Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_068863251.1 I603_RS04065 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_001677335.1:WP_068863251.1 Length = 528 Score = 183 bits (464), Expect = 9e-51 Identities = 111/320 (34%), Positives = 170/320 (53%), Gaps = 5/320 (1%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEGA 60 K +++ K P + ++ V + + +A + + DG I SS K+T A+L+ A Sbjct: 5 KVLISDKMDPNAARIFEERGCDVDVITGETPEQLIARIGEYDGLAIRSSTKVTKAVLDAA 64 Query: 61 TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120 T LK + +G D D+ + +G+V+ NTP + +TA+ +L+ A AR++ + Sbjct: 65 TNLKVIGRAGIGVDNVDIPYASSKGVVVMNTPFGNSITTAEHAIALMFALARQIPDANAQ 124 Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180 +AG W S GV++ KTLG++G G IG VA RA LG MKV+ + Sbjct: 125 TQAGLWPKS---GFMGVELTNKTLGLIGAGNIGSIVASRA-LGLRMKVIAYDPFLTEDRA 180 Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240 G +V+L LL+ ADFV L PLT ET++++ L+ KK +IN +RG +DE Sbjct: 181 VEMGVEKVDLDTLLSRADFVTLHTPLTEETRNILSRERLEGAKKGIRIINCARGGLIDEA 240 Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300 AL + L++G + GA LDVFETEP D PL N + PH+G++T E + +A AE Sbjct: 241 ALRDCLESGQVAGAALDVFETEPPAKDHPLFGTPNFICTPHLGASTTEAQVNVALQVAEQ 300 Query: 301 LVAALDGTLTSNIVNREVLS 320 L L +N +N LS Sbjct: 301 LSDYLVNGGVTNALNVPSLS 320 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: 346 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: 528 Length adjustment: 31 Effective length of query: 290 Effective length of database: 497 Effective search space: 144130 Effective search space used: 144130 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 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