Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_057687229.1 ABB28_RS15235 D-glycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_001431535.1:WP_057687229.1 Length = 345 Score = 232 bits (592), Expect = 9e-66 Identities = 136/308 (44%), Positives = 188/308 (61%), Gaps = 8/308 (2%) Query: 5 VAWKSLP--EDVLAYLQQHAQVVQVDATQ---HDAFVAALKDADGGIGS-SVKITPAMLE 58 V W S P + V+ L+ +++ DA + L+ DG I + + +I A L Sbjct: 7 VVWVSQPLIDAVIEPLRAQVELITTDAVTAWTQEQLAERLRGVDGAIITLNERIGAAQLA 66 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 GA RL+ ++ + VG++ DV L+ G++ +NTPDVLTE+TAD F+L++A+ARR+ E Sbjct: 67 GADRLQVIANVGVGYNNLDVDALSAAGVLASNTPDVLTETTADLGFALLMAAARRITESE 126 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 W++ G W + G D+ G TLGI+G+GRIG +ARR A GF M+VLY NRS P Sbjct: 127 RWLRDGQWGQWSFQTMLGADIHGSTLGILGMGRIGQGIARRGAHGFGMRVLYHNRSRLPA 186 Query: 179 AEEA-YGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATV 237 A EA GA+ EL LLA +D + L +P T + HLI A+ L MK +A L+N +RG V Sbjct: 187 ATEAEVGAQYAELDALLAQSDHLVLVLPYTAASHHLINASALAKMKPTATLVNIARGGIV 246 Query: 238 DEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNA 297 DE AL +AL +G + AGLDV+E EP LL L NVV PHIGSA+ TR AM + A Sbjct: 247 DELALADALAHGRLAAAGLDVYEGEPQVRPE-LLALRNVVLTPHIGSASLGTRKAMVQLA 305 Query: 298 AENLVAAL 305 +NL+AAL Sbjct: 306 VDNLLAAL 313 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: 239 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: 345 Length adjustment: 28 Effective length of query: 293 Effective length of database: 317 Effective search space: 92881 Effective search space used: 92881 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 24 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