Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate 3607860 Dshi_1268 PfkB domain protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_21335 (645 letters) >FitnessBrowser__Dino:3607860 Length = 333 Score = 157 bits (398), Expect = 5e-43 Identities = 107/341 (31%), Positives = 163/341 (47%), Gaps = 26/341 (7%) Query: 10 RQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLKSAMLSRVGD 69 R + + +GR+G+DL G +ED + +GGSSANIA G + G ++A+++RV D Sbjct: 9 RSRNFLVIGRVGMDLSPAPAGTAIEDATDLMVAMGGSSANIAAGLVKFGARAALVTRVSD 68 Query: 70 DHMGRFLVESLAREGCD---VSGIKVDPERLTAMVLLGLKDRETFPLVFYRENCADMALR 126 D +GR+ + LA G D V+ + + A+ L D + V YR AD + Sbjct: 69 DAVGRYCLNQLAAYGVDATHVTPVAGEFRNSLALYESRLADHNS---VIYRNGAADFQMS 125 Query: 127 AEDISEAFIASSKALLITGTHFSTDGVYKASIQALEYAEKHNVKRILDIDYRPVLWGLAG 186 D+ + AL+ GT F+ + A+ +A E A + I D+DYRP W Sbjct: 126 VADVEAVDYSQYGALITAGTVFAAEPSRSATFRAFELARAAGLPIIFDVDYRPYSW---- 181 Query: 187 KADGETRFVADQQVSQHVQKILPRFDLIVGTEEEF-LIAGGSEDLLSALRNVRRLTAATL 245 + Q + + + D+IV +EEF +AGG + L+ R + + +A + Sbjct: 182 --------PSPQVAEEVLSRAGALSDIIVANDEEFGFMAGGIDKGLAKARELAQTSAGIV 233 Query: 246 VVKLGPQGCTVIHGVIPVRLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDASDERC 305 V K+GP+G +R IYP V L GAGD+FM+GFL+ E Sbjct: 234 VYKMGPEGAITFANGTELRT---GIYP---VTALKPTGAGDSFMAGFLASLAEGRELREA 287 Query: 306 CQLANACGGLVVSRHACAPAMPTRAELD-YLFNSPVPITRP 345 +AC +VV++ CAPAMP ELD +L P P P Sbjct: 288 VLRGSACAAIVVAKPGCAPAMPDARELDAFLARHPGPRNAP 328 Lambda K H 0.321 0.138 0.412 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: 464 Number of extensions: 23 Number of successful extensions: 5 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: 645 Length of database: 333 Length adjustment: 33 Effective length of query: 612 Effective length of database: 300 Effective search space: 183600 Effective search space used: 183600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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