Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BPHYT_RS14520 BPHYT_RS14520 2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__BFirm:BPHYT_RS14520 Length = 329 Score = 236 bits (603), Expect = 4e-67 Identities = 146/328 (44%), Positives = 195/328 (59%), Gaps = 9/328 (2%) Query: 1 MKKIVAWKSLPEDVLAYLQQHAQVV--QVDATQHDAFVAALKDADGGIGSSVKITPAMLE 58 M+KI+ + + DV+ L+Q+ V Q D D L D DG + + + A L Sbjct: 1 MQKILVARPIFPDVIERLKQYFDVDWNQGDVLAADELKRRLADKDGALTAGDPVGAAELA 60 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 A RL+ +S ++VG++ FDVA ++ NTPDVL ESTAD ++L++A+ARR+ E Sbjct: 61 AAPRLRVVSNMAVGYNNFDVAAFNAANVLGTNTPDVLNESTADFGWALMMAAARRITESE 120 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS-ANP 177 W++ G WQ A G D+ G TLG++G+GRIG A+ARRA GF+M+V+Y NRS P Sbjct: 121 HWLRGGQWQKWAYDAFLGSDLHGSTLGVIGMGRIGQALARRAK-GFDMQVIYHNRSRVAP 179 Query: 178 QAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATV 237 + E A V +LL AD V L +P T E H IGAAEL MK +A L N +RG V Sbjct: 180 EIEAELNAEYVSKQDLLRRADHVVLVLPYTKENHHTIGAAELALMKPTATLTNIARGGIV 239 Query: 238 DEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNA 297 D+ AL+EAL++ I AGLDVFE EP + LL + NVV PHI SAT TR AMA A Sbjct: 240 DDAALVEALRSKQIAAAGLDVFEGEP-NLNQDLLSVPNVVLTPHIASATEATRRAMANLA 298 Query: 298 AENLVAAL-DGTLTS---NIVNREVLSK 321 A+NL+A L +G N VN EV+ K Sbjct: 299 ADNLIAGLGEGPRAGRPPNPVNPEVIGK 326 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: 257 Number of extensions: 16 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: 321 Length of database: 329 Length adjustment: 28 Effective length of query: 293 Effective length of database: 301 Effective search space: 88193 Effective search space used: 88193 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