Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BPHYT_RS31960 BPHYT_RS31960 hypothetical protein
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__BFirm:BPHYT_RS31960 Length = 316 Score = 160 bits (406), Expect = 3e-44 Identities = 107/316 (33%), Positives = 157/316 (49%), Gaps = 5/316 (1%) Query: 3 KIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATR 62 +++A + L L+ ++V + + DAD I V++ + + A R Sbjct: 6 RVLATSPIHLSALPILEPSCELVVAPDDSEETLRKFVADADALI-VRVRLPDDIFDHAPR 64 Query: 63 LKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVK 122 LKA VG D V TR I +AN PD T++ A+ V ILA AR L + Sbjct: 65 LKACVRHGVGLDFIPVERATRADIAVANLPDSNTQAVAEHVVGAILAMARGFDRLPRAWR 124 Query: 123 AGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEA 182 W + G++++ +T+GIVGLGRIG VA GF M+VL + A Sbjct: 125 NDGWL--VRQTFQGIELRDRTVGIVGLGRIGLQVAAALHHGFGMRVLGCDNGAREGLPSY 182 Query: 183 YGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKAL 242 +E + + +DF+ L PL T+HL+ A L K A+L+NA+RG +D+ AL Sbjct: 183 VDQTSIE--NVFSGSDFITLHAPLVKSTRHLVNAELLSLAKPGALLVNAARGGLIDDDAL 240 Query: 243 IEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLV 302 + AL++G I A LDVFE EPLP D P + NV+ PH+ + T E M+ AA +V Sbjct: 241 VAALRSGQIGCAALDVFEPEPLPPDHPYWSIDNVLLTPHVAAFTSEGLVRMSTGAARAVV 300 Query: 303 AALDGTLTSNIVNREV 318 L G ++VN EV Sbjct: 301 EILHGRRPEHLVNEEV 316 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: 226 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: 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