Align D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized)
to candidate RR42_RS32885 RR42_RS32885 LacI family transcriptional regulator
Query= CharProtDB::CH_003593 (296 letters) >FitnessBrowser__Cup4G11:RR42_RS32885 Length = 321 Score = 134 bits (338), Expect = 2e-36 Identities = 92/285 (32%), Positives = 150/285 (52%), Gaps = 9/285 (3%) Query: 2 NMKKLATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLV- 60 N+K LA L++ L+A A+ + IA+ NPFF ++ GA A + + Sbjct: 5 NLKPLAGLLALGILAAPAHADG---ERIAVFTKNQTNPFFQVVRQGADAAAKSMNARVTH 61 Query: 61 -VLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATK 119 + ++ ++++ ++D+ V+ ++ P D A+G VK N ANIPV+ + ++ Sbjct: 62 YIPTKPDSIPEQMSQIEDVIVKKADAIVFVPVDYKAMGPGVKKINAANIPVVNVTDKSDV 121 Query: 120 GEVVSHI-ASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHK 178 G VS I ASD LG K A G+G V+ L+GI G+ +R G A+ A Sbjct: 122 GNFVSFIGASDYDLGLKTATHLFKAMGGKG-NVVLLEGIKGSLTNIDRVRGMHDALKAFP 180 Query: 179 -FNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVV 237 ++ASQPA++ R++ L VM+NL+ ++P + A+FA ND MA+GA+ ALQ A + +V Sbjct: 181 GIKLVASQPANYQRLQALQVMENLMQSYPQIDAIFATNDAMAIGAIEALQGANRK-ALVS 239 Query: 238 GFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKV 282 G +GT + A+ G + AT G G+ A + L+G V Sbjct: 240 GINGTQEAIDAIKAGTMLATGDYNGFAQGCLGMTAAIRKLRGMPV 284 Lambda K H 0.313 0.129 0.344 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: 220 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 296 Length of database: 321 Length adjustment: 27 Effective length of query: 269 Effective length of database: 294 Effective search space: 79086 Effective search space used: 79086 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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