Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_043772030.1 U743_RS11935 threonine ammonia-lyase, biosynthetic
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000733765.1:WP_043772030.1 Length = 510 Score = 212 bits (540), Expect = 1e-59 Identities = 117/308 (37%), Positives = 181/308 (58%), Gaps = 7/308 (2%) Query: 19 RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78 R+ A +TP+ + ++ ++ K E+ Q + +FK RGA N ++QL+EA+R GV+ Sbjct: 13 RVYDVAIRTPLSPAPRLSARIGNKLLLKREDLQPVHSFKLRGAFNRIAQLSEAERAKGVV 72 Query: 79 TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAK 138 S+GNHAQ +AL+A+ LG A I+MP P+ KV A +G+GG+V+++ D+ A Sbjct: 73 CASAGNHAQGVALAARTLGCTAWIVMPRTTPQIKVDAVRGFGGKVVLHGDAYDEASAHAA 132 Query: 139 EISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVG-----PLDALFVCLGGGGLLSGSAL 193 +I E G T IPPYD P V+AGQGT A+E+ E++ PLD +FVC+GGGGLL+G A Sbjct: 133 KIVEERGATYIPPYDDPLVIAGQGTIAREIVEQLAEAGEKPLDVIFVCVGGGGLLAGVAA 192 Query: 194 AARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEK 253 + +P +V GVEPE + ++ G V + ADG + G F + + Sbjct: 193 YIKAVSPTTKVIGVEPEDSDCMGRALAAGRRVILPQVGLFADGVAVRQAGKEPFRVARAC 252 Query: 254 VDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGN 311 VD +LTVS +E+ ++ + V EP G L+ A A+ A++ ++KR+G I+SG N Sbjct: 253 VDAMLTVSIDEICAAVRDVFYENRSVPEPAGALAVAGAKRWALETGARDKRLGAIVSGAN 312 Query: 312 VDIERYAH 319 V+ +R H Sbjct: 313 VNFDRLRH 320 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: 335 Number of extensions: 15 Number of successful extensions: 3 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: 510 Length adjustment: 31 Effective length of query: 292 Effective length of database: 479 Effective search space: 139868 Effective search space used: 139868 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