Align Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 (characterized)
to candidate SM_b20432 SM_b20432 threonine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__Smeli:SM_b20432 Length = 334 Score = 175 bits (443), Expect = 2e-48 Identities = 103/312 (33%), Positives = 173/312 (55%), Gaps = 8/312 (2%) Query: 21 IHSIREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALD 80 I I A RI+ V TP+ S S+ + G + K E Q G+FK+RGA+N++ +L Sbjct: 9 IDDIEVAARRISGRVLTTPLAMSGSLSELCGVPVGLKLEHHQTTGSFKLRGATNAVLSLS 68 Query: 81 DDEASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVS 140 + + GV+ S+GNH A+A AAK G A I + P KV ++R G ++ S Sbjct: 69 AGDRALGVIAASTGNHGRALAHAAKAEGSVATICMSHLVPVNKVSEIRRLGANVRIVGNS 128 Query: 141 IESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLIS 200 + + +R+ E G ++V PF+++ ++GQGT+ LE++ ++P++ ++VP+SGGGL + Sbjct: 129 QDEAQEEVERLVAENGLVMVPPFDHRAIVAGQGTLGLEVVAQMPDVAMVLVPVSGGGLAA 188 Query: 201 GVALAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRAFLG---DLTW 257 GVA A KA P+ R++ + S AAG + ++AD L +G +T+ Sbjct: 189 GVAAAVKARRPATRVIGLTMERGAAMKASFAAGGPALVDEQPSLADSLGGGIGLDNRVTF 248 Query: 258 PVVRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSK 317 + R+L+DDII++ + I M+ Y + VE +GA+G++A L+ + K Sbjct: 249 RMCRELLDDIILLTEAEIAAGMRHAYAEEREIVEGAGAVGISALLAGKIKDI-----DGP 303 Query: 318 IGIIVSGGNVDL 329 I +I+SG NVD+ Sbjct: 304 IAVIISGRNVDM 315 Lambda K H 0.316 0.133 0.381 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: 221 Number of extensions: 16 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: 339 Length of database: 334 Length adjustment: 28 Effective length of query: 311 Effective length of database: 306 Effective search space: 95166 Effective search space used: 95166 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 (21.6 bits) S2: 49 (23.5 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