Align fructokinase (EC 2.7.1.4) (characterized)
to candidate Ac3H11_700 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
Query= BRENDA::Q42896 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_700 Length = 319 Score = 117 bits (293), Expect = 4e-31 Identities = 102/327 (31%), Positives = 151/327 (46%), Gaps = 32/327 (9%) Query: 12 IVSFGEMLIDFVPTVSGVSLAEAPGFLKAPGGAPANVAIAVTRLGGKSAFVGKLGDDEFG 71 +V+ GE L++F T G P +L+ GG +N IA R G ++A++ +LG D FG Sbjct: 11 VVALGEALVEFNQTRPG-----EPQYLQGFGGDTSNAVIAAARAGARTAYLTRLGSDAFG 65 Query: 72 HMLAGILKTNGVQAEGINFDKGARTALAFVTLRADGEREFMFYRNPSADMLLTPAELNLD 131 L + GV + D T + FVT A G EF + R SA + PA L + Sbjct: 66 QALLDLWAREGVDTTAVERDAQHPTGIYFVTHGAAG-HEFSYLRAGSAASRMAPAWLADE 124 Query: 132 -------LIRSAKVFHYGSISLIV--EPCRAAHMKAMEVAKEAGALLSYDPNLRLPLWPS 182 +++ ++ H ISL V C A+ +AM VA+ AGA +++DPNLRL LWP Sbjct: 125 SVKGPAAVLQQCRILHVSGISLAVSASACDTAY-EAMRVARAAGARVAFDPNLRLKLWPL 183 Query: 183 AEEAKKQIKSIWDSADVIKVSDVELEFLTGSNKIDDESAMSLW--HPNLKLLLVTLGEKG 240 A A+ I D+ ++ L G + D A++ W ++V LG G Sbjct: 184 A-RARACIAHAVSLCDIFLPGLDDMAALLG---LSDADAIADWGHAQGAATVVVKLGADG 239 Query: 241 CNYYTKK---FHGTVGGFHVKTVDTTGAGDSFVGALLTKIVDDQTILEDEARLKEVLRFS 297 + V G V VD TGAGD F G LL ++ L D+ L +R++ Sbjct: 240 VLLSSADPAVPRQRVPGRSVALVDATGAGDCFDGNLLARLA-----LGDD--LAAAVRYA 292 Query: 298 CACGAITTTKKGAIPALPTASEALTLL 324 ++ GA+ LPTA + LL Sbjct: 293 NTAASLAVQGFGAVAPLPTAQQVQALL 319 Lambda K H 0.318 0.135 0.389 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: 238 Number of extensions: 15 Number of successful extensions: 4 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: 328 Length of database: 319 Length adjustment: 28 Effective length of query: 300 Effective length of database: 291 Effective search space: 87300 Effective search space used: 87300 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 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