Align L-rhamnonate dehydratase; RhamD; EC 4.2.1.90 (characterized)
to candidate BPHYT_RS28240 BPHYT_RS28240 L-rhamnonate dehydratase
Query= SwissProt::Q12DF1 (395 letters) >FitnessBrowser__BFirm:BPHYT_RS28240 Length = 392 Score = 716 bits (1848), Expect = 0.0 Identities = 338/392 (86%), Positives = 362/392 (92%), Gaps = 2/392 (0%) Query: 4 MPTIKHVRAFTVRGGGADYHDQGSGHWIDDHISTPMGRYPEYRQSRQSFGINVLGTLVVE 63 MPTI+HVRAF VRGGGADYHDQ GHWIDDHISTPM RYPEYRQSRQSFGINVLGTLVVE Sbjct: 3 MPTIRHVRAFIVRGGGADYHDQPGGHWIDDHISTPMARYPEYRQSRQSFGINVLGTLVVE 62 Query: 64 IEASDGTVGFSVTTGGELGCWIVEKHLARFIEGAKVTDIEKIWDQMFNATLYYGRKGIVL 123 IEASDGTVGF+VTTGGE+G +IVEKHLARF+EG VTDIEK+WDQM+ +TLYYGRKG+VL Sbjct: 63 IEASDGTVGFAVTTGGEIGAFIVEKHLARFLEGQLVTDIEKMWDQMYFSTLYYGRKGVVL 122 Query: 124 NTISGVDLALWDLLAKVRKEPVHALLGGPVRDELTFYATGARPDLAKKMGFIGGKLPLHH 183 NTISGVDLALWDLLAKVRKEPV+ LLGGPVRDEL FYATGARPDLAK+MGFIGGKLPL H Sbjct: 123 NTISGVDLALWDLLAKVRKEPVYQLLGGPVRDELVFYATGARPDLAKEMGFIGGKLPLQH 182 Query: 184 GPAEREEGLKKNLELLGEMRQRVGDDFWLMYDCWMSLDVEYATRLANAASEYKLKWIEEA 243 GPAE E GLK+NLE L +MR RVGDDFWLMYDCWMSLDV YATRLA AA EY LKWIEE Sbjct: 183 GPAEGEAGLKQNLEKLADMRSRVGDDFWLMYDCWMSLDVPYATRLAQAAHEYGLKWIEEC 242 Query: 244 LPPDDYWGYAELRRNVPRGMLVTTGEHEATRWGFRMLLEMECCDILQPDVGWCGGITELL 303 LPPDDYWGYAELRRNVPRGM+V+TGEHEATRWGFRMLLEM+CCD++QPDVGWCGGITEL+ Sbjct: 243 LPPDDYWGYAELRRNVPRGMMVSTGEHEATRWGFRMLLEMQCCDLIQPDVGWCGGITELI 302 Query: 304 KISALADAHGKLVVPHGSSVYSYHFVITRHNSPFSEFLMMAPKADEVVPMFNPMLLDEPV 363 KISALADAH +VVPHGSSVYSYHFV+TRHNSPF+EFLMMAPKADEVVPMF P+LLDEPV Sbjct: 303 KISALADAHNVMVVPHGSSVYSYHFVVTRHNSPFAEFLMMAPKADEVVPMFTPLLLDEPV 362 Query: 364 PVNGRMKASALDAPGFGVRLNPECALQRPFPR 395 PVNGRMK D PGFGVRLNPECAL RP+PR Sbjct: 363 PVNGRMKVP--DTPGFGVRLNPECALVRPYPR 392 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: 628 Number of extensions: 12 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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