Align D-galactonate dehydratase family member Dd703_0947; EC 4.2.1.-; D-gluconate dehydratase; EC 4.2.1.39; D-mannonate dehydratase; EC 4.2.1.8 (uncharacterized)
to candidate WP_086510675.1 BZY95_RS14785 mandelate racemase/muconate lactonizing enzyme family protein
Query= curated2:C6CBG9 (417 letters) >NCBI__GCF_002151265.1:WP_086510675.1 Length = 378 Score = 99.0 bits (245), Expect = 2e-25 Identities = 94/355 (26%), Positives = 151/355 (42%), Gaps = 71/355 (20%) Query: 60 LIGKDPTRIEDIWQSA--AVSGYWRNGPIMNNALSGVDMALWDIKGKLAGMPVYELLGGK 117 LIG+DP + E +W + + G + ALSG+D+ALWDIKGK G+P+ LLGG+ Sbjct: 66 LIGQDPLQTERLWLELYNRLRDQGQRG-LTVTALSGIDIALWDIKGKRFGVPISTLLGGR 124 Query: 118 CRDGIPLYC----HTDGGDEVEVEDNIR---ARMEEGYQYVRCQMGMYGGAGTD-DLKLI 169 RD + Y G D VE DN R EG+ V+ ++G G D DL++I Sbjct: 125 FRDSVRAYATGSFRRAGVDRVE--DNAREVAGYRREGFHAVKIKIGF----GVDEDLRVI 178 Query: 170 ATQLARAKNIQPKRSPRSKTPGIYFDPEAYAKSVPRLFEHLRNKLGFGIEFIHDVHERVT 229 E +R +G + + D + Sbjct: 179 --------------------------------------EAVRESIGPDMRLMIDANHGYD 200 Query: 230 PVTAIQLAKTLEPYQLFYLEDPVAPENIDWLRMLRQQSSTPISMGELFVNINEWKPLIDN 289 + A+++ + + + + E+PV PE++ R +R P++ GE + + Sbjct: 201 YLEAVEVGRRAAKFGIDWFEEPVLPEHVSAYRAVRADQPIPVAGGETWHGRYAMHEPLAT 260 Query: 290 KLIDYIRCHVSTIGGITPAKKLAVYSELNGVRTAWHGPGDISPVGVCANMHLDMSS---- 345 + +D I+ + +GG T +++A + L+GVR H G VC L + Sbjct: 261 RAVDIIQPDICGVGGFTEIRRVADMAALHGVRLVPHVWG----TAVCLAASLQFMAALLP 316 Query: 346 ------PNFGIQEYTPMNDALREVFPGCP-EIDQGYAYVNDKPGLGIDIN-ETLA 392 P I E+ + R+ P E D+G + D PGLGI+I+ E LA Sbjct: 317 NPPRRDPIEPILEFDRTENPFRQAVVTTPIEHDRGVVAIPDGPGLGIEIDREALA 371 Lambda K H 0.319 0.139 0.430 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: 412 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 417 Length of database: 378 Length adjustment: 31 Effective length of query: 386 Effective length of database: 347 Effective search space: 133942 Effective search space used: 133942 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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