Align serine racemase (EC 5.1.1.18) (characterized)
to candidate RR42_RS02315 RR42_RS02315 threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Cup4G11:RR42_RS02315 Length = 508 Score = 167 bits (422), Expect = 7e-46 Identities = 100/304 (32%), Positives = 166/304 (54%), Gaps = 6/304 (1%) Query: 19 RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78 ++ A +T + ++ ++ +V+FK E+ Q + +FK RGA N ++ L+ + K GV+ Sbjct: 15 KVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLSPEELKRGVI 74 Query: 79 TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQ---VIMYDRYKDDREK 135 S+GNHAQ +ALSA L A I MP+ P+ K+ A + GG+ ++++ D Sbjct: 75 AASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEWVEIVLHGDSYSDAYN 134 Query: 136 MAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEE-VGPLDALFVCLGGGGLLSGSALA 194 A + ++ LT I P+D P V+AGQGT A E+ + GPL A+FV +GGGGL+SG A Sbjct: 135 HAAVLEKKHKLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGGGLISGIASY 194 Query: 195 ARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKV 254 + P +V GV+ + ++S G V + +DG + +G TF I +E V Sbjct: 195 IKAVRPEIKVIGVQTVDSDAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKETFRITRELV 254 Query: 255 DDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGNV 312 D+I+ V + + LK + ++EP G ++ A + A +EKLK + + I G N+ Sbjct: 255 DEIILVDTDAICAGLKDVFQDTRSILEPAGAMAVAGLKLYAEREKLKGQHLVAIACGANM 314 Query: 313 DIER 316 + +R Sbjct: 315 NFDR 318 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: 341 Number of extensions: 14 Number of successful extensions: 4 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: 508 Length adjustment: 31 Effective length of query: 292 Effective length of database: 477 Effective search space: 139284 Effective search space used: 139284 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 17 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