Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate HSERO_RS19280 HSERO_RS19280 D-2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__HerbieS:HSERO_RS19280 Length = 316 Score = 171 bits (432), Expect = 3e-47 Identities = 118/302 (39%), Positives = 163/302 (53%), Gaps = 13/302 (4%) Query: 10 LPEDVLAYLQQHAQVVQVDATQH-DAFVAALKDADGGIGSS--VKITPAMLEGATRLKAL 66 LP+ +L LQQH + H +A +AA+ GI ++ K++ + L+ + Sbjct: 15 LPQHLLDLLQQHYTCHNLILQPHSEAELAAIAPQIRGIAANGEAKVSREFMARFPALEIV 74 Query: 67 STISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHW 126 S VG+D DV RGI + +TPDVL + AD +L+LA+AR VV + ++G W Sbjct: 75 SVFGVGYDGVDVPAARERGIHVTHTPDVLNDDVADLAMALMLATARNVVRADRFARSGEW 134 Query: 127 QHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGAR 186 + GP F V G LGIVGLGRIG A+A+RAA F+M++ Y NRS + Sbjct: 135 KK--GPFPFTTKVSGARLGIVGLGRIGQAIAKRAA-AFDMQISYHNRSRKDVPYTYVDS- 190 Query: 187 RVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEAL 246 + L DF+ + P T+ L+ A L+++ LIN +RG+ VDE ALI AL Sbjct: 191 ---ITALAREVDFLVMITPGGAGTRALVNAEVLEALGPKGFLINVARGSVVDEAALIAAL 247 Query: 247 QNGTIHGAGLDVFETEP-LPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAAL 305 + G I GAGLDVF EP +P++ L L NVV PH+ S T TR AMA A NL A Sbjct: 248 KTGVIAGAGLDVFADEPNVPAE--LAALDNVVLTPHMASGTLVTRTAMADLAFNNLQAHF 305 Query: 306 DG 307 G Sbjct: 306 SG 307 Lambda K H 0.317 0.131 0.366 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: 244 Number of extensions: 11 Number of successful extensions: 4 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: 321 Length of database: 316 Length adjustment: 27 Effective length of query: 294 Effective length of database: 289 Effective search space: 84966 Effective search space used: 84966 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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