Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate PfGW456L13_1617 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1617 Length = 321 Score = 141 bits (355), Expect = 2e-38 Identities = 93/283 (32%), Positives = 136/283 (48%), Gaps = 11/283 (3%) Query: 30 TQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLA 89 T D + LK A I + + I A + + LK + + G + D+A GI + Sbjct: 38 TLPDQVIEHLKGATVAISNKILIDAAAMAASPDLKLILITATGTNNVDLAAARAHGITVC 97 Query: 90 NTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFG---VDVQGKTLGI 146 N T S A L+L A R+ + + V G WQ + L V+++GKTLG+ Sbjct: 98 NCQGYGTPSVAQHTIMLLLNLATRLADYQKAVGEGRWQQAKQFCLLDYPIVELEGKTLGL 157 Query: 147 VGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPL 206 +G G +GGAVAR A F M+V+ P + R+ L ELL D + L PL Sbjct: 158 LGHGELGGAVARLAE-AFGMRVVLGQIPGRPARPD-----RLPLDELLPQVDALTLHCPL 211 Query: 207 TPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPS 266 T+H IGA EL +MK A ++N +RG +DE+AL AL+NG + GA DV EP + Sbjct: 212 NEHTRHFIGARELAAMKPGAFVVNTARGGLIDEQALANALRNGHLGGAATDVLSVEPPVN 271 Query: 267 DSPLL--KLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 +PLL + ++ PH + E R + EN + G Sbjct: 272 GNPLLAHDIPRLIVTPHNAWGSREARQRIVGQVTENALGYFSG 314 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: 209 Number of extensions: 9 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: 321 Length of database: 321 Length adjustment: 28 Effective length of query: 293 Effective length of database: 293 Effective search space: 85849 Effective search space used: 85849 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