Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate 3607475 Dshi_0888 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= BRENDA::Q54HH2 (324 letters) >FitnessBrowser__Dino:3607475 Length = 324 Score = 303 bits (776), Expect = 4e-87 Identities = 149/319 (46%), Positives = 212/319 (66%), Gaps = 4/319 (1%) Query: 1 MEPMATVTLKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGA 60 ++P T D+ AH+RI+ +IH+TPVLT+S N+L G EL+FKCEN QK G+FK+RGA Sbjct: 5 IDPAVIPTYDDVVAAHERIKPHIHRTPVLTSSYFNDLVGAELFFKCENFQKAGAFKVRGA 64 Query: 61 CNAIFSLDEEELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGA 120 CNA+F L + +GV THSSGNH +LSYA+ R + C VV+P AP K A+ GYG Sbjct: 65 CNAVFGLSDALAERGVATHSSGNHALSLSYAAGRRGIPCNVVMPRTAPEAKKAAVRGYGG 124 Query: 121 TVTKCKATLEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENLDAIITP 180 +T+C+ + +RE+ ++ E+ + +HP+++ +V+AGQGT S E MEQ + LD +I P Sbjct: 125 IITECEPSTTSREAVFAEVQERTGAEFVHPYNDPRVVAGQGTCSREFMEQTDGLDMMIAP 184 Query: 181 VGGGGLLSGTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLT 240 +GGGG++SG C+T ++ P +++ AAEP ADD YRS +G I P TIADGL Sbjct: 185 IGGGGMISGCCLTLSNIAPEVQIIAAEPEQADDAYRSFKAGHI--IADDAPVTIADGLKV 242 Query: 241 TVGSLTFPIIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKK 300 + LT+ + + ++ +E EI AMKL W+RMKI++EPS A LA ILK KDK Sbjct: 243 PLKDLTWHFVSNHVSDILTASEQEIIDAMKLTWQRMKIVMEPSCAVPLATILKN--KDKF 300 Query: 301 DIKKVGIIISGGNVDLSSI 319 K+VG+I++GGNVDL + Sbjct: 301 AGKRVGVIVTGGNVDLDKL 319 Lambda K H 0.315 0.132 0.374 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: 296 Number of extensions: 8 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: 324 Length of database: 324 Length adjustment: 28 Effective length of query: 296 Effective length of database: 296 Effective search space: 87616 Effective search space used: 87616 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 (21.5 bits) S2: 48 (23.1 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