Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate WP_011842465.1 RSPH17029_RS18080 mandelate racemase/muconate lactonizing enzyme family protein
Query= curated2:A8MA91 (398 letters) >NCBI__GCF_000015985.1:WP_011842465.1 Length = 387 Score = 106 bits (265), Expect = 1e-27 Identities = 84/279 (30%), Positives = 131/279 (46%), Gaps = 28/279 (10%) Query: 68 VEVESSDGEVGFGISTGGYPAAWIIENHLSRF---VVGKYVGEVEKTWDQMFKATIYYGR 124 VE+ + G VG G S G + E L+++ ++G+ +E+ W M + + G Sbjct: 17 VEITTDSGIVGIGES-GAWGHLEASEAALAKYCDYLIGEDPRRIERHWQVMHRFAHFNG- 74 Query: 125 RGIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYATGPRPDVAKSLGF---- 180 + AISAVD+ALWD+ + G+P+Y+LLGG VRD L YA V + + F Sbjct: 75 -AAIGGAISAVDIALWDIKARSYGVPIYELLGGAVRDSLRVYAHVYSKTVDEVVSFAAEK 133 Query: 181 -------IGGKLPLIHGPAD-----GIEGL-RENVRIFKEAREKVGDDFLLMYDCWMSLD 227 IG P + P D G GL R + + RE VG + L+ + L Sbjct: 134 ARDGYTAIGHFNPFLDEPEDKPYFLGHAGLVRMGIETVRRTREAVGPEVDLLLEMHRRLT 193 Query: 228 LPYAQRLLSELKPYGLFWIEEPFIPDDYWSFGALANIA--PPTLVASGEHESTVHGFRLL 285 A Y W+E+P P+ + A+A +A P +A+GE ++ F++ Sbjct: 194 PAEAISFAEAAADYTPGWLEDPIRPE---NIDAMAEVARRSPVPIATGERYFNIYQFKMA 250 Query: 286 LELGKVNVIQPDVTWVGGVTPMIKIAALAEAYGAWVIPH 324 +E ++ + V GG+T +KIAA+AEA V PH Sbjct: 251 IERRALSFARVSVGICGGITAAVKIAAIAEANDVQVAPH 289 Lambda K H 0.321 0.141 0.440 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: 360 Number of extensions: 17 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: 398 Length of database: 387 Length adjustment: 31 Effective length of query: 367 Effective length of database: 356 Effective search space: 130652 Effective search space used: 130652 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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