Align Putative L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (uncharacterized)
to candidate WP_050462203.1 AKL27_RS07595 galactonate dehydratase
Query= curated2:A8MA91 (398 letters) >NCBI__GCF_001189915.1:WP_050462203.1 Length = 379 Score = 124 bits (310), Expect = 6e-33 Identities = 109/347 (31%), Positives = 160/347 (46%), Gaps = 33/347 (9%) Query: 66 VVVEVESSD-GEVGFG-ISTGGYPAAWI-IENHLSRFVVGKYVGEVEKTWDQMFKATIYY 122 V V+VE+ G +G+G S G P A + L + VVG E W +M++ + Sbjct: 19 VFVKVETDQPGLIGWGECSLPGKPNAMLGAVADLEKLVVGADPTNTEWCWQRMYRHAFWR 78 Query: 123 GRRGIVMNAISAVDLALWDLMGKVRGLPVYDLLGGPVRDELTFYAT----------GPRP 172 G I A+S VD+ALWD+ GK+ PVY L+GG VRD + YA R Sbjct: 79 GGP-IQTAALSGVDIALWDIRGKLANQPVYKLMGGAVRDRIRLYANCGLSSDPEELRRRV 137 Query: 173 DVAKSLGFIGGK---LPLIHGPADGIEGLRENVRIFKEAREKVGDDFLLMYDCWMSLDLP 229 A SLG+ K LP ++ D + +R+ V + R+++G + D L Sbjct: 138 RHAVSLGYTAVKFYPLPAVNA-VDSLATIRQVVACCEAVRDEIGAERDFALDFHGRLSSG 196 Query: 230 YAQRLLSELKPYGLFWIEEPFIPDDYWSFGALANIAPPTLV--ASGEHESTVHGFRLLLE 287 +A + S ++ WIEEP +P+ + ALA +A ++ A GE T FR +LE Sbjct: 197 FAVEIESAIRHTKPLWIEEPVLPE---TPKALARLAEKCVIPIAVGERLFTRFDFREVLE 253 Query: 288 LGKVNVIQPDVTWVGGVTPMIKIAALAEAYGAWVIPHG-----SSVYGYHFIITRVNSPF 342 VIQPDV GG+T M+KIAA AE YG + PH S+ G H Sbjct: 254 NEWATVIQPDVANAGGITEMMKIAAFAETYGVALAPHNPNGPVQSIAGMHLAAALQPFVI 313 Query: 343 AEYLVVSPDATKIVPQFHPLLRDEPIPQNGKVRLSRKPGFGVELNRD 389 E+ D + + P + +G V L + PG G+ +N + Sbjct: 314 LEHRHEHHDFLEQLADNIP-----KVGADGYVGLPKGPGLGIHVNEE 355 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: 440 Number of extensions: 27 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: 398 Length of database: 379 Length adjustment: 30 Effective length of query: 368 Effective length of database: 349 Effective search space: 128432 Effective search space used: 128432 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 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