Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AZOBR_RS10940 AZOBR_RS10940 3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__azobra:AZOBR_RS10940 Length = 415 Score = 142 bits (359), Expect = 1e-38 Identities = 101/278 (36%), Positives = 143/278 (51%), Gaps = 16/278 (5%) Query: 45 GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104 GI S +T +LE A+RL ++ +G +Q D+ R GI + N P T S A+ V Sbjct: 58 GIRSRTHLTAKVLEAASRLFSVGCFCIGTNQVDLKAARRLGIPVFNAPYSNTRSVAELVI 117 Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164 I+ R + + V G W S A +++GKTLGIVG G IG V+ A Sbjct: 118 GEIIMLMRGIFSKSNLVHGGGWMKS---AKDSYEIRGKTLGIVGYGHIGTQVSIMAE-SM 173 Query: 165 NMKVLY---TNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKS 221 MKV Y N+ A A+ + L ELLA +D V L VP TP+T+ +IG A++++ Sbjct: 174 GMKVRYYDVVNKLALGNAQPCHS-----LEELLAVSDVVTLHVPDTPQTRDMIGEAQIRA 228 Query: 222 MKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPS----DSPLLKLANVV 277 MKK A LINA+RG V +AL AL++ + GA +DVF EP +S L L N + Sbjct: 229 MKKGAHLINAARGKVVVIEALAAALRDKHLLGAAIDVFPKEPGGDKEVFESALRGLDNAI 288 Query: 278 ALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 PHIG +T E + + ++ L+ D T VN Sbjct: 289 LTPHIGGSTMEAQANIGTEVSQKLIEYSDNGSTMGAVN 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: 262 Number of extensions: 15 Number of successful extensions: 2 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: 415 Length adjustment: 30 Effective length of query: 291 Effective length of database: 385 Effective search space: 112035 Effective search space used: 112035 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: 49 (23.5 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