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 WP_086510078.1 BZY95_RS11575 hydroxyectoine utilization dehydratase EutB
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_002151265.1:WP_086510078.1 Length = 334 Score = 172 bits (435), Expect = 1e-47 Identities = 111/323 (34%), Positives = 168/323 (52%), Gaps = 12/323 (3%) Query: 17 YAADIHSIREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSI 76 + + SI +A+ RIA +TP++ S ++ + K E Q +GAFK+RGA+N I Sbjct: 6 HGVTLASIYQARRRIAGQALRTPLVRSHALSERFDADILLKLETLQPSGAFKLRGAANMI 65 Query: 77 FALDD----DEASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGG 132 AL + D GVVT S+GNH AVA AA G+PA I + R PA KV ++ G Sbjct: 66 AALIERHGCDALEAGVVTASTGNHGRAVAYAAARLGVPATICLSRLVPANKVAAIEALGA 125 Query: 133 HIIWSDVSIESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVP 192 + S + +R+ E G L+ PF++ +GQGT+ LEL+E+ P++D +IV Sbjct: 126 EVRRVGESQDEAFGEVERLIRERGMTLIPPFDDPLIAAGQGTIGLELMEDAPDLDRVIVG 185 Query: 193 ISGGGLISGVALAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRAFL 252 +SGGGL+ G+ A KAI P RI QS AG+ + + ++AD L + Sbjct: 186 LSGGGLLGGIGAAVKAIRPEARITGVSLSRGAAMWQSLQAGRPVAVEEVESLADSLGGGI 245 Query: 253 G---DLTWPVVRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQS 309 G T+ +VR+++D+ V + AI AM E K+ VE + A+GLAA + Sbjct: 246 GLDNRCTFSLVREVMDEHYQVSEAAIAQAMVDILEHEKLLVEGAAAVGLAALAEHGIEV- 304 Query: 310 SAWHESSKIGIIVSGGNVDLGVL 332 ++ +I+SG V L L Sbjct: 305 ----RGQRVALILSGNGVALETL 323 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: 225 Number of extensions: 9 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: 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 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