Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate HSERO_RS05485 HSERO_RS05485 phosphoesterase
Query= SwissProt::P0DOW0 (331 letters) >FitnessBrowser__HerbieS:HSERO_RS05485 Length = 345 Score = 114 bits (284), Expect = 5e-30 Identities = 97/326 (29%), Positives = 151/326 (46%), Gaps = 22/326 (6%) Query: 23 EPGWIALRVAGVGICGSELSGYL--GHNELR-KPPLVMGHEFSGVVEEVGHGVTNVKIGD 79 +P + ++V GICGS+L Y G +R K P+V+GHE SG + EVG VT++ G Sbjct: 24 QPQQLKVKVKAGGICGSDLHYYHHGGFGVVRIKEPMVLGHEVSGQIAEVGTAVTDIAPGT 83 Query: 80 LVTANPLVTCGRCIHCLRGERQRCESRRIIGI-----DFPGAYAERVLVPSNQCYAVKDA 134 + +P CG C +C G++ C R G GA+ + +++ +Q + V D Sbjct: 84 RIAISPSRPCGACKYCQEGKQNHCLDMRFYGSAMRTPHVQGAFRQEIIIERSQAHVVADH 143 Query: 135 I---DGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIAVVDPN 191 + + A+ EPL+ A+ AV A VG +V G G IG + V +GA + V D Sbjct: 144 VSDGEAAMAEPLSVALHAVRRAGPLVGKRVLVTGCGPIGALVVVAARRAGALEVVVTDVA 203 Query: 192 DERLKISQLWGA------TEMAPNLGALLTDNHPQSFDCVIDAVGLSTTRRDSLNALIRG 245 L+ + GA E L A D +FD + +A G +L AL Sbjct: 204 SMPLQAALQVGADSAINMAETPAALKAYAADK--GTFDVLFEASGNERALVGALEALRPQ 261 Query: 246 GRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQKFLPVDRQWLDV 305 V +GL + N +V ELE RG+F + +EF AV L+N +K + V Sbjct: 262 AIIVQVGLGGDI-QFPANLLVGKELEWRGAFRF-HEEFAMAVELMN-RKLVDVKPLITAT 318 Query: 306 RSLEEGPAAFKELVNGSPFSKIILTF 331 + + AF+ + S K+ ++F Sbjct: 319 YPIAQAVEAFEIAGDRSRMMKVQISF 344 Lambda K H 0.322 0.139 0.424 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: 260 Number of extensions: 18 Number of successful extensions: 3 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: 331 Length of database: 345 Length adjustment: 28 Effective length of query: 303 Effective length of database: 317 Effective search space: 96051 Effective search space used: 96051 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: 49 (23.5 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