Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate Ac3H11_2732 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2732 Length = 278 Score = 105 bits (261), Expect = 1e-27 Identities = 78/251 (31%), Positives = 116/251 (46%), Gaps = 19/251 (7%) Query: 16 LISGGAAGIGEVLAAAYLEAGAQVHVCDVS-ESALAVFRDKYPGTVATRADVSDAAQIEA 74 +++GGA+GIGE + GA V V DV+ E A A+ + P A D +D IE Sbjct: 20 IVTGGASGIGEATCRRLVAEGATVVVADVNAERAAALASELGPRASAQVFDAADVRSIER 79 Query: 75 VFKVQREHLGGLDVLVNNAGIAGPT------GGIDAISDAEWQATININLTAQYRFAHHA 128 + + E G LDVL NNA ++ P ID I W + +NL +A Sbjct: 80 LVQGTVERFGRLDVLHNNAALSSPAIHAKDKNAID-IEFEVWDQVMAVNLRGYLAGCKYA 138 Query: 129 VPMLKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLP 188 +P + G +++ AS G G R Y+ +K AI+GL + +A+ G +R NA+ P Sbjct: 139 LPTMIAQGGGAIVNTASTGGFSGDITRMAYSVSKAAIIGLTRQIATHHGAQGVRCNAVAP 198 Query: 189 GIVEGPRMDGVIRARAEQVGVPEAEMRQEYLNKISLKRMVTAEDVAAMALFLCSPAARNV 248 G+V P G A A + V + + + ED+AA+ FL S AR + Sbjct: 199 GLVLTP---GTRGAAASVIDVMQ--------RHLLVPEFGEPEDIAALVCFLASGEARYI 247 Query: 249 TGQAISVDGNV 259 GQ DG + Sbjct: 248 NGQTYIADGGM 258 Lambda K H 0.318 0.133 0.383 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: 185 Number of extensions: 9 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: 262 Length of database: 278 Length adjustment: 25 Effective length of query: 237 Effective length of database: 253 Effective search space: 59961 Effective search space used: 59961 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 (21.7 bits) S2: 47 (22.7 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