVIMYD 127 A + V S+GNHAQ +A + L I MP+ PE K+ T+ +GG QV + Sbjct: 64 ADKDVFVCA-SAGNHAQGVAYVCRHLQKKGVIFMPVTTPEQKIRKTRLFGGAWVQVQLVG 122 Query: 128 RYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVC-LGGGG 186 Y DD + ++ G + P+D P V+ GQ T E+ E++G +FV +GGGG Sbjct: 123 DYFDDTLRASQAYCAEVGGHFLSPFDDPDVIEGQATVTYEMLEQLGRSPDVFVVPVGGGG 182 Query: 187 LLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYT 246 L S + AP E++ VEP G + + G+ + ++ T DGA +G T Sbjct: 183 LSSSARRLLSERAPETEIFYVEPSGGKSLAAAVQAGAPIALEQVDTFVDGAAVAKMGVNT 242 Query: 247 FSIIKE-KVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGI 305 F+ +K D +L + ++ + + IV+EP G L+ A + +K+K+K K + Sbjct: 243 FAALKGIDADHVLDIPEDRICTTILDMLNTEGIVLEPAGALALDALKDLKDKIKGKTVVC 302 Query: 306 IISGGNVDIER 316 + SGGN D ER Sbjct: 303 VSSGGNFDFER 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: 287 Number of extensions: 21 Number of successful extensions: 6 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: 411 Length adjustment: 29 Effective length of query: 294 Effective length of database: 382 Effective search space: 112308 Effective search space used: 112308 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