Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_142248010.1 BK574_RS21120 D-glycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_002019605.1:WP_142248010.1 Length = 326 Score = 235 bits (600), Expect = 1e-66 Identities = 128/286 (44%), Positives = 178/286 (62%), Gaps = 10/286 (3%) Query: 22 AQVVQVDATQHDAFVAALKDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADL 81 ++V+Q + + DA + + D + L +LK ++ ++VG+D DV Sbjct: 37 SEVLQKELERADALFSLVSDP---------LRSQQLAKCPKLKVIANMAVGYDNIDVEHA 87 Query: 82 TRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQG 141 T +GIV+ +TPDVLT++TAD F+L+LA+AR++ E +++K WQ L G DV Sbjct: 88 TNKGIVVCHTPDVLTDTTADLTFALLLATARKIPEATDYIKNDQWQQWSPYLLAGTDVHH 147 Query: 142 KTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVC 201 KT+GIVG+GRIG AVA+RA GF+M++LY NRS + E+ GA+ ELL +D+V Sbjct: 148 KTIGIVGMGRIGEAVAKRAK-GFDMEILYHNRSRKMETEQQLGAKYCSFEELLQQSDYVV 206 Query: 202 LQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFET 261 P TP TK L + MK SAI INASRG V+E AL EAL+ G I AGLDVF Sbjct: 207 CLAPFTPVTKELFDQQAFQQMKNSAIFINASRGGLVNEAALQEALEKGVIQAAGLDVFAE 266 Query: 262 EPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 EP+ ++ PL++L NVVA+PHIGSAT ETR AM + EN+ L+G Sbjct: 267 EPVRANHPLVQLPNVVAIPHIGSATVETRDAMVKMTVENIKKVLEG 312 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: 228 Number of extensions: 8 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: 326 Length adjustment: 28 Effective length of query: 293 Effective length of database: 298 Effective search space: 87314 Effective search space used: 87314 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 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