Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (characterized)
to candidate PfGW456L13_3930 Gluconate dehydratase (EC 4.2.1.39)
Query= SwissProt::Q12DF1 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3930 Length = 394 Score = 696 bits (1797), Expect = 0.0 Identities = 326/392 (83%), Positives = 355/392 (90%) Query: 4 MPTIKHVRAFTVRGGGADYHDQGSGHWIDDHISTPMGRYPEYRQSRQSFGINVLGTLVVE 63 +PTIKHVRAFT+RGGGADYHDQ GHWIDDHI+TPM +YPEYRQSR++FGINVLGTLVVE Sbjct: 3 IPTIKHVRAFTLRGGGADYHDQADGHWIDDHIATPMSKYPEYRQSRRTFGINVLGTLVVE 62 Query: 64 IEASDGTVGFSVTTGGELGCWIVEKHLARFIEGAKVTDIEKIWDQMFNATLYYGRKGIVL 123 IEASDGTVGF+VTTGGE +IVEKHLARF+EG +VTDIEKIWDQM+ +TLYYGRKGIV+ Sbjct: 63 IEASDGTVGFAVTTGGEPAAYIVEKHLARFLEGVRVTDIEKIWDQMYQSTLYYGRKGIVI 122 Query: 124 NTISGVDLALWDLLAKVRKEPVHALLGGPVRDELTFYATGARPDLAKKMGFIGGKLPLHH 183 NTISGVDLALWDLL K+R+EPVH LLGG VRDEL FYATGARPDLA+KMGFIGGK+PLHH Sbjct: 123 NTISGVDLALWDLLGKIRQEPVHQLLGGAVRDELQFYATGARPDLAQKMGFIGGKMPLHH 182 Query: 184 GPAEREEGLKKNLELLGEMRQRVGDDFWLMYDCWMSLDVEYATRLANAASEYKLKWIEEA 243 GPAE EEGL+KNLE L MR+RVG DFWLM DCWMSLD+ YAT+LA A EY LKWIEEA Sbjct: 183 GPAEGEEGLRKNLEELATMRERVGPDFWLMLDCWMSLDLNYATKLAVGAHEYGLKWIEEA 242 Query: 244 LPPDDYWGYAELRRNVPRGMLVTTGEHEATRWGFRMLLEMECCDILQPDVGWCGGITELL 303 LPPDDYWGYA LR NVP+GMLVTTGEHEATRWGFRMLLEM CCDI+QPDVGWCGGITEL+ Sbjct: 243 LPPDDYWGYAALRNNVPKGMLVTTGEHEATRWGFRMLLEMGCCDIIQPDVGWCGGITELV 302 Query: 304 KISALADAHGKLVVPHGSSVYSYHFVITRHNSPFSEFLMMAPKADEVVPMFNPMLLDEPV 363 KISALADAH LV+PHGSSVYSYHFV TRHNSPF+EFLMMAPKADEVVPMF+P LL EPV Sbjct: 303 KISALADAHNALVIPHGSSVYSYHFVATRHNSPFAEFLMMAPKADEVVPMFHPQLLGEPV 362 Query: 364 PVNGRMKASALDAPGFGVRLNPECALQRPFPR 395 PVNGRM+ SALD PGFGV LNPEC L RP+ R Sbjct: 363 PVNGRMRLSALDQPGFGVTLNPECQLHRPYNR 394 Lambda K H 0.321 0.140 0.444 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: 625 Number of extensions: 16 Number of successful extensions: 1 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: 395 Length of database: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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 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