Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate CA265_RS09010 CA265_RS09010 3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Pedo557:CA265_RS09010 Length = 315 Score = 127 bits (320), Expect = 3e-34 Identities = 92/291 (31%), Positives = 142/291 (48%), Gaps = 17/291 (5%) Query: 25 VQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTR 83 V + D ALK+ D + S+ K+ +++ +K + VG D DV Sbjct: 24 VDTETVPQDQLAEALKNYDAITVRSATKVRKELIDAVPNIKLIGRGGVGMDNIDVEYARS 83 Query: 84 RGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKA-GHWQHSIGPALF--GVDVQ 140 +GI + NTP + S A+ VFS + R + + + G Q + + G ++ Sbjct: 84 QGINVVNTPAASSLSVAELVFSHLFTGIRFLQDANRKMPVEGSTQFNNLKKAYAKGTELS 143 Query: 141 GKTLGIVGLGRIGGAVARRAALGFNMKVLYTNR--SANPQAEEAYGARRVE-------LA 191 GKT+GI+G GRIG A A+ ALG M VL + S + E G + V L Sbjct: 144 GKTIGIIGFGRIGRATAK-VALGLGMNVLAYDLYPSESEITLEFQGGKSVSIPIKTVSLD 202 Query: 192 ELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTI 251 E++ +DF L P K ++GA E MK ++N SRG T+DE ALI+AL +G + Sbjct: 203 EVITGSDFFSLHTPFAD--KPILGAEEFAKMKNGVGIVNCSRGGTIDELALIDALNSGKV 260 Query: 252 HGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLV 302 AGLDVF+ EP P + +L + PHIG++T+E + + A ++ Sbjct: 261 SFAGLDVFDNEPTPL-AEILTHPKISLTPHIGASTNEAQERIGTELATLII 310 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: 215 Number of extensions: 11 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: 315 Length adjustment: 27 Effective length of query: 294 Effective length of database: 288 Effective search space: 84672 Effective search space used: 84672 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