Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_078430830.1 BK574_RS10245 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_002019605.1:WP_078430830.1 Length = 524 Score = 183 bits (464), Expect = 9e-51 Identities = 110/304 (36%), Positives = 164/304 (53%), Gaps = 14/304 (4%) Query: 18 LQQHAQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFD 77 +Q++ VQ + DA + + S+ +T ++E LK ++ VG D D Sbjct: 27 IQKNVTEVQQELHTFDAIL---------VRSATTVTAELIEKMPNLKIIARAGVGVDNID 77 Query: 78 VADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGV 137 + T+ GIV+ N PD T STA+ FS+I A AR++ + + +K G W A G Sbjct: 78 IEAATKAGIVVVNAPDGNTISTAEHTFSMICALARKIPQANQSIKLGEWNRK---AFQGT 134 Query: 138 DVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATA 197 +++GKTLGIVG GRIG +A+RA F M+ L + E G L E+L A Sbjct: 135 ELRGKTLGIVGFGRIGSQLAKRAK-AFEMQPLVFDPFLTKARAEKLGVVPATLEEVLEKA 193 Query: 198 DFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLD 257 D + + PLT +TK ++G + K+ LIN +RG +DE AL L+NG + GA LD Sbjct: 194 DIITVHTPLTKDTKGILGMENIGKTKRGVYLINCARGGIIDEVALKHYLENGHVAGAALD 253 Query: 258 VFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVNRE 317 VFE EP D+ L++L NV+A PHI ++T E + +A +E ++ L+G SN +N Sbjct: 254 VFEEEP-AIDNALIELDNVIATPHIAASTKEAQLNVAAQVSEEVLLFLEGNPVSNSINLP 312 Query: 318 VLSK 321 LSK Sbjct: 313 TLSK 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: 310 Number of extensions: 12 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: 524 Length adjustment: 31 Effective length of query: 290 Effective length of database: 493 Effective search space: 142970 Effective search space used: 142970 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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