Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_093428290.1 BM272_RS08145 threonine ammonia-lyase, biosynthetic
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_900112605.1:WP_093428290.1 Length = 504 Score = 195 bits (495), Expect = 2e-54 Identities = 104/301 (34%), Positives = 166/301 (55%), Gaps = 3/301 (0%) Query: 19 RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78 R+ A +TP+ ++ ++ +VF K E+ Q + ++K RGA N + L QR GV+ Sbjct: 13 RVYDVARETPLDPATGLSNRLGNQVFLKREDLQPVFSYKLRGAYNKIIHLAPEQRARGVI 72 Query: 79 TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAK 138 S+GNHAQ +ALSA+ LGIPA+I+MP P+ K+ A + G +++++ D+ Sbjct: 73 AASAGNHAQGVALSARRLGIPARIVMPKTTPDIKIEAVRALGAEIVLHGSSYDEAFAHCM 132 Query: 139 EISEREGLTIIPPYDHPHVLAGQGTAAKELFEEV-GPLDALFVCLGGGGLLSGSALAARH 197 +I+E G+ IPPYD P V+AGQGT A EL + PL+A+FV +GGGGLL+G + R Sbjct: 133 QIAEEAGMAFIPPYDDPDVIAGQGTVAMELARQAPQPLEAVFVPVGGGGLLAGVSAYFRA 192 Query: 198 FAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDI 257 P + GVEP + G V + ADG + +G F I++E VD++ Sbjct: 193 LYPGVRIIGVEPADAPTLHSALAAGERVQLPQVGIFADGVAVRRIGEEPFRILRESVDEV 252 Query: 258 LTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKE--KLKNKRIGIIISGGNVDIE 315 + VS + + +K + + EP G LS A + E +L+ + ++SG N++ + Sbjct: 253 VLVSTDAICAAIKDIFDNTRSIAEPAGALSVAGLKQYVENHRLEGANLAAVVSGANINFD 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: 351 Number of extensions: 15 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: 504 Length adjustment: 31 Effective length of query: 292 Effective length of database: 473 Effective search space: 138116 Effective search space used: 138116 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 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